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PDBID Method Resolution Release Date NLP types # NLPs H3 H4 H2A H2B H1 Dna variant Dna length Title Authors DOI Publication H3 taxa H4 taxa H2A taxa H2B taxa H1 taxa Release Year Interactors Interactor categories Interactor UIDS Histone UIDS Q-score
0 3C1B X-ray 2.20 2008-10-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure Lu, X., Simon, M.D., Chodaparambil, J.V., Hansen, J.C., Shokat, K.M., Luger, K. 10.1038/nsmb.1489 18794842 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2008 P06897, Q28D68, P84233, P62799 -
1 3LZ1 X-ray 2.50 2010-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2) Vasudevan, D., Chua, E.Y., Davey, C.A. 10.1016/j.jmb.2010.08.039 20800598 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P84233, P62799, P02281 -
2 9R2P EM 4.18 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Na, N.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.196
3 6ZHX EM 2.50 2020-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class. Lehmann, L.C., Bacic, L., Hewitt, G., Brackmann, K., Sabantsev, A., Gaullier, G., Pytharopoulou, S., Degliesposti, G., Okkenhaug, H., Tan, S., Costa, A., Skehel, J.M., Boulton, S.J., Deindl, S. 10.1016/j.celrep.2020.108529 33357431 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.625
4 5B2J X-ray 2.60 2016-06-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146_4CpG 142 Human nucleosome containing CpG methylated DNA Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S. 10.1002/2211-5463.12064 27419055 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P04908, P68431, P62805, P06899 -
5 8HAL EM 4.40 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 151 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Transcription-associated, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P04908, P68431, P62805, P06899 0.195
6 8X15 EM 3.20 2024-03-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 137 Structure of nucleosome-bound SRCAP-C in the apo state Yu, J., Sui, F., Gu, F., Li, W., Yu, Z., Wang, Q., He, S., Wang, L., Xu, Y. 10.1038/s41421-023-00640-1 38331872 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2, Actin, cytoplasmic 1, N-terminally processed, Actin-like protein 6A, DNA methyltransferase 1-associated protein 1, YEATS domain-containing protein 4 Transcription-associated, Chromatin remodelers, Cell cycle, SRCAP (INO80), Histone chaperones, Histone PTM readers, INO80, Histone_acetylation_reader, Euchromatin-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P68431, P62807, P62805, Q93077 0.218
7 8H0V EM 3.80 2022-12-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.2 601 201 RNA polymerase II transcribing a chromatosome (type I) Hirano, R., Ehara, H., Kujirai, T., Uejima, T., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1038/s41467-022-35003-z 36435862 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P68431, P06899, P04908, P62805, P16403 0.228
8 1M19 X-ray 2.30 2003-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1016/S0022-2836(02)01407-9 12559907 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2003 P02302, P06897, P62799, P02281 -
9 2F8N X-ray 2.90 2006-05-23 octamer 1 canonical_H3 canonical_H4 macroH2A,canonical_H2A canonical_H2B alphasat_146 145 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Chakravarthy, S., Luger, K. 0 Xenopus laevis Xenopus laevis Homo sapiens,Mus musculus Xenopus laevis Xenopus laevis 2006 O75367, Q9D2U9, P62799, P02281, P84233, Q8CGP6 -
10 3AFA X-ray 2.50 2010-05-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The human nucleosome structure Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H. 10.1073/pnas.1003064107 20498094 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2010 P04908, P68431, P62805, P06899 -
11 3AZF X-ray 2.70 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
12 3AZH X-ray 3.49 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
13 3AZM X-ray 2.89 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
14 3MGR X-ray 2.30 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Rubidium ions to the Nucleosome Core Particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P84233, P62799, P02281 -
15 3REI X-ray 2.65 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P06897, P84233, P62799, P02281 -
16 3MNN X-ray 2.50 2011-04-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Wu, B., Ong, M.S., Groessl, M., Adhireksan, Z., Hartinger, C.G., Dyson, P.J., Davey, C.A. 10.1002/chem.201100298 21344528 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2011 P06897, P84233, P62799, P02281 -
17 3UTB X-ray 2.20 2012-04-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b) Chua, E.Y.D., Vasudevan, D., Davey, G.E., Wu, B., Davey, C.A. 10.1093/nar/gks261 22453276 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P06897, P84233, P62799, P02281 -
18 5AV8 X-ray 2.20 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
19 5AV9 X-ray 2.20 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
20 5B1M X-ray 2.34 2017-02-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The mouse nucleosome structure containing H3.1 Ueda, J., Harada, A., Urahama, T., Machida, S., Maehara, K., Hada, M., Makino, Y., Nogami, J., Horikoshi, N., Osakabe, A., Taguchi, H., Tanaka, H., Tachiwana, H., Yao, T., Yamada, M., Iwamoto, T., Isotani, A., Ikawa, M., Tachibana, T., Okada, Y., Kimura, H., Ohkawa, Y., Kurumizaka, H., Yamagata, K. 10.1016/j.celrep.2016.12.065 28099840 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2017 P62806, C0HKE1, Q9D2U9, P68433 -
21 5CPI X-ray 2.90 2015-10-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_2R 146 Nucleosome containing unmethylated Sat2R DNA Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H. 10.1098/rsob.150128 26446621 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
22 5F99 X-ray 2.63 2016-02-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B MMTV 147 X-ray Structure of the MMTV-A Nucleosome Core Particle Frouws, T.D., Duda, S.C., Richmond, T.J. 10.1073/pnas.1524607113 26787910 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P06897, P84233, P62799, P02281 -
23 5NL0 X-ray 5.40 2017-05-17 octamer, hemisome 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0-B 601L 193 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Bednar, J., Garcia-Saez, I., Boopathi, R., Cutter, A.R., Papai, G., Reymer, A., Syed, S.H., Lone, I.N., Tonchev, O., Crucifix, C., Menoni, H., Papin, C., Skoufias, D.A., Kurumizaka, H., Lavery, R., Hamiche, A., Hayes, J.J., Schultz, P., Angelov, D., Petosa, C., Dimitrov, S. 10.1016/j.molcel.2017.04.012 28475873 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P22844, P06897, P62799, P02281, P84233 -
24 5ONW X-ray 2.80 2017-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 146 X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C Frouws, T.D., Barth, P.D., Richmond, T.J. 10.1016/j.jmb.2017.10.029 29113904 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P06897, P84233, P62799, P02281 -
25 5XF6 X-ray 2.63 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P06897, P84233, P62799, P02281 -
26 6A5O EM 9.90 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 178 RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P62805, P06899, P84243 0.083
27 6LER X-ray 3.00 2021-03-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 169 169 bp nucleosome harboring non-identical cohesive DNA termini. Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 P04908, P68431, P62805, P06899 -
28 8UXQ EM 6.30 2024-09-25 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 97 Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Sokolova, V., Miratsky, J., Svetlov, V., Brenowitz, M., Vant, J., Lewis, T.S., Dryden, K., Lee, G., Sarkar, S., Nudler, E., Singharoy, A., Tan, D. 10.1016/j.str.2024.09.013 39383876 Xenopus laevis Xenopus laevis Mus musculus Xenopus laevis Xenopus laevis 2024 Chromobox protein homolog 5 Heterochromatin-associated, Histone PTM readers, Histone_methylation_H3K9_reader, Transcription-associated P45973 P0C0S6, P84233, P62799, P02281 0.143
29 6X5A EM 4.36 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. 10.1038/s41586-020-2749-z 32911481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.265
30 6R8Y EM 4.30 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.313
31 9W74 EM 4.94 2025-12-10 hexamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 207 Cryo-EM structure of the close-packed di-hexasome (CPDH) Ho, C.H., Kobayashi, Y., Ogasawara, M., Takizawa, Y., Kurumizaka, H. 10.1016/j.isci.2025.114453 41541688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 P06897, P84233, P62799, P02281 0.224
32 9E1R EM 3.10 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassB4 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.616
33 9E1V EM 3.10 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassC2 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.586
34 9E1W EM 3.20 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassC3 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.578
35 9E2D EM 6.08 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 316 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.083
36 9E2Q EM 3.14 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 319 Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.145
37 9E3R EM 6.90 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 319 Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.068
38 9JAO EM 3.10 2025-04-30 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 104 The structure of SMARCAD1 bound to the hexasome in the presence of ADP-BeFx Hu, P., Sun, J., Sun, H., Chen, K., Sia, Y., Xia, X., Xi, Q., Chen, Z. 10.1038/s41586-025-09100-0 40468067 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 Heterochromatin-associated, SWI/SNF, DNA repair, Chromatin remodelers Q9H4L7 A0A310TTQ1, P06897, P62799, P02281 0.445
39 9JNP EM 2.30 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ATP state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.587
40 9JO5 EM 2.80 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP-B state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.482
41 9M76 EM 4.10 2026-03-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 UHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain. Naschberger, A., Baradaran, R., Sayed, A., Fischle, W. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 E3 ubiquitin-protein ligase UHRF1 Histone PTM readers, Histone PTM writers, E3 ubiquitin-protein ligation Q96T88 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.239
42 9OGS EM 3.05 2025-11-05 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_2R 128 Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v1) Shih, R.M., Arimura, Y., Konishi, H.A., Funabiki, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, P06899, P0C0S5 0.562
43 9S0U EM 6.72 2025-09-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 175 State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Histone-lysine N-methyltransferase SETD2, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit SPT16 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A8D1KNW4, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q9BYW2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.108
44 9WBZ EM 2.90 2026-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 154 The structure of NCP-motor-ARP module of ncBAF-nucleosome complex Chen, K., Du, L., Liu, Y., Chen, M., Chen, Z. 10.1038/s41421-025-00858-1 41402274 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 Isoform 2 of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4, Actin, cytoplasmic 1, Actin-like protein 6A, B-cell CLL/lymphoma 7 protein family member A SWI/SNF, Transcription-associated, Chromatin remodelers P51532, P60709, O96019, Q4VC05 Q6AZJ8, P84233, P62799, P02281 0.343
45 8PP7 EM 2.91 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 human RYBP-PRC1 bound to mononucleosome Ciapponi, M., Karlukova, E., Schkolziger, S., Benda, C., Muller, J. 10.1038/s41594-024-01258-x 38528151 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Polycomb, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496 P84040, P84051, P02283, P02299 0.511
46 9Y4P EM 3.84 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 321 Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 Isoform 7 of DNA (cytosine-5)-methyltransferase 3B, DNA (cytosine-5)-methyltransferase 3A DNA modification, Transcription-associated Q9UBC3, Q9Y6K1 P06897, P62799, P02281, A0A310TTQ1, P84233 -
47 5OY7 X-ray 5.77 2017-09-20 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 619 Structure of the 4_601_157 tetranucleosome (P1 form) Ekundayo, B., Richmond, T.J., Schalch, T. 10.1016/j.jmb.2017.09.002 28893533 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P06897, P84233, P62799, P02281 -
48 9R5S EM 3.80 2026-01-28 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 160 Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Hughes, A.L., Sundaramoorthy, R., Owen-Hughes, T. 10.7554/eLife.52513 41439750 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 P06897, P84233, P62799, P02281 0.256
49 5AVB X-ray 2.40 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
50 5B2I X-ray 3.00 2016-06-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146_4CpG 146 Human nucleosome containing CpG unmethylated DNA Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S. 10.1002/2211-5463.12064 27419055 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P04908, P68431, P62805, P06899 -
51 8JH3 EM 3.70 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P62805, P06899, P84243 0.255
52 5CPK X-ray 2.63 2015-10-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_2L 139 Nucleosome containing methylated Sat2L DNA Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H. 10.1098/rsob.150128 26446621 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
53 6UH5 EM 3.50 2019-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structural basis of COMPASS eCM recognition of the H2Bub nucleosome Hsu, P.L., Shi, H., Leonen, C., Kang, J., Chatterjee, C., Zheng, N. 10.1016/j.molcel.2019.10.013 31733991 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, Ubiquitin, Spp1 Telomere-associated, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Ubiquitin, Euchromatin-associated Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, P0CG47, Q6CRQ4 P62799, P02281, Q6AZJ8, Q92133, P84233 0.372
54 2CV5 X-ray 2.50 2005-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of human nucleosome core particle Tsunaka, Y., Kajimura, N., Tate, S., Morikawa, K. 10.1093/nar/gki663 15951514 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2005 O60814, P04908, P68431, P62805 -
55 6V2K X-ray 2.60 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The nucleosome structure after H2A-H2B exchange Hirano, R., Arimura, Y., Kujirai, T., Shibata, M., Okuda, A., Morishima, K., Inoue, R., Sugiyama, M., Kurumizaka, H. 10.1038/s42003-021-01707-z 33580188 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P68431, P62805, P06899 -
56 7E8D EM 2.80 2021-11-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 172 NSD2 E1099K mutant bound to nucleosome Sato, K., Kumar, A., Hamada, K., Okada, C., Oguni, A., Machiyama, A., Sakuraba, S., Nishizawa, T., Nureki, O., Kono, H., Ogata, K., Sengoku, T. 10.1038/s41467-021-26913-5 34782608 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Histone-lysine N-methyltransferase NSD2 Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated O96028 P68431, P62805, P06899, P0C0S8 0.556
57 9GMK EM 3.50 2025-01-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 SIRT7:H3K18DTU nucleosome complex Moreno-Yruela, C., Ekundayo, B.E., Foteva, P.N., Ni, D., Calvino-Sanles, E., Stahlberg, H., Fierz, B. 10.1038/s41467-025-56529-y 39900593 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 NAD-dependent protein deacetylase sirtuin-7 Histone_deacetylation_H3K36, Histone PTM erasers, Histone_deacetylation_H3K18 Q9NRC8 Q71DI3, P62805, Q6FI13, P06899 0.24
58 6NJ9 EM 2.96 2019-02-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C. 10.1016/j.cell.2019.02.002 30765112 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P06897, P84233, P62799, P02281 0.551
59 6R8Z EM 3.90 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP_THF2(-1)-UV-DDB Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.307
60 9DWJ EM 3.40 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 106 Nucleosome containing a 1-nt gap at SHL-3.5 Weaver, T.M., Ryan, B.J., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62807, P62805, P0C0S8 0.453
61 8V28 EM 3.36 2024-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2BK120ub-modified nucleosome ubiquitin position 4 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P06897, P84233, P62799, P02281 0.505
62 8OSL EM 4.90 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription factors, Transcription-associated O08785, Q9WTL8 P04908, P68431, P62805, P06899 0.177
63 8Q36 X-ray 2.60 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Batchelor, L.K., De Falco, L., Dyson, P.J., Davey, C.A. 10.1039/d4ra01617c 38495982 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 GAG structural protein DNA integration, Viral P14349 O60814, P04908, P68431, P62805 -
64 8Q3E X-ray 2.17 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Batchelor, L.K., De Falco, L., Dyson, P.J., Davey, C.A. 10.1039/d4ra01617c 38495982 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 GLY-GLY-TYR-ASN-LEU-ARG-PRO-ARG-THR-TYR-GLN-PRO-GLN-ARG-TYR-GLY-GLY-GLY DNA integration, Viral P14349 O60814, P04908, P68431, P62805 -
65 8QYV EM 3.50 2024-10-02 hexamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 118 SWR1-hexasome complex Jalal, A.S.B., Girvan, P., Chua, E.Y.D., Liu, L., Wang, S., McCormack, E.A., Skehan, M.T., Knight, C.L., Rueda, D.S., Wigley, D.B. 10.1016/j.molcel.2024.08.015 39226902 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, SWR1-complex protein 5, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, P38326, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04911, P61830 0.324
66 8SIY EM 2.90 2023-08-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome Sahu, S., Ekundayo, B.E., Kumar, A., Bleichert, F. 10.15252/embj.2023114654 37551430 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Leucine-rich repeat and WD repeat-containing protein 1, Origin recognition complex subunit 2 Heterochromatin-associated, DNA replication, ORC A0A140UHX1, Q75PQ8 P06897, P84233, P62799, P02281 0.497
67 8SKZ EM 3.50 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome Nartey, W., Williams, G.J. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera Heterochromatin-associated, Chromatin remodelers Q9XFH4 P06897, P84233, A0A8J1LTD2, P02281 0.458
68 8SMY EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.544
69 8SMZ EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.535
70 8SN6 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.434
71 8SNA EM 4.00 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.405
72 8T9G EM 6.20 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 215 Automethylated PRC2 dimer bound to nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Transcription-associated, Histone_methylation_H3K27_writer, Histone PTM writers, Heterochromatin-associated, Histone chaperones, Polycomb Q15022, Q15910, O75530, Q09028, Q6ZN18 P06897, P84233, P62799, P02281 0.163
73 8T9H EM 3.37 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 99 Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. 10.1016/j.molcel.2023.07.020 37595555 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 P06897, P84233, P62799, P02281 0.393
74 8VG2 EM 3.04 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 196 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Hepatocyte nuclear factor 3-alpha Transcription factors, Transcription-associated P55317 P68431, P04908, P10412, P62805, P06899 0.493
75 8OOA EM 3.18 2023-07-26 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 102 CryoEM Structure INO80core Hexasome complex Hexasome refinement state1 Zhang, M., Jungblut, A., Kunert, F., Hauptmann, L., Hoffmann, T., Kolesnikova, O., Metzner, F., Moldt, M., Weis, F., DiMaio, F., Hopfner, K.P., Eustermann, S. 10.1126/science.adf6287 37384673 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 P62807, P68431, P62805, Q93077 0.525
76 8VWS EM 3.10 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nucleosome containing 8oxoG at SHL-6 Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Q71DI3, P62807, P62805, P0C0S8 0.534
77 8W9D EM 3.90 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Wang, C., Chu, C., Guo, Z., Zhan, X. 10.1126/sciadv.adk7678 38598631 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Unclear peptide Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 O60814, P04908, P68431, P62805 0.263
78 8WH5 EM 3.58 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Structure of DDM1-nucleosome complex in the apo state Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9LD28, P59226, P59259, O23629 0.394
79 8XBT EM 4.12 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.199
80 8Y3F EM 4.54 2025-01-29 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Shimizu, M., Tanaka, H., Nishimura, M., Sato, N., Nozawa, K., Ehara, H., Sekine, S.I., Morishima, K., Inoue, R., Takizawa, Y., Kurumizaka, H., Sugiyama, M. 10.1093/pnasnexus/pgae484 39539301 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P04908, P68431, P62805, P06899 -
81 8YBJ EM 2.38 2024-07-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Kimura, T., Hirai, S., Kujirai, T., Fujita, R., Ogasawara, M., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1111/gtc.13143 38972377 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P04908, P68431, P62805, P06899 0.631
82 8YBK EM 2.69 2024-07-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 114 Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Kimura, T., Hirai, S., Kujirai, T., Fujita, R., Ogasawara, M., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1111/gtc.13143 38972377 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P04908, P68431, P62805, P06899 0.598
83 8ZJT EM 3.20 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 139 Structure of free nucleosome Xue, W., Han, Y., Tian, Y., Wang, J., Xie, Z., Zheng, X., Yue, X., Dong, S., Li, H., Luo, Z., Zhang, S., Yang, Y., Zou, Z., Li, W., Ma, N., Zhu, F., Chen, C., Yin, Y., Zhang, Y., Xu, K. 10.1093/nar/gkaf734 40744500 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 O60814, Q71DI3, P04908, P62805 0.511
84 9D3L EM 2.80 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 124 Two Dsup molecules in complex with the nucleosome open from the left side Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Damage suppressor protein Q71DI3, P62805, Q6FI13, Q99879 0.573
85 9E1N EM 3.40 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Snf2h bound nucleosome complex-ClassA3 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.512
86 9EH1 EM 3.10 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerase I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, Superkiller complex protein 8, N-terminally processed, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Transcription factors, Histone PTM writers, Transcription-associated, RNA polymerases, Histone_methylation_H3K4_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q96ST2, Q6PD62, Q92541, B7Z4W0, Q9GZS3, A0A2R8YHB3, P63272, Q9BYW2 A0A310TTQ1, P06897, P62799, P02281 0.237
87 9GE4 EM 3.52 2025-08-20 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 152 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., Hopfner, K.P. 10.1093/nar/gkag138 41775336 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P68431, P62805, Q16778, P0C0S5 0.448
88 8OSK EM 3.60 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 124 Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription factors, Transcription-associated O08785, Q9WTL8 P04908, P68431, P62805, P06899 0.267
89 8KD5 EM 2.90 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.378
90 6UXW EM 8.96 2020-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 SWI/SNF nucleosome complex with ADP-BeFx Han, Y., Reyes, A.A., Malik, S., He, Y. 10.1038/s41586-020-2087-1 32188938 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Transcription regulatory protein SNF2, SWI/SNF chromatin-remodeling complex subunit SWI1, SWI/SNF chromatin-remodeling complex subunit SNF5, SWI/SNF complex subunit SWI3, Transcription regulatory protein SNF12, Transcription regulatory protein SNF6, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 SWI/SNF, RSC (SWI/SNF), Transcription-associated, Chromatin remodelers P22082, P09547, P18480, P32591, P53628, P18888, Q12406, Q05123, P53330 P06897, P84233, P62799, P02281 0.122
91 7V9J EM 8.00 2022-07-27 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 399 Telomeric trinucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, P04908, P68431, P62805 0.107
92 6WZ5 EM 2.20 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Bilokapic, S., Suskiewicz, M.J., Ahel, I., Halic, M. 10.1038/s41586-020-2725-7 32939087 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 P06897, P84233, P62799, P02281 0.504
93 7BWD EM 4.32 2021-04-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Dot1L-H2BK34ub Nucleosome Complex Liu, L., Lou, Z.Y., Ai, H.S., Cao, L. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P62979 O60814, P04908, P68431, P62805 0.332
94 7EA8 EM 3.10 2021-07-14 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 122 Human SETD2 bound to a nucleosome containing oncohistone mutations Liu, Y., Zhang, Y., Xue, H., Cao, M., Bai, G., Mu, Z., Yao, Y., Sun, S., Fang, D., Huang, J. 10.1038/s41421-021-00261-6 33972509 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Histone-lysine N-methyltransferase SETD2 Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated Q9BYW2 P06899, P20671, Q6PI79, P62799 0.509
95 7K78 EM 3.10 2021-03-31 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 116 antibody and nucleosome complex Guan, R., Lian, T., Zhou, B.R., He, E., Wu, C., Singleton, M., Bai, Y. 10.1038/s41467-021-21985-9 33741944 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2021 scFv P02309, P02293, P04911, None 0.556
96 7OHA EM 2.90 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 122 nucleosome with TBP and TFIIA bound at SHL +2 Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription factors, Transcription-associated P13393, P32773, P32774 P06897, P84233, P62799, P02281 0.516
97 7PEZ EM 7.90 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 182 Nucleosome 4 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.203
98 7PF0 EM 11.00 2022-08-03 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 541 Trinucleosome of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.101
99 7PF3 EM 4.00 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Nucleosome 4 of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.351
100 7PFA EM 9.70 2022-08-03 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 561 Trinucleosome of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.084
101 7SSA EM 3.20 2023-04-05 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 137 Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome Donovan, B.T., Chen, H., Eek, P., Meng, Z., Jipa, C., Tan, S., Bai, L., Poirier, M.G. 10.1016/j.molcel.2023.03.006 36996811 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2023 Centromere-binding protein 1 Transcription-associated P17106 P02293, P84233, P04911, P62799 0.449
102 7UX9 EM 3.20 2023-08-09 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 141 Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA) Lee, S.C., Adams, D.W., Ipsaro, J.J., Cahn, J., Lynn, J., Kim, H.S., Berube, B., Major, V., Calarco, J.P., LeBlanc, C., Bhattacharjee, S., Ramu, U., Grimanelli, D., Jacob, Y., Voigt, P., Joshua-Tor, L., Martienssen, R.A. 10.1016/j.cell.2023.08.001 37643610 Arabidopsis thaliana Xenopus laevis Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2023 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9FJE8, O23629, P62799, P59169 0.445
103 7V9C EM 4.50 2022-07-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 273 Telomeric Dinucleosome in open state Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, P04908, P68431, P62805 0.109
104 7VDV EM 3.40 2022-05-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 The overall structure of human chromatin remodeling PBAF-nucleosome complex Yuan, J.J., Chen, K.J., Zhang, W.B., Chen, Z.C. 10.1038/s41586-022-04658-5 35477757 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Isoform 2 of Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2, PHD finger protein 10, Isoform 2 of Bromodomain-containing protein 7, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Protein polybromo-1 Transcription-associated, Chromatin remodelers, Cell cycle, PBAF (SWI/SNF), SWI/SNF P51532, O96019, P60709, Q68CP9, Q8WUB8, Q9NPI1, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q86U86 P06897, P84233, P62799, P02281 0.315
105 8JH4 EM 3.20 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 178 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P62805, P06899, P84243 0.313
106 7XFI EM 2.90 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 136 Structure of nucleosome-DI complex (-50I, Apo state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P06897, P84233, P62799, P02281 0.525
107 7XFM EM 3.10 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-3-methyladenine glycosylase DNA modification, DNA repair P29372 P06897, P84233, P62799, P02281 0.466
108 7XVM X-ray 2.84 2023-05-24 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H5 601L 169 Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Gallus gallus 2023 P02259, P68431, P04908, P62805, P06899 -
109 7YRG EM 4.20 2023-12-13 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 histone methyltransferase Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. 10.1016/j.molcel.2023.07.001 37536340 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 P84233, P02281, P62799, P0C0S5 0.227
110 8CZE EM 2.58 2023-06-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of a Xenopus Nucleosome with Widom 601 DNA Milano, C.R., Ur, S.N., Gu, Y., Zhang, J., Allison, R., Brown, G., Neale, M.J., Tromer, E.C., Corbett, K.D., Hochwagen, A. 10.1038/s44318-024-00034-3 38332377 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P06897, P84233, P62799, P02281 0.598
111 8DU4 EM 3.55 2022-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Rahman, S., Hoffmann, N.A., Worden, E.J., Smith, M.L., Namitz, K.E.W., Knutson, B.A., Cosgrove, M.S., Wolberger, C. 10.1073/pnas.2205691119 36095189 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 WD repeat-containing protein 5, Retinoblastoma-binding protein 5, Polyubiquitin-B Transcription-associated, COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Ubiquitin, Euchromatin-associated P61964, Q15291, P0CG47 P02302, P06897, P62799, P02281 0.237
112 8EUJ EM 3.36 2023-07-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2 of the INO80-Nucleosome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus Xenopus Xenopus Xenopus Xenopus laevis 2023 A0A310TTQ1, Q6AZJ8, P62798, A0A1B8Y854 0.322
113 8EVG EM 2.75 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 162bp CX3CR1 nucleosome (further classified with better nucleosome end) Tengfei, L., Ruifang, G., Yawen, B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Single-chain variable fragment P68431, P62805, Q16778, Q16777 0.531
114 8G6H EM 3.06 2024-02-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P06897, P84233, P62799, P02281 0.552
115 8HAG EM 3.20 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.29
116 8HQY EM 3.05 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 136 Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom Tong, Z., Ai, H., Xu, Z., He, K., Chu, G.C., Shi, Q., Deng, Z., Xue, Q., Sun, M., Du, Y., Liang, L., Li, J.B., Pan, M., Liu, L. 10.1038/s41594-023-01141-1 38177667 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Protein SSX2, Polyubiquitin-B (Fragment) Histone_ubiquitination_H2AK119_reader, Ubiquitin, Histone PTM readers, Transcription-associated Q16385, P0CG47 O60814, Q71DI3, P04908, P62805 0.47
117 8HR1 EM 3.02 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom Tong, Z., Ai, H., Xu, Z., He, K., Chu, G.C., Shi, Q., Deng, Z., Xue, Q., Sun, M., Du, Y., Liang, L., Li, J.B., Pan, M., Liu, L. 10.1038/s41594-023-01141-1 38177667 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 SSX1 Histone_ubiquitination_H2AK119_reader, Histone PTM readers, Transcription-associated Q16384 O60814, Q71DI3, P04908, P62805 0.532
118 9DWM EM 4.20 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 126 DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.31
119 9DWG EM 3.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite) Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.364
120 7XSZ EM 3.40 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 155 RNA polymerase II elongation complex transcribing a nucleosome (EC115) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.248
121 9JNV EM 3.00 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP(S) state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.49
122 8Y3D EM 5.10 2025-01-29 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Shimizu, M., Tanaka, H., Nishimura, M., Sato, N., Nozawa, K., Ehara, H., Sekine, S.I., Morishima, K., Inoue, R., Takizawa, Y., Kurumizaka, H., Sugiyama, M. 10.1093/pnasnexus/pgae484 39539301 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P04908, P68431, P62805, P06899 -
123 8YV8 EM 3.00 2024-07-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Wassing, I.E., Nishiyama, A., Shikimachi, R., Jia, Q., Kikuchi, A., Hiruta, M., Sugimura, K., Hong, X., Chiba, Y., Peng, J., Jenness, C., Nakanishi, M., Zhao, L., Arita, K., Funabiki, H. 10.1126/sciadv.adp5753 39178260 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Cell division cycle-associated protein 7 Methylated DNA binding Q9BWT1 O60814, P04908, P68431, P62805 0.524
124 9C9G EM 2.91 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 144 S.c INO80 in complex with S.c 0/80 nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62799, P02293, P04911, P61830 0.445
125 9C9X EM 2.83 2025-07-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 A0A310TTQ1, P06897, P62799, P02281 0.494
126 9DBY EM 2.80 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, RING1 and YY1-binding protein, Ubiquitin Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Histone PTM readers, Histone_ubiquitination_reader, Polycomb, Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496, Q8N488, P0CG48 P06897, P84233, P62799, P02281 0.39
127 9DGG EM 2.98 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 ncPRC1RYBP bound to unmodified nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Polycomb, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496 P06897, P84233, P62799, P02281 0.47
128 9E1O EM 3.30 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Snf2h bound nucleosome complex - ClassB1 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.538
129 9E1Y EM 2.60 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Empty Nucleosome with 601 widom sequence Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1101/2024.12.31.630910 39803580 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 P06897, P84233, P62799, P02281 0.685
130 9E3U EM 4.90 2026-01-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 165 Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Isoform 3 of DNA (cytosine-5)-methyltransferase 3B, DNA (cytosine-5)-methyltransferase 3A DNA modification, Transcription-associated Q9UBC3, Q9Y6K1 Q71DI3, A0A1B8Y854, P62805, None 0.124
131 9EGZ EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_methylation_H3K36_writer, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 A0A310TTQ1, P06897, P62799, P02281 0.261
132 9GD1 EM 4.00 2024-09-18 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 259 Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Engeholm, M., Roske, J.J., Oberbeckmann, E., Dienemann, C., Lidschreiber, M., Cramer, P., Farnung, L. 10.1016/j.molcel.2024.08.022 39270644 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 P06897, P84233, P62799, P02281 0.332
133 9II7 EM 3.50 2025-06-11 hexamer 1 H3.3 canonical_H4 H2A.B canonical_H2B 601_modified 114 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Akatsu, M., Hirano, R., Kujirai, T., Ogasawara, M., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1038/s44318-025-00473-6 40447801 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, C4QWA8, C4QZ45, C4R0E6, C4R370 P0C5Z0, P62805, P06899, P84243 0.285
134 9K3Z EM 2.75 2025-05-14 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 145 Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Wang, Y., Wu, J., Yang, S., Li, X., Wang, J., Lv, Q., Zhu, X., Lu, G., Zhang, J., Shen, W.H., Liu, B., Lin, J., Dong, A. 10.1016/j.str.2025.04.015 40359943 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2025 Q9C944, P59226, P59259, Q9LQQ4 0.498
135 8VWT EM 3.30 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA modification, DNA repair O15527 Q71DI3, P62807, P62805, P0C0S8 0.41
136 9OB1 EM 3.20 2026-03-04 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 145 S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2026 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62798, P02293, P04911, P61830 0.374
137 9OGR EM 2.78 2025-11-05 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_2R 116 Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v1) Shih, R.M., Arimura, Y., Konishi, H.A., Funabiki, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, P06899, P0C0S5 0.579
138 6MUP EM 3.50 2019-07-24 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 147 CENP-A nucleosome bound by two copies of CENP-C(CD) and two copies CENP-N(NT) Allu, P.K., Dawicki-McKenna, J.M., Van Eeuwen, T., Slavin, M., Braitbard, M., Xu, C., Kalisman, N., Murakami, K., Black, B.E. 10.1016/j.cub.2019.06.062 31353180 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 Centromere protein C, Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188, Q96H22 P49450, Q5QNW6, P62805, Q93077 0.401
139 7BY0 EM 4.50 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C Ariyoshi, M., Makino, F., Watanabe, R., Nakagawa, R., Kato, T., Namba, K., Arimura, Y., Fujita, R., Kurumizaka, H., Okumura, E.I., Hara, M., Fukagawa, T. 10.15252/embj.2020105671 33463726 Gallus gallus Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Maltose Binding Protein tag, linker,CENP-C P0AEX9 P04908, P62805, P06899, P84229 0.297
140 7XZZ EM 4.07 2022-10-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Cryo-EM structure of the nucleosome in complex with p53 Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.192
141 6HTS EM 4.80 2018-11-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Cryo-EM structure of the human INO80 complex bound to nucleosome Ayala, R., Willhoft, O., Aramayo, R.J., Wilkinson, M., McCormack, E.A., Ocloo, L., Wigley, D.B., Zhang, X. 10.1038/s41586-018-0021-6 29643506 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit B Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q9C086 P04908, P68431, P62805, P06899 0.181
142 8SN3 EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.429
143 7ZI4 EM 3.20 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Vance, N.R., Ayala, R., Willhoft, O., Tvardovskiy, A., McCormack, E.A., Bartke, T., Zhang, X., Wigley, D.B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit C, INO80 complex subunit B Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q6PI98, Q9C086 P04908, P68431, P62805, P06899 0.462
144 5B0Z X-ray 1.99 2016-01-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Suzuki, Y., Horikoshi, N., Kato, D., Kurumizaka, H. 10.1016/j.bbrc.2015.12.041 26694698 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 Q71DI3, P04908, P62805, P06899 -
145 6UPL EM 7.40 2019-12-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 79 Structure of FACT_subnucleosome complex 2 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription-associated, Histone chaperones, FACT, DNA replication, DNA repair Q9Y5B9, Q08945 P62807, P68431, P62805, Q93077 0.173
146 6UPK EM 4.90 2019-12-11 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 72 Structure of FACT_subnucleosome complex 1 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription-associated, Histone chaperones, FACT, DNA replication, DNA repair Q9Y5B9, Q08945 P62807, P68431, P62805, Q93077 0.203
147 8X1C EM 3.20 2024-03-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of nucleosome-bound SRCAP-C in the ADP-bound state Yu, J., Sui, F., Gu, F., Li, W., Yu, Z., Wang, Q., He, S., Wang, L., Xu, Y. 10.1038/s41421-023-00640-1 38331872 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2, Actin, cytoplasmic 1, Actin-like protein 6A, DNA methyltransferase 1-associated protein 1, YEATS domain-containing protein 4 Transcription-associated, Chromatin remodelers, Cell cycle, SRCAP (INO80), Histone chaperones, Histone PTM readers, INO80, Histone_acetylation_reader, Euchromatin-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P68431, P62807, P62805, Q93077 0.297
148 8WH8 EM 3.60 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 125 Structure of DDM1-nucleosome complex in ADP state Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9LD28, P59226, P59259, O23629 0.403
149 8VO0 EM 3.30 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 Q71DI3, Q6AZJ8, P62805, P02281 0.258
150 9E00 EM 3.75 2026-02-25 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 321 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, None -
151 8KCY EM 2.80 2025-03-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 193 Structure of nucleosome complexed with two DEK molecules Kujirai, T., Echigoya, K., Kishi, Y., Saeki, M., Ito, T., Kato, J., Negishi, L., Kimura, H., Masumoto, H., Takizawa, Y., Gotoh, Y., Kurumizaka, H. 10.1038/s41594-025-01493-w 39984731 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Protein DEK P35659 P04908, P68431, P62805, P06899 0.479
152 7YYH EM 8.90 2022-05-18 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 153 Structure of the human CCANdeltaT CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein U, Centromere protein C CENP-A NAC/CAD, Transcription-associated, Cell cycle, Centromere-associated, Nuclear division, Kinetochore Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q71F23, Q03188 P49450, P62807, P62805, Q93077 0.075
153 7ZS9 EM 3.10 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription factors, RNA polymerases, Transcription-associated, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P06897, P84233, P62799, P02281 0.34
154 5B32 X-ray 2.35 2016-08-03 octamer 1 H3.3 canonical_H4 canonical_H2A,H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Horikoshi, N., Arimura, Y., Taguchi, H., Kurumizaka, H. 10.1098/rsob.160127 27358293 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P0C0S5, P84243, P04908, P62805, P06899 -
155 8BVW EM 4.00 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 206 RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Cell cycle, Transcription factors, RNA polymerases, DNA repair, Euchromatin-associated P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P06897, P84233, P62799, P02281 0.234
156 8CWW EM 2.74 2023-06-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of S. cerevisiae Hop1 CBR bound to a nucleosome Milano, C.R., Ur, S.N., Gu, Y., Zhang, J., Allison, R., Brown, G., Neale, M.J., Tromer, E.C., Corbett, K.D., Hochwagen, A. 10.1038/s44318-024-00034-3 38332377 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Meiosis-specific protein HOP1 Nuclear division P20050 P06897, P84233, P62799, P02281 0.574
157 8G6G EM 2.93 2024-02-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P06897, P84233, P62799, P02281 0.575
158 8GRM EM 3.05 2023-04-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.chempr.2023.01.012 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 COMMD3 protein, Ring1B, Ubiquitin, UbcH5b Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Polycomb, Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496, P0CG47, P62837 O60814, P04908, P68431, P62805 0.516
159 8HAI EM 4.70 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.212
160 8HAJ EM 4.80 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 164 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.2
161 8HAN EM 4.20 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Transcription-associated, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P04908, P68431, P62805, P06899 0.209
162 8IEG EM 3.44 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.molcel.2023.08.001 37633270 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1, Ubiquitin-conjugating enzyme E2 2 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, DNA repair, Telomere-associated Q07457, P06104 O60814, P04908, P68431, P62805 0.393
163 8JLA EM 3.44 2023-10-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 156 Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Ehara, H., Sekine, S.I., Hayashi, G., Takizawa, Y., Kurumizaka, H. 10.1093/nar/gkad754 37718728 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 P04908, P68431, P62805, P06899 0.453
164 8OX1 EM 2.70 2023-08-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 Structure of TRF1core in complex with telomeric nucleosome Hu, H., van Roon, A.M., Ghanim, G.E., Ahsan, B., Oluwole, A.O., Peak-Chew, S.Y., Robinson, C.V., Nguyen, T.H.D. 10.1126/sciadv.adi4148 37624885 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Telomeric repeat-binding factor 1 Cell cycle, DNA repair, Telomere-associated, Shelterin P54274 P62807, P68431, P62805, Q93077 0.579
165 8VMJ EM 3.10 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K4me3 nucleosome bound to PRC2_AJ119-450 Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 Q71DI3, Q6AZJ8, P62805, A0A8J1LZU9 0.402
166 8PKJ EM 2.50 2024-02-28 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of the nucleosome containing Nr5a2 motif at SHL+5.5 Kobayashi, W., Sappler, A.H., Bollschweiler, D., Kummecke, M., Basquin, J., Arslantas, E.N., Ruangroengkulrith, S., Hornberger, R., Duderstadt, K., Tachibana, K. 10.1038/s41594-024-01239-0 38409506 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2024 P62806, P84244, C0HKE1, Q6ZWY9 0.6
167 8SMW EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.526
168 8SN4 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.439
169 8SN7 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.445
170 8SN9 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.424
171 8T9F EM 2.60 2023-09-06 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 122 Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. 10.1016/j.molcel.2023.07.020 37595555 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 P84233, P02281, P62799, P0C0S5 0.516
172 8U5H EM 3.23 2024-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome Chen, X., Guo, Y., Zhao, T., Lu, J., Fang, J., Wang, Y., Wang, G.G., Song, J. 10.1038/s41467-024-50526-3 39043678 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA (cytosine-5)-methyltransferase 3A, Ubiquitin Ubiquitin, DNA modification Q9Y6K1, P0CG48 P02302, P06897, P62799, P02281 0.443
173 8UBL EM 2.80 2026-01-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 162 Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 scFv, Achaete-scute homolog 1, Transcription factor E2-alpha Heterochromatin-associated, Transcription factors, Transcription-associated Q02067, P15806 P04908, P68431, P62805, P06899 0.506
174 8UPF EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.464
175 8V27 EM 3.34 2024-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2BK120ub-modified nucleosome ubiquitin position 3 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P06897, P84233, P62799, P02281 0.516
176 8VFX EM 2.65 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 158 Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 scFv P04908, P68431, P62805, P06899 0.559
177 8VFY EM 2.89 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 171 Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Hepatocyte nuclear factor 3-alpha Transcription factors, Transcription-associated P55317 P04908, P68431, P62805, P06899 0.463
178 8TAS EM 4.10 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 193 PRC2 monomer bound to nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Transcription-associated, Histone_methylation_H3K27_writer, Histone PTM writers, Heterochromatin-associated, Histone chaperones, Polycomb Q15022, Q15910, O75530, Q09028, Q6ZN18 P06897, P84233, P62799, P02281 0.259
179 9CAB EM 3.94 2025-06-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 169 Cryo-EM structure of human SRCAP-nucleosome complex in the encounter state (composite structure) Park, G., Patel, A.B., Wu, C., Louder, R.K. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2 Transcription-associated, Chromatin remodelers, Cell cycle, SRCAP (INO80), Histone chaperones, INO80, Euchromatin-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230 P06897, P62799, P84233, P02281 0.266
180 9CAN EM 3.30 2025-07-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 S.c INO80 in complex with Xenopus 0/40 nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.36
181 8IHL EM 7.64 2024-01-17 octamer, hexamer, hexamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 353 Overlapping tri-nucleosome Nishimura, M., Fujii, T., Tanaka, H., Maehara, K., Morishima, K., Shimizu, M., Kobayashi, Y., Nozawa, K., Takizawa, Y., Sugiyama, M., Ohkawa, Y., Kurumizaka, H. 10.1038/s42003-023-05694-1 38191828 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P04908, P68431, P62805, P06899 0.109
182 7XVL X-ray 3.51 2023-05-24 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 169 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Adhireksan, Z., Sharma, D., Qiuye, B., Lee, P.L., Padavattan, S., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P68431, P07305, P04908, P62805, P06899 -
183 8AV6 EM 4.68 2022-12-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 CryoEM structure of INO80 core nucleosome complex in closed grappler conformation Kunert, F., Metzner, F.J., Jung, J., Hopfler, M., Woike, S., Schall, K., Kostrewa, D., Moldt, M., Chen, J.X., Bantele, S., Pfander, B., Eustermann, S., Hopfner, K.P. 10.1126/sciadv.add3189 36490333 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 RuvB-like helicase, Ino80, PAPA-1 domain-containing protein, YL1_C domain-containing protein, DASH complex subunit DAD4 INO80, Chromatin remodelers G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 Q71DI3, P62807, P62805, P0C0S8 -
184 8BZ1 EM 3.80 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2 Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, I3LJZ9, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657 P06897, P84233, P62799, P02281 0.244
185 8COM EM 3.30 2023-07-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 Structure of the Nucleosome Core Particle from Trypanosoma brucei Deak, G., Wapenaar, H., Sandoval, G., Chen, R., Taylor, M.R.D., Burdett, H., Watson, J.A., Tuijtel, M.W., Webb, S., Wilson, M.D. 10.1093/nar/gkad577 37427792 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Xenopus laevis 2023 Q57Z31, Q4GYX7, Q389T1, Q57YA3 0.439
186 8EU2 EM 2.93 2023-07-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Class3 of the INO80-Hexasome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.434
187 8EVJ EM 4.10 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 138 CX3CR1 nucleosome bound PU.1 and C/EBPa Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 ScFv, Transcription factor PU.1 Transcription factors, Euchromatin-associated, Transcription-associated P17433 P68431, P62805, Q16778, Q16777 0.31
188 8G6S EM 3.47 2024-02-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2AK119ub-modified nucleosome ubiquitin position 2 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P06897, P84233, P62799, P02281 0.445
189 8GUJ EM 2.80 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1-nucleosome complex (Model II) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK120_writer Q5VTR2, O75150 P68431, P62805, P06899, P0C0S8 0.532
190 8GUK EM 2.51 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Human nucleosome core particle (free form) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 P68431, P62805, P06899, P0C0S8 0.588
191 8HAH EM 3.90 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 164 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.159
192 8HE5 EM 6.95 2023-07-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, DNA repair protein Transcription factors, Transcription-associated, RNA polymerases, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R198 P04908, P68431, P62805, P06899 0.105
193 8HY0 EM 3.10 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.463
194 8IHT EM 3.72 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Rpd3S bound to the nucleosome Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. 10.1038/s41422-023-00884-2 37845487 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, RCO1 isoform 1, Chromatin modification-related protein EAF3 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q04779, Q12432 P06897, P84233, P62799, P02281 0.345
195 7U4D EM 8.10 2022-03-30 octamer, octamer 2 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 139 CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and 601 DNA sequence Zhou, K., Gebala, M., Woods, D., Sundararajan, K., Edwards, G., Krzizike, D., Wereszczynski, J., Straight, A.F., Luger, K. 10.1038/s41594-022-00758-y 35422519 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q96H22 P49450, P62807, P62805, Q93077 0.114
196 8J90 EM 4.71 2024-07-03 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 111 Cryo-EM structure of DDM1-nucleosome complex Osakabe, A., Takizawa, Y., Horikoshi, N., Hatazawa, S., Negishi, L., Sato, S., Berger, F., Kakutani, T., Kurumizaka, H. 10.1038/s41467-024-49465-w 38992002 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9FJE8, P59226, P59259, O23629 0.243
197 8J92 EM 2.90 2024-07-03 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 149 Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W Osakabe, A., Takizawa, Y., Horikoshi, N., Hatazawa, S., Negishi, L., Sato, S., Berger, F., Kakutani, T., Kurumizaka, H. 10.1038/s41467-024-49465-w 38992002 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 Q9FJE8, P59226, P59259, O23629 0.53
198 8JHF EM 3.68 2023-11-15 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 160 Native SUV420H1 bound to 167-bp nucleosome Lin, F., Zhang, R., Shao, W., Lei, C., Ma, M., Zhang, Y., Wen, Z., Li, W. 10.1038/s41421-023-00620-5 38052811 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 O60814, P68431, P62805, P0C0S5 0.433
199 8JNE EM 4.68 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.13
200 8QZ0 EM 3.80 2024-10-02 octamer 1 H3.3 canonical_H4 H2A.X,H2A.Z canonical_H2B 601 113 SWR1-hexasome-dimer complex Jalal, A.S.B., Girvan, P., Chua, E.Y.D., Liu, L., Wang, S., McCormack, E.A., Skehan, M.T., Knight, C.L., Rueda, D.S., Wigley, D.B. 10.1016/j.molcel.2024.08.015 39226902 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Histone H2A.Z-specific chaperone CHZ1, Helicase SWR1, SWR1-complex protein 5, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 Transcription-associated, Chromatin remodelers, Histone chaperones, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated P40019, Q05471, P38326, Q12509, Q03433, Q03940, Q12464, Q03388 P61830, Q12692, P02309, P02293, P04911 0.293
201 8RUQ EM 2.29 2025-02-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Borealin N-terminus in complex with H3.T3p-nucleosome Ruza, R.R., Chung, C.W., Gold, D.B.H., Serena, M., Roberts, E., Gruneberg, U., Barr, F.A. 10.1038/s44319-025-00523-4 40664717 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Borealin Nuclear division, CPC Q53HL2 P62799, P02281, A0A310TTQ1, Q6AZJ8, P84233 0.618
202 8SN5 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.41
203 8T3W EM 3.25 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state2 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Telomere-associated Q07457 P06897, P84233, P62799, P02281 0.52
204 8VX6 EM 3.20 2024-10-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Human OGG1 bound at the nucleosomal DNA entry site You, Q., Feng, X., Cai, Y., Baylin, S.B., Li, H. 10.1038/s42003-024-06919-7 39341999 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 N-glycosylase/DNA lyase DNA modification, DNA repair O15527 P06897, P84233, P62799, P02281 0.424
205 8X7K EM 3.27 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair P61077, Q8IYW5 O60814, Q71DI3, P04908, P62805 0.423
206 8YTI X-ray 2.70 2024-04-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.10 601L 169 Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Adhireksan, Z., Sharma, D., Qiuye, B., Lee, P.L., Padavattan, S., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Q92522, P68431, P04908, P62805, P06899 -
207 9C9S EM 3.09 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 147 S.c INO80 in complex with S.c 0/40 nucleosome, Class 1 Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62799, P02293, P04911, P61830 0.424
208 7V9S EM 11.00 2022-07-27 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 388 Telomeric trinucleosome in open state Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, P04908, P68431, P62805 0.093
209 7U0I EM 2.60 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of LIN28b nucleosome bound 2 OCT4 Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Single-chain variable fragment, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 P0AEX9 P68431, P62805, Q16778, Q16777 0.548
210 1P3A X-ray 3.00 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
211 6KW4 EM 7.55 2019-11-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 The ClassB RSC-Nucleosome Complex Ye, Y., Wu, H., Chen, K., Clapier, C.R., Verma, N., Zhang, W., Deng, H., Cairns, B.R., Gao, N., Chen, Z. 10.1126/science.aay0033 31672915 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Chromatin structure-remodeling complex protein RSC58, Chromatin structure-remodeling complex protein RSC30, Chromatin structure-remodeling complex protein RSC8, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC6, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex subunit RSC4, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Cell cycle, RSC (SWI/SNF), Transcription-associated, Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P06897, P84233, P62799, P02281 0.099
212 5WCU X-ray 5.53 2018-10-31 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H5 601 164 Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Zhou, B.R., Jiang, J., Ghirlando, R., Norouzi, D., Sathish Yadav, K.N., Feng, H., Wang, R., Zhang, P., Zhurkin, V., Bai, Y. 10.1016/j.jmb.2018.06.020 29959925 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Gallus gallus 2018 P84040, P02283, P02259, P02299, P84051 -
213 9ZEO EM 3.10 2026-03-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Chakraborty, U., Saccone, E.C., Becerra, G.C., Khan, L.F., Arslanovic, N., Aguilar, R., Gloor, S.L., Hunt, S.R., Folkwein, H.J., Husby, N.L., Maier, K.E., Marunde, M.R., Schomburg, N.K., Vaidya, A., Cowles, M.W., Venters, B.J., Kassavetis, G., Sun, Z.-W., Kadonaga, J.T., Armache, J.-P., Keogh, M.-C., Tyler, J.K. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Single-chain antibody (VHH) 1G1 O60814, P04908, P68431, P62805 0.532
214 3O62 X-ray 3.22 2011-01-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link Todd, R.C., Lippard, S.J. 10.1016/j.chembiol.2010.10.018 21168769 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2011 P06897, P84233, P62799, P02281 -
215 3REJ X-ray 2.55 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P06897, P84233, P62799, P02281 -
216 3UT9 X-ray 2.20 2012-04-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L) Chua, E.Y.D., Vasudevan, D., Davey, G.E., Wu, B., Davey, C.A. 10.1093/nar/gks261 22453276 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P06897, P84233, P62799, P02281 -
217 4KGC X-ray 2.69 2014-03-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM Adhireksan, Z., Davey, G.E., Campomanes, P., Groessl, M., Clavel, C.M., Yu, H., Nazarov, A.A., Yeo, C.H., Ang, W.H., Droge, P., Rothlisberger, U., Dyson, P.J., Davey, C.A. 10.1038/ncomms4462 24637564 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2014 Q6AZJ8, P84233, P62799, P02281 -
218 5O9G EM 4.80 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 162 Structure of nucleosome-Chd1 complex Farnung, L., Vos, S.M., Wigge, C., Cramer, P. 10.1038/nature24046 29019976 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 P06897, P84233, P62799, P02281 0.018
219 5Z23 X-ray 2.73 2019-02-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Arimura, Y., Tachiwana, H., Takagi, H., Hori, T., Kimura, H., Fukagawa, T., Kurumizaka, H. 10.1038/s41467-019-08314-x 30718488 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P04908, P68431, P62805, P06899 -
220 6A5T EM 6.70 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P62805, P06899, P84243 0.151
221 6J99 EM 4.10 2019-02-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Yao, T., Jing, W., Hu, Z., Tan, M., Cao, M., Wang, Q., Li, Y., Yuan, G., Lei, M., Huang, J. 10.1038/s41422-019-0146-7 30770869 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P62979 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.132
222 6JR1 X-ray 2.40 2019-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the human nucleosome phased with 16 selenium atoms Saotome, M., Horikoshi, N., Urano, K., Kujirai, T., Yuzurihara, H., Kurumizaka, H., Kagawa, W. 10.1107/S2059798319012713 31588924 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P04908, P68431, P62805, P06899 -
223 6KVD X-ray 2.21 2019-12-18 octamer 1 canonical_H3 canonical_H4 H2A.J canonical_H2B alphasat_146 146 Crystal structure of human nucleosome containing H2A.J Tanaka, H., Sato, S., Koyama, M., Kujirai, T., Kurumizaka, H. 10.1093/jb/mvz109 31793981 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P06899, P68431, P62805, Q9BTM1 -
224 6NQA EM 3.54 2019-02-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C. 10.1016/j.cell.2019.02.002 30765112 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG48 P06897, P84233, P62799, P02281 0.436
225 7U0G EM 2.60 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 133 structure of LIN28b nucleosome bound 3 OCT4 Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Maltodextrin-binding protein,POU domain, class 5, transcription factor 1, Single-chain variable fragment P0AEX9 P68431, P62805, Q16778, Q16777 0.531
226 6R1U EM 4.36 2019-04-24 octamer 1 H3.3,canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Marabelli, C., Marrocco, B., Pilotto, S., Chittori, S., Picaud, S., Marchese, S., Ciossani, G., Forneris, F., Filippakopoulos, P., Schoehn, G., Rhodes, D., Subramaniam, S., Mattevi, A. 10.1016/j.celrep.2019.03.061 30970244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Lysine-specific histone demethylase 1B, Putative oxidoreductase GLYR1 Histone_methylation_H3K36_reader, Transcription-associated, Histone PTM readers, Histone PTM erasers, Histone_demethylation_H3K4, Euchromatin-associated Q8NB78, Q49A26 P06897, P84233, P62799, P02281 0.198
227 6R25 EM 4.61 2019-04-24 octamer 1 H3.3,canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3 Marabelli, C., Marrocco, B., Pilotto, S., Chittori, S., Picaud, S., Marchese, S., Ciossani, G., Forneris, F., Filippakopoulos, P., Schoehn, G., Rhodes, D., Subramaniam, S., Mattevi, A. 10.1016/j.celrep.2019.03.061 30970244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Lysine-specific histone demethylase 1B, NPAC Histone_methylation_H3K36_reader, Transcription-associated, Histone PTM readers, Histone PTM erasers, Histone_demethylation_H3K4, Euchromatin-associated Q8NB78, Q49A26 P06897, P84233, P62799, P02281 0.186
228 6S01 EM 3.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Wang, H., Farnung, L., Dienemann, C., Cramer, P. 10.1038/s41594-019-0345-4 31819277 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.529
229 6UGM EM 3.70 2019-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structural basis of COMPASS eCM recognition of an unmodified nucleosome Hsu, P.L., Shi, H., Leonen, C., Kang, J., Chatterjee, C., Zheng, N. 10.1016/j.molcel.2019.10.013 31733991 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, H3 N-terminus, Spp1 Telomere-associated, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, Q6CRQ4 Q6AZJ8, Q92133, P62799, P02281 0.385
230 6V92 EM 20.00 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 RSC-NCP Patel, A.B., Moore, C.M., Greber, B.J., Luo, J., Zukin, S.A., Ranish, J., Nogales, E. 10.7554/eLife.54449 31886770 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Actin-related protein 7, Actin-like protein ARP9, High temperature lethal protein 1, Chromatin structure-remodeling complex protein RSC14, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC4, Chromatin structure-remodeling complex protein RSC8, Chromatin structure-remodeling complex protein RSC6, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex protein RSC58, Regulator of Ty1 transposition protein 102, Chromatin structure-remodeling complex subunit SFH1, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC30 Cell cycle, RSC (SWI/SNF), Transcription-associated, Chromatin remodelers Q12406, Q05123, Q9URQ5, P38210, P32832, Q06488, Q06639, Q02206, P43609, P25632, Q03124, Q07979, P53330, Q06168, P32597, P38781 O60814, P04908, P68431, P62805 0.053
231 6VYP X-ray 4.99 2020-05-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 191 Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Kim, S.A., Zhu, J., Yennawar, N., Eek, P., Tan, S. 10.1016/j.molcel.2020.04.019 32396821 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Lysine-specific histone demethylase 1A, REST corepressor 1 Histone_demethylation_H3K9, Histone_demethylation_H3K4, Histone PTM erasers, Transcription-associated O60341, Q9UKL0 P06897, P84233, P62799, P02281 -
232 7A08 EM 3.11 2020-09-23 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 132 CryoEM Structure of cGAS Nucleosome complex Michalski, S., de Oliveira Mann, C.C., Stafford, C.A., Witte, G., Bartho, J., Lammens, K., Hornung, V., Hopfner, K.P. 10.1038/s41586-020-2748-0 32911480 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 P84243, P62807, P62805, Q93077 0.533
233 7CRP EM 3.20 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode) Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD3 Histone_methylation_H3K4_writer, Histone_methylation_H3K27_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated Q9BZ95 P06897, Q92133, P62799, P02281 0.542
234 7EA5 EM 3.30 2021-07-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Yeast Set2 bound to a nucleosome containing oncohistone mutations Liu, Y., Zhang, Y., Xue, H., Cao, M., Bai, G., Mu, Z., Yao, Y., Sun, S., Fang, D., Huang, J. 10.1038/s41421-021-00261-6 33972509 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-36 specific Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated P46995 Q6AZJ8, P84233, P62799, P02281 0.473
235 7ENN EM 2.80 2021-07-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The structure of ALC1 bound to the nucleosome Wang, L., Chen, K., Chen, Z. 10.1038/s41467-021-24320-4 34210977 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P62799, P84233, P02281 0.567
236 7PEW EM 4.60 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 176 Nucleosome 1 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P04908, P62805 0.29
237 7R5R EM 2.44 2022-04-27 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 133 Structure of the human CCAN CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 P49450, P62807, P62805, Q93077 0.571
238 9GEO EM 2.79 2025-08-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome core particle Burn, G.L., Raisch, T., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Gimber, N., Raunser, S., Zychlinsky, A. 10.1038/s41586-025-09523-9 40963017 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 P06897, P84233, P62799, P02281 0.608
239 9IHE EM 2.95 2025-08-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome core particle bound by two molecules of DTT-reduced native monomeric myeloperoxidase Burn, G.L., Raisch, T., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Gimber, N., Raunser, S., Zychlinsky, A. 10.1038/s41586-025-09523-9 40963017 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Myeloperoxidase light chain Neutrophil extracellular traps P05164 P06897, P84233, P62799, P02281 0.578
240 9JNW EM 2.90 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of isw1-nucleosome complex in ADP+ state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.496
241 7NL0 EM 3.50 2021-08-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 131 Cryo-EM structure of the Lin28B nucleosome core particle Roberts, G.A., Ozkan, B., Gachulincova, I., O'Dwyer, M.R., Hall-Ponsele, E., Saxena, M., Robinson, P.J., Soufi, A. 10.1038/s41556-021-00727-5 34354236 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 P04908, P68431, P62805, P06899 0.519
242 6LA8 X-ray 3.40 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 349 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A. 10.1038/s41467-020-18533-2 32958761 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P68431, P07305, P04908, P62805, P06899 -
243 6M44 X-ray 3.81 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 355 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A. 10.1038/s41467-020-18533-2 32958761 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P68431, P62805, P06899 -
244 6M4G EM 2.80 2020-09-23 octamer 1 canonical_H3 canonical_H4 H2A.B canonical_H2B 601 93 Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Zhou, M., Dai, L., Li, C., Shi, L., Huang, Y., Guo, Z., Wu, F., Zhu, P., Zhou, Z. 10.15252/embj.2020105907 33073403 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P68431, P62805, Q16778, P0C5Z0 0.493
245 6RNY EM 3.90 2019-09-25 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B Human-D02 128 PFV intasome - nucleosome strand transfer complex Wilson, M.D., Renault, L., Maskell, D.P., Ghoneim, M., Pye, V.E., Nans, A., Rueda, D.S., Cherepanov, P., Costa, A. 10.1038/s41467-019-12007-w 31519882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 Integrase DNA integration, Viral P14350 P0C0S8, P62807, P62805, P84243 0.349
246 6RYR EM 3.10 2020-07-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Nucleosome-CHD4 complex structure (single CHD4 copy) Farnung, L., Ochmann, M., Cramer, P. 10.7554/eLife.56178 32543371 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 4,Chromodomain-helicase-DNA-binding protein 4,Chromodomain-helicase-DNA-binding protein 4 NuRD (CHD), Chromatin remodelers Q14839 P06897, P84233, P62799, P02281 0.52
247 6ZHY EM 3.00 2020-12-23 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class. Lehmann, L.C., Bacic, L., Hewitt, G., Brackmann, K., Sabantsev, A., Gaullier, G., Pytharopoulou, S., Degliesposti, G., Okkenhaug, H., Tan, S., Costa, A., Skehel, J.M., Boulton, S.J., Deindl, S. 10.1016/j.celrep.2020.108529 33357431 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.516
248 7AT8 EM 4.40 2020-12-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Finogenova, K., Bonnet, J., Poepsel, S., Schafer, I.B., Finkl, K., Schmid, K., Litz, C., Strauss, M., Benda, C., Muller, J. 10.7554/eLife.61964 33211010 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2, Polycomb protein SUZ12 Transcription-associated, Histone_methylation_H3K27_writer, Histone PTM writers, Heterochromatin-associated, Polycomb Q15910, Q15022 P06897, P84233, P62799, P02281 0.29
249 7BXT EM 4.20 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain Ariyoshi, M., Makino, F., Watanabe, R., Nakagawa, R., Kato, T., Namba, K., Arimura, Y., Fujita, R., Kurumizaka, H., Okumura, E.I., Hara, M., Fukagawa, T. 10.15252/embj.2020105671 33463726 Gallus gallus Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 CENP-C, Maltodextrin-binding protein,Centromere protein N Nuclear division, Centromere-associated, Kinetochore O57392, P0AEX9 P04908, P62805, Q16778, P84229 0.387
250 7COW X-ray 2.86 2021-08-11 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 353 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P68431, P07305, P04908, P62805, P06899 -
251 7EGP EM 6.90 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 166 The structure of SWI/SNF-nucleosome complex He, Z.Y., Chen, K.J., Ye, Y.P., Chen, Z.C. 10.1038/s41421-021-00262-5 33907182 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Transcription regulatory protein SNF2, SWI/SNF chromatin-remodeling complex subunit SWI1, SWI/SNF chromatin-remodeling complex subunit SNF5, SWI/SNF complex subunit SWI3, Transcription regulatory protein SNF12, Transcription regulatory protein SNF6, SWI/SNF global transcription activator complex subunit SWP82, Regulator of Ty1 transposition protein 102, Actin-related protein 7, Actin-like protein ARP9 SWI/SNF, RSC (SWI/SNF), Transcription-associated, Chromatin remodelers P22082, P09547, P18480, P32591, P53628, P18888, P43554, P53330, Q12406, Q05123 Q6AZJ8, P84233, P62799, P02281 0.105
252 7LYA EM 2.91 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 P04908, P68431, P62805, P06899 0.59
253 7NKX EM 2.90 2021-08-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 139 RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Chromo domain-containing protein 1, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Chromatin remodelers, RNA polymerases, Transcription factors, Centromere-associated, Heterochromatin-associated, CHD, SPT4-SPT5 complex, Euchromatin-associated P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P32657, P32914, P27692 P06897, P84233, P62799, P02281 0.444
254 7OHB EM 3.40 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 TBP-nucleosome complex Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein Transcription factors, Transcription-associated P13393 P06897, P84233, P62799, P02281 0.435
255 6KIV EM 4.00 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Ubiquitin, Euchromatin-associated Q03164, Q15291, P62979, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.343
256 7PEU EM 7.20 2022-08-03 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 520 Trinucleosome of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.138
257 7PFC EM 6.40 2022-08-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 344 Nucleosome stack of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.177
258 7PFT EM 9.80 2022-08-03 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 591 Trinucleosome of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.109
259 7PFV EM 4.40 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 177 Nucleosome 1 of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.268
260 7SCZ EM 3.50 2022-01-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to multiple BRCTs Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 Histone_PARylation_writer, DNA repair, Histone PTM writers P09874 P04908, P68431, P62805, P06899 0.425
261 7SWY EM 2.60 2022-03-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 2.6 A structure of a 40-601[TA-rich+1]-40 nucleosome Nodelman, I.M., Das, S., Faustino, A.M., Fried, S.D., Bowman, G.D., Armache, J.P. 10.1038/s41594-021-00719-x 35173352 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 P06897, P84233, P62799, P02281 -
262 7TAN EM 3.00 2022-05-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of VRK1 C-terminal tail bound to nucleosome core particle Budziszewski, G.R., Zhao, Y., Spangler, C.J., Kedziora, K.M., Williams, M.R., Azzam, D.N., Skrajna, A., Koyama, Y., Cesmat, A.P., Simmons, H.C., Arteaga, E.C., Strauss, J.D., Kireev, D., McGinty, R.K. 10.1093/nar/gkac198 35390161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Serine/threonine-protein kinase VRK1 Nuclear division, Histone_phosphorylation_H3T3_writer, Cell cycle, Histone PTM writers Q99986 Q71DI3, P62807, P62805, P0C0S8 0.56
263 7U0J EM 2.70 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of 162bp LIN28b nucleosome Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Single-chain variable fragment P68431, P62805, Q16778, Q16777 0.568
264 7U50 EM 3.40 2022-09-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Weaver, T.M., Hoitsma, N.M., Spencer, J.J., Gakhar, L., Schnicker, N.J., Freudenthal, B.D. 10.1038/s41467-022-33057-7 36104361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-(apurinic or apyrimidinic site) endonuclease DNA repair P27695 Q71DI3, P62807, P62805, P0C0S8 0.415
265 7UND EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 131 Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 Q6AZJ8, P84233, P62799, P02281 0.216
266 7UV9 EM 3.20 2023-02-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate Spangler, C.J., Skrajna, A., Foley, C.A., Nguyen, A., Budziszewski, G.R., Azzam, D.N., Arteaga, E.C., Simmons, H.C., Smith, C.B., Wesley, N.A., Wilkerson, E.M., McPherson, J.E., Kireev, D., James, L.I., Frye, S.V., Goldfarb, D., McGinty, R.K. 10.1038/s41589-023-01256-y 36797403 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Lysine-specific demethylase 2A Centromere-associated, Heterochromatin-associated, Histone_demethylation_H3K36, Histone PTM erasers Q9Y2K7 Q71DI3, P62807, P62805, P0C0S8 0.42
267 7XD1 EM 3.20 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 cryo-EM structure of unmodified nucleosome Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, P04908, P68431, P62805 0.558
268 6KIW EM 4.00 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2C, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Ubiquitin, Euchromatin-associated Q8NEZ4, Q15291, P62979, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.33
269 6J4X EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.233
270 7XX6 X-ray 3.39 2023-05-31 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601L 169 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P68431, P07305, P04908, P62805, P06899 -
271 2NZD X-ray 2.65 2007-04-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing 145 bp of DNA Ong, M.S., Richmond, T.J., Davey, C.A. 10.1016/j.jmb.2007.02.062 17379244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2007 P06897, P84233, P62799, P02281 -
272 9E3D EM 3.80 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 320 Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.153
273 7PET EM 9.50 2022-08-03 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 698 The 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.105
274 9R2Q EM 3.20 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Chakraborty, D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.361
275 9QMS EM 5.00 2026-01-14 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 141 DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.168
276 6HKT X-ray 9.70 2018-10-31 octamer, octamer, octamer, octamer, octamer, octamer 6 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 1122 Structure of an H1-bound 6-nucleosome array Garcia-Saez, I., Menoni, H., Boopathi, R., Shukla, M.S., Soueidan, L., Noirclerc-Savoye, M., Le Roy, A., Skoufias, D.A., Bednar, J., Hamiche, A., Angelov, D., Petosa, C., Dimitrov, S. 10.1016/j.molcel.2018.09.027 30392928 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 P04908, P68431, P62805, P06899 -
277 9CA7 EM 3.35 2025-06-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 121 Cryo-EM structure of human SRCAP-nucleosome complex in the fully-engaged state (composite structure) Park, G., Patel, A.B., Wu, C., Louder, R.K. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2 Transcription-associated, Chromatin remodelers, Cell cycle, SRCAP (INO80), Histone chaperones, INO80, Euchromatin-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230 P06897, P62799, P84233, P02281 0.554
278 5Y0C X-ray 2.09 2018-07-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of the human nucleosome at 2.09 angstrom resolution Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T., Kurumizaka, H. 10.1093/nar/gky661 30053102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 P04908, P68431, P62805, P06899 -
279 3MGS X-ray 3.15 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Cesium ions to the Nucleosome Core particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P84233, P62799, P02281 -
280 7YI4 EM 3.96 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.23
281 7JZV EM 3.90 2021-02-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Witus, S.R., Burrell, A.L., Farrell, D.P., Kang, J., Wang, M., Hansen, J.M., Pravat, A., Tuttle, L.M., Stewart, M.D., Brzovic, P.S., Chatterjee, C., Zhao, W., DiMaio, F., Kollman, J.M., Klevit, R.E. 10.1038/s41594-020-00556-4 33589814 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 BRCA1,Ubiquitin-conjugating enzyme E2 D3, BRCA1-associated RING domain protein 1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair P38398, Q99728 O60814, Q71DI3, P62805, Q6FI13 0.313
282 7DBH EM 3.60 2022-01-19 octamer 1 canonical_H3,H3.3 canonical_H4 canonical_H2A canonical_H2B 601 126 The mouse nucleosome structure containing H3mm18 Hirai, S., Tomimatsu, K., Miyawaki-Kuwakado, A., Takizawa, Y., Komatsu, T., Tachibana, T., Fukushima, Y., Takeda, Y., Negishi, L., Kujirai, T., Koyama, M., Ohkawa, Y., Kurumizaka, H. 10.1093/nar/gkab1137 34929737 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2022 P62806, C0HKE1, Q9D2U9, A0A8X6EH29 0.391
283 1ZLA X-ray 2.90 2006-02-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bound to the nucleosomal core Barbera, A.J., Chodaparambil, J.V., Kelley-Clarke, B., Joukov, V., Walter, J.C., Luger, K., Kaye, K.M. 10.1126/science.1120541 16469929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2006 latent nuclear antigen Viral Q9DUM3 P06897, P84233, P62799, P02281 -
284 3A6N X-ray 2.70 2010-05-26 octamer 1 TS_H3.4 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 The nucleosome containing a testis-specific histone variant, human H3T Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H. 10.1073/pnas.1003064107 20498094 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2010 Q16695, P04908, P62805, P06899 -
285 6FML EM 4.34 2018-04-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 CryoEM Structure INO80core Nucleosome complex Eustermann, S., Schall, K., Kostrewa, D., Lakomek, K., Strauss, M., Moldt, M., Hopfner, K.P. 10.1038/s41586-018-0029-y 29643509 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 RuvB-like helicase, Ino80, les2, Ies6, Actin related protein 5 INO80, Chromatin remodelers G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 Q71DI3, P62807, P62805, P0C0S8 0.33
286 3AN2 X-ray 3.60 2011-07-20 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_4_palindorm 121 The structure of the centromeric nucleosome containing CENP-A Tachiwana, H., Kagawa, W., Shiga, T., Osakabe, A., Miya, Y., Saito, K., Hayashi-Takanaka, Y., Oda, T., Sato, M., Park, S.-Y., Kimura, H., Kurumizaka, H. 10.1038/nature10258 21743476 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P49450, P04908, P62805, P06899 -
287 3W98 X-ray 3.42 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P04908, P68431, P62805, P06899 -
288 4YM5 X-ray 4.00 2015-12-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 143 Crystal structure of the human nucleosome containing 6-4PP (inside) Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H. 10.1038/srep16330 26573481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
289 4YS3 X-ray 3.00 2015-10-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Chatterjee, N., North, J.A., Dechassa, M.L., Manohar, M., Prasad, R., Luger, K., Ottesen, J.J., Poirier, M.G., Bartholomew, B. 10.1128/MCB.00441-15 26416878 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P06897, P84233, P62799, P02281 -
290 5AV5 X-ray 2.40 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
291 5B31 X-ray 2.20 2016-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A,H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Horikoshi, N., Arimura, Y., Taguchi, H., Kurumizaka, H. 10.1098/rsob.160127 27358293 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P68431, P0C0S5, P04908, P62805, P06899 -
292 5JRG X-ray 2.50 2017-03-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 144 Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Osakabe, A., Arimura, Y., Matsumoto, S., Horikoshi, N., Sugasawa, K., Kurumizaka, H. 10.1038/srep41783 28139742 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P04908, P68431, P62805, P06899 -
293 5MLU X-ray 2.80 2017-05-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Crystal structure of the PFV GAG CBS bound to a mononucleosome Lesbats, P., Serrao, E., Maskell, D.P., Pye, V.E., O'Reilly, N., Lindemann, D., Engelman, A.N., Cherepanov, P. 10.1073/pnas.1621159114 28490494 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 PFV GAG peptide DNA integration, Viral P14349 P06897, P84233, P62799, P02281 -
294 5X0Y EM 4.69 2017-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome Liu, X., Li, M., Xia, X., Li, X., Chen, Z. 10.1038/nature22036 28424519 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Transcription regulatory protein SNF2 SWI/SNF, Transcription-associated, Chromatin remodelers P22082 P06897, P84233, P62799, P02281 0.315
295 5XF4 X-ray 2.87 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P04908, P68431, P62805, P06899 -
296 5XF5 X-ray 2.82 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P04908, P68431, P62805, P06899 -
297 5Z3U EM 4.31 2019-05-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 SWI/SNF, Transcription-associated, Chromatin remodelers P22082 Q6AZJ8, P84233, P62799, P02281 0.372
298 7XFL EM 2.80 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 134 Structure of nucleosome-AAG complex (A-53I, free state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P06897, P84233, P62799, P02281 0.55
299 7Y7I EM 3.42 2022-07-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 chicken KNL2 in complex with the CENP-A nucleosome Jiang, H., Ariyoshi, M., Watanabe, R., Makino, F., Namba, K., Fukagawa, T. 10.1101/2022.06.24.497480 0 Gallus gallus Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Myb-like domain-containing protein F1NE16 P04908, P68431, P62805, P06899 0.454
300 9JNX EM 3.00 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP*+ state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.497
301 7K60 EM 3.12 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.10 601 197 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 scFv20 Q92522, P68431, P04908, P62805, P06899 0.435
302 9NY4 EM 2.98 2025-09-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 USP21 bound to H2AK119ub nucleosome Rahman, S., Hicks, C.W., Gwizdala, A., Wolberger, C. 10.1126/sciadv.ady2604 41071870 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Ubiquitin carboxyl-terminal hydrolase 21, Ubiquitin Histone_deubiquitination_H2AK119, Ubiquitin, Histone PTM erasers, Transcription-associated Q9UK80, J3QS39 P06897, P84233, P62799, P02281 0.398
303 9Q8X EM 2.94 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 151 Ku70/80 bound to a 153 bp H2AX nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P16104, P68431, P62805, P06899 0.321
304 9RN2 EM 4.10 2026-02-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 138 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Vecchia, L., Weiss, J., Cavadini, S., Kempf, G., Kater, L., Pathare, G., Thoma, N.H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, N-terminally processed, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, Zinc finger protein ubi-d4, Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Cell cycle, Transcription factors, Transcription-associated, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q92785, P42212, P48431 P04908, P68431, P62805, P06899 0.141
305 9RZC EM 3.66 2025-09-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16 Transcription-associated, Histone PTM writers, Histone_methylation_H3K36_writer, Histone chaperones, FACT, DNA replication, DNA repair, Euchromatin-associated Q9BYW2, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.434
306 9SLJ EM 3.80 2025-10-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Double Occupancy) Gireesh, A., Abad, M.A., Nozawa, R.S., Sotelo-Parrilla, P., Dury, L.C., Likhodeeva, M., Wear, M., Spanos, C., Peralta, C.C., Rappsilber, J., Hopfner, K.P., Wilson, M.D., Vanderlinden, W., Hirota, T., Jeyaprakash, A.A. 10.1038/s44318-025-00594-y 41145915 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2025 Borealin, Baculoviral IAP repeat-containing protein 5, Inner centromere protein Nuclear division, Centromere-associated, CPC Q53HL2, O15392, Q9NQS7 P06899, P84233, P0C0S8, P62799 0.397
307 9UX9 EM 3.05 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 119 local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state Sun, F., Zou, B., Li, H., Xu, C., Luo, Q., Wang, C., Xu, P., Pei, D., Chen, J., Qin, D., Zhang, Y., He, J. 10.1093/nar/gkag092 41657245 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 SWI/SNF, Transcription-associated, Chromatin remodelers P51532 A0A310TTQ1, Q6AZJ8, A0A8J0U496, P62799 0.299
308 7V9K EM 8.10 2022-07-27 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 539 Telomeric tetranucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, P04908, P68431, P62805 0.076
309 6IRO EM 3.40 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 the crosslinked complex of ISWI-nucleosome in the ADP-bound state Yan, L., Wu, H., Li, X., Gao, N., Chen, Z. 10.1038/s41594-019-0199-9 30872815 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 P06897, P84233, P62799, P02281 0.435
310 8F86 EM 3.10 2023-04-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 SIRT6 bound to an H3K9Ac nucleosome Wang, Z.A., Markert, J.W., Whedon, S.D., Yapa Abeywardana, M., Lee, K., Jiang, H., Suarez, C., Lin, H., Farnung, L., Cole, P.A. 10.1021/jacs.2c13512 36930461 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P06897, P84233, P62799, P02281 0.434
311 9E2F EM 5.90 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 318 Cryo-EM structure of a di-nucleosome with a five base pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Q71DI3, P62805, P06899, P0C0S8 0.167
312 8KD6 EM 3.07 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.311
313 9XYC EM 3.50 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q Syau, D., Farnung, L. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.356
314 8DK5 EM 2.71 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of 187bp LIN28b nucleosome with site 0 mutation Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Single-chain variable fragment P68431, P62805, Q16778, Q16777 0.535
315 9MPP EM 3.10 2025-10-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 166 The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L Yan, Y., Zhou, X.E., Thomas, S.L., Liu, M., Lai, G.Q., Worden, E.J., Jones, P.A., Xu, T.H. 10.1038/s41594-025-01704-4 41174279 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 DNA (cytosine-5)-methyltransferase 3A, DNA (cytosine-5)-methyltransferase 3-like DNA modification Q9Y6K1, Q9UJW3 P06897, P84233, P62799, P02281 0.282
316 7E8I EM 3.10 2021-06-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Dai, L., Dai, Y., Han, J., Huang, Y., Wang, L., Huang, J., Zhou, Z. 10.1016/j.molcel.2021.05.010 34102105 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 BRCA1-associated RING domain protein 1, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Ubiquitin, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair Q99728, P0CG47 P06897, P84233, P62799, P02281 0.456
317 9GCG EM 3.43 2025-08-13 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 152 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Aggarwal, P., Sharma, M., Hopfner, K.P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, INO80 complex subunit B, INO80 complex subunit C, Actin-related protein 5 Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9C086, Q6PI98, Q9H9F9 P68431, P62805, Q16778, P0C0S5 0.424
318 5B1L X-ray 2.35 2017-02-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 The mouse nucleosome structure containing H3t Ueda, J., Harada, A., Urahama, T., Machida, S., Maehara, K., Hada, M., Makino, Y., Nogami, J., Horikoshi, N., Osakabe, A., Taguchi, H., Tanaka, H., Tachiwana, H., Yao, T., Yamada, M., Iwamoto, T., Isotani, A., Ikawa, M., Tachibana, T., Okada, Y., Kimura, H., Ohkawa, Y., Kurumizaka, H., Yamagata, K. 10.1016/j.celrep.2016.12.065 28099840 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2017 P62806, C0HKE1, Q9D2U9, P68433 -
319 7X3W EM 3.10 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of ISW1-N1 nucleosome Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 P06897, P84233, P62799, P02281 0.489
320 10YI EM 2.90 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite) Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q96KK5, Q71DI3, P62805, Q99879 0.524
321 1P3O X-ray 2.75 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
322 10YH EM 2.90 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite) Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q96KK5, Q71DI3, P62805, Q99879 0.522
323 6KE9 X-ray 2.22 2020-04-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Soman, A., Liew, C.W., Teo, H.L., Berezhnoy, N.V., Olieric, V., Korolev, N., Rhodes, D., Nordenskiold, L. 10.1093/nar/gkaa289 32374876 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 O60814, P04908, P68431, P62805 -
324 6JXD X-ray 2.25 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 147 Human nucleosome core particle with cohesive end DNA termini Sharma, D., De Falco, L., Padavattan, S., Rao, C., Geifman-Shochat, S., Liu, C.F., Davey, C.A. 10.1038/s41467-019-13641-0 31848352 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P68431, P62805, P06899 -
325 3WA9 X-ray 3.07 2013-12-18 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The nucleosome containing human H2A.Z.1 Horikoshi, N., Sato, K., Shimada, K., Arimura, Y., Osakabe, A., Tachiwana, H., Hayashi-Takanaka, Y., Iwasaki, W., Kagawa, W., Harata, M., Kimura, H., Kurumizaka, H. 10.1107/S090744491302252X 24311584 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P68431, P62805, P06899, P0C0S5 -
326 9MMK EM 3.20 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosome, Canonical (Class 1) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.552
327 7MBN EM 4.02 2021-12-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Ayoub, A., Park, S.H., Lee, Y.T., Cho, U.S., Dou, Y. 10.1021/acs.biochem.1c00603 34928138 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.217
328 9N6K EM 2.90 2025-06-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 162 2.88 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex with DNA-binding domain Nodelman, I.M., Folkwein, H.J., Glime, W.S., Armache, J.P., Bowman, G.D. 10.1038/s41594-025-01556-y 40437259 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 Q6AZJ8, P84233, P62799, P02281 0.422
329 9MMN EM 3.60 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosomes, Left offset stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.189
330 7YI5 EM 3.96 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.254
331 8TB9 EM 4.00 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601 193 PRC2-J119-450 monomer bound to H1-nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Homo sapiens 2024 Protein Jumonji, Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Histone chaperones, Polycomb, Histone PTM erasers Q92833, Q15022, Q15910, O75530, Q09028, Q6ZN18 P06897, P07305, P62799, P02281, P84233 0.261
332 7ZSB EM 6.60 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 219 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription factors, RNA polymerases, Transcription-associated, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P06897, P84233, P62799, P02281 0.277
333 8ETV EM 3.16 2023-07-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Class2 of the INO80-Hexasome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02302, Q6AZJ8, P62799, P02281 0.387
334 8G6Q EM 3.41 2024-02-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2AK119ub-modified nucleosome ubiquitin position 1 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P06897, P84233, P62799, P02281 0.434
335 8GUI EM 2.81 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1-nucleosome complex (Model I) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK120_writer Q5VTR2, O75150 P68431, P62805, P06899, P0C0S8 0.532
336 8HXZ EM 3.40 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Cryo-EM structure of Eaf3 CHD in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, DNA repair Q12432 P06897, P84233, P62799, P02281 0.326
337 8JH2 EM 5.70 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.145
338 8KB5 EM 2.26 2023-10-18 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Cryo-EM structure of the human nucleosome containing H3.8 Hirai, S., Kujirai, T., Akatsu, M., Ogasawara, M., Ehara, H., Sekine, S.I., Ohkawa, Y., Takizawa, Y., Kurumizaka, H. 10.1093/jb/mvad069 37757444 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 P04908, P62805, P06899, P84243 0.655
339 8OL1 EM 3.50 2024-02-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Xu, P., Liu, Y., Liu, C., Guey, B., Li, L., Melenec, P., Ricci, J., Ablasser, A. 10.1038/s41586-024-07112-w 38418882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Cyclic GMP-AMP synthase, SPRY domain-containing SOCS box protein 3, Elongin-C, Elongin-B Transcription factors, Transcription-associated, E3 ubiquitin-protein ligation, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884, Q6PJ21, Q15369, Q15370 Q99877, Q96KK5, Q99878, Q71DI3, Q93079, P62805 0.4
340 8OSJ EM 6.20 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 128 Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription factors, Transcription-associated O08785, Q9WTL8 P04908, P68431, P62805, P06899 0.219
341 8OTT EM 3.30 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 MYC-MAX bound to a nucleosome at SHL+5.8 Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Myc proto-oncogene protein, Protein max Transcription factors, Transcription-associated P01106, P61244 P68431, P04908, P62805, Q8CGP7, P06899 0.411
342 8PC6 EM 3.04 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.484
343 8SYP EM 2.60 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 Genomic CX3CR1 nucleosome Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Single-chain variable fragment P68431, P62805, Q16778, Q16777 0.559
344 8TOF EM 2.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 176 Rpd3S bound to an H3K36Cme3 modified nucleosome Markert, J.W., Vos, S.M., Farnung, L. 10.1038/s41467-023-43968-8 38065958 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Rco1, histone N-terminal tail Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P02302, P06897, P62799, P02281 0.464
345 9MLN EM 3.30 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 GammaH2AX containing nucleosome, Canonical (Class 1) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.419
346 8VWU EM 3.00 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Nucleosome containing 8oxoG at SHL4 Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Q71DI3, P62807, P62805, P0C0S8 0.559
347 8X2Z EM 3.90 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.237
348 8XBU EM 4.24 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.171
349 9B2T EM 2.99 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Haspin bound to nucleosome in position 2 Hicks, C.W., Gliech, C.R., Rahman, S., Zhang, X., Eneim, A.S., Vasquez, S.J., Holland, A.J., Wolberger, C. 10.1038/s41594-025-01502-y 39979508 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Serine/threonine-protein kinase haspin Nuclear division, Histone_phosphorylation_H3T3_writer, Histone PTM writers Q8TF76 P06897, P84233, P62799, P02281 0.502
350 9D3N EM 3.00 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 5S_somatic 96 167-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, Q6FI13, Q99879 0.466
351 9DG3 EM 3.46 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 RING1 and YY1-binding protein, Ubiquitin Transcription-associated, Heterochromatin-associated, Histone PTM readers, Histone_ubiquitination_reader, Polycomb, Ubiquitin Q8N488, P0CG48 P06897, P84233, P62799, P02281 0.382
352 9GFM EM 3.80 2025-08-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 CryoEM structure of the human INO80 core-nucleosome complex state N-7 Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., Hopfner, K.P. 10.1093/nar/gkag138 41775336 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 INO80 complex subunit B INO80, Chromatin remodelers Q9C086 P04908, P68431, P62805, Q16778 0.372
353 9GMR EM 2.80 2025-01-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 SIRT7-H3K36MTUnucleosome complex Moreno-Yruela, C., Ekundayo, B.E., Foteva, P.N., Ni, D., Calvino-Sanles, E., Stahlberg, H., Fierz, B. 10.1038/s41467-025-56529-y 39900593 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 NAD-dependent protein deacetylase sirtuin-7 Histone_deacetylation_H3K36, Histone PTM erasers, Histone_deacetylation_H3K18 Q9NRC8 Q71DI3, P62805, Q6FI13, P06899 0.545
354 9IPU EM 4.30 2024-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601L 170 cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Shi, Q., Deng, Z., Zhang, L., Tong, Z., Li, J.B., Chu, G.C., Ai, H., Liu, L. 10.1002/anie.202413651 39363740 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair P61077, Q8IYW5, P62979 P07305, Q71DI3, O60814, P04908, P62805 0.237
355 9J8M EM 3.82 2025-02-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 184 Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Horikoshi, N., Miyake, R., Sogawa-Fujiwara, C., Ogasawara, M., Takizawa, Y., Kurumizaka, H. 10.1038/s41467-025-56823-9 39929866 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Barrier-to-autointegration factor, Lamin-A/C Nuclear division O75531, P02545 P04908, P68431, P62805, P06899 0.345
356 9J8N EM 7.14 2025-02-26 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 189 Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Horikoshi, N., Miyake, R., Sogawa-Fujiwara, C., Ogasawara, M., Takizawa, Y., Kurumizaka, H. 10.1038/s41467-025-56823-9 39929866 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Barrier-to-autointegration factor, Lamin-A/C Nuclear division O75531, P02545 P04908, P68431, P62805, P06899 0.164
357 9K42 EM 3.14 2025-05-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with 147bp Widom 601 DNA (C2 symmetry) Wang, Y., Wu, J., Yang, S., Li, X., Wang, J., Lv, Q., Zhu, X., Lu, G., Zhang, J., Shen, W.H., Liu, B., Lin, J., Dong, A. 10.1016/j.str.2025.04.015 40359943 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2025 Q9LD28, P59226, P59259, Q9LQQ4 0.424
358 9E49 EM 5.93 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 314 Cryo-EM structure of a di-nucleosome with an eight base-pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Q71DI3, P62805, P06899, P0C0S8 0.216
359 6NN6 EM 3.90 2019-02-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of Dot1L-H2BK120ub nucleosome complex Anderson, C.J., Baird, M.R., Hsu, A., Barbour, E.H., Koyama, Y., Borgnia, M.J., McGinty, R.K. 10.1016/j.celrep.2019.01.058 30759380 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, F5H388 P06897, P84233, P62799, P02281 0.371
360 6JYL EM 3.37 2019-05-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state Yan, L., Wu, H., Li, X., Gao, N., Chen, Z. 10.1038/s41594-019-0199-9 30872815 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.452
361 5E5A X-ray 2.81 2016-02-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle Fang, Q., Chen, P., Wang, M., Fang, J., Yang, N., Li, G., Xu, R.M. 10.7554/eLife.11911 26812545 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 C-terminal domain of Regulatory protein IE1 Viral P03169 P06897, P84233, P62799, P02281 -
362 1ID3 X-ray 3.10 2001-09-28 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B alphasat_146 146 CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS White, C.L., Suto, R.K., Luger, K. 10.1093/emboj/20.18.5207 11566884 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2001 P02294, P02309, P04911, P61830 -
363 1KX4 X-ray 2.60 2002-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 X-Ray Structure of the Nucleosome Core Particle, NCP146b, at 2.6 A Resolution Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J. 10.1016/S0022-2836(02)00386-8 12079350 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2002 P06897, P84233, P62799, P02281 -
364 1M18 X-ray 2.45 2003-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1016/S0022-2836(02)01407-9 12559907 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2003 P02302, P06897, P62799, P02281 -
365 1P3M X-ray 2.90 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
366 3AV1 X-ray 2.50 2011-06-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The human nucleosome structure containing the histone variant H3.2 Tachiwana, H., Osakabe, A., Shiga, T., Miya, Y., Kimura, H., Kagawa, W., Kurumizaka, H. 10.1107/S0907444911014818 21636898 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 Q71DI3, P04908, P62805, P06899 -
367 3KXB X-ray 3.20 2010-06-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Watanabe, S., Resch, M., Lilyestrom, W., Clark, N., Hansen, J.C., Peterson, C., Luger, K. 10.1016/j.bbagrm.2010.01.009 20100606 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P84233, P62799, P02281 -
368 3W96 X-ray 3.00 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P04908, P68431, P62805, P06899 -
369 4J8X X-ray 2.87 2013-05-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P06897, P84233, P62799, P02281 -
370 4R8P X-ray 3.28 2014-11-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle McGinty, R.K., Henrici, R.C., Tan, S. 10.1038/nature13890 25355358 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2014 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Polycomb, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496 P06897, P84233, P62799, P02281 -
371 4WU9 X-ray 2.60 2015-09-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of cisPtNAP-NCP145 Chua, E.Y., Davey, G.E., Chin, C.F., Droge, P., Ang, W.H., Davey, C.A. 10.1093/nar/gkv356 25916851 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P06897, P84233, P62799, P02281 -
372 4X23 X-ray 3.50 2014-12-10 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Kato, H., Jiang, J.S., Zhou, B.R., Rozendaal, M., Feng, H., Ghirlando, R., Xiao, T.S., Straight, A.F., Bai, Y. 10.1126/science.1235532 23723239 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2014 CENP-C Nuclear division, Centromere-associated, Kinetochore Q66LH7 P84040, P84051, P02283, P02299 -
373 4ZUX X-ray 3.82 2016-02-24 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Morgan, M.T., Haj-Yahya, M., Ringel, A.E., Bandi, P., Brik, A., Wolberger, C. 10.1126/science.aac5681 26912860 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 Ubiquitin carboxyl-terminal hydrolase 8, Transcription and mRNA export factor SUS1, SAGA-associated factor 11, Polyubiquitin-B, SAGA-associated factor 73 Transcription-associated, Ubiquitin, Histone PTM erasers, SAGA, Histone_deubiquitination P50102, Q6WNK7, Q03067, P0CG47, P53165 P06897, P84233, P62799, P02281 -
374 5XF3 X-ray 2.60 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P04908, P68431, P62805, P06899 -
375 1EQZ X-ray 2.50 2000-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION Harp, J.M., Hanson, B.L., Timm, D.E., Bunick, G.J. 10.1107/S0907444900011847 11092917 Gallus gallus Gallus gallus Gallus gallus Gallus gallus Xenopus laevis 2000 P0C1H5, P62801, P02263, P84229 -
376 5Z30 X-ray 2.45 2018-07-18 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T., Kurumizaka, H. 10.1093/nar/gky661 30053102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 P68431, P62805, P06899, P0C0S5 -
377 5Z3V EM 4.22 2019-05-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 SWI/SNF, Transcription-associated, Chromatin remodelers P22082 Q6AZJ8, P84233, P62799, P02281 0.356
378 6A5P EM 7.00 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 168 RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P62805, P06899, P84243 0.138
379 6BUZ EM 3.92 2017-12-20 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N Chittori, S., Hong, J., Saunders, H., Feng, H., Ghirlando, R., Kelly, A.E., Bai, Y., Subramaniam, S. 10.1126/science.aar2781 29269420 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 Maltose-binding periplasmic protein, Centromere protein N chimera P0AEX9 P49450, P04908, P62805, P06899 0.372
380 6C0W EM 4.00 2018-01-17 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 139 Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A Pentakota, S., Zhou, K., Smith, C., Maffini, S., Petrovic, A., Morgan, G.P., Weir, J.R., Vetter, I.R., Musacchio, A., Luger, K. 10.7554/eLife.33442 29280735 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q96H22 P49450, P62807, P62805, Q93077 0.39
381 6FQ5 EM 3.80 2018-04-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Class 1 : canonical nucleosome Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41467-018-03677-z 29626188 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2018 P06897, P84233, P62799, P02281 0.301
382 6INQ EM 6.90 2019-04-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 125 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P62805, P06899, P84243 0.149
383 6IY2 EM 3.47 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B MMTV 147 Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 SWI/SNF, Transcription-associated, Chromatin remodelers P22082 P06897, P84233, P62799, P02281 0.427
384 6J4W EM 7.90 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 171 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, F2QTN1, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.123
385 6J50 EM 4.70 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.195
386 6JR0 X-ray 2.50 2019-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the human nucleosome phased with 12 selenium atoms Saotome, M., Horikoshi, N., Urano, K., Kujirai, T., Yuzurihara, H., Kurumizaka, H., Kagawa, W. 10.1107/S2059798319012713 31588924 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P04908, P68431, P62805, P06899 -
387 6K1I X-ray 2.75 2020-01-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601_modified 147 Human nucleosome core particle with gammaH2A.X variant Sharma, D., De Falco, L., Padavattan, S., Rao, C., Geifman-Shochat, S., Liu, C.F., Davey, C.A. 10.1038/s41467-019-13641-0 31848352 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P16104, P68431, P62805, P06899 -
388 1F66 X-ray 2.60 2000-11-27 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z Suto, R.K., Clarkson, M.J., Tremethick, D.J., Luger, K. 10.1038/81971 11101893 Xenopus laevis Mus musculus Homo sapiens Xenopus laevis Xenopus laevis 2000 P62806, P84233, P02281, P0C0S5 -
389 1AOI X-ray 2.80 1998-09-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J. 10.1038/38444 9305837 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 1998 P02302, P06897, P62799, P02281 -
390 6K1P EM 3.87 2019-05-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The complex of ISWI-nucleosome in the ADP.BeF-bound state Yan, L., Wu, H., Li, X., Gao, N., Chen, Z. 10.1038/s41594-019-0199-9 30872815 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.42
391 6T93 EM 3.49 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Nucleosome with OCT4-SOX2 motif at SHL-6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P68431, P62805, P06899 0.419
392 9JO2 EM 3.00 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in Apo* state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.476
393 9K44 EM 3.22 2025-11-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 145 Cryo-EM structure of Arabidopsis thaliana H2A-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Wang, Y., Dong, A. 0 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2025 Q9LD28, Q9LQQ4, P59259, P59169 0.431
394 9L1X EM 2.69 2025-05-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 162 hDEK-nucleosome complex (conformation 1) Shen, Y., Liu, Y., Guo, M., Mao, S., Chen, R., Wang, M., Li, Z., Li, Y., Chen, W., Chen, F., Wu, B., Wang, C., Chen, W., Cui, H., Yuan, K., Huang, H. 10.1038/s41594-025-01559-9 40379883 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Protein DEK P35659 P04908, P62805, P06899, P84243 0.541
395 9LRW EM 3.04 2026-02-04 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 140 Cryo-EM structure of Fission yeast centromeric nucleosome Class 2 Xiong, Y., Jian, Y., Zhang, Y., Zhang, M., Zhang, X., Zhang, K., Fu, C., Tian, T., Zang, J. 10.1093/jmcb/mjaf056 41453208 Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Xenopus laevis 2026 P04913, Q9Y812, P04909, P09322 0.436
396 9MU4 EM 3.29 2025-02-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Structure of a native Drosophila melanogaster octameric nucleosome Venette-Smith, N.L., Vishwakarma, R.K., Dollinger, R., Schultz, J., Venkatakrishnan, V., Babitzke, P., Anand, G., Gilmour, D.S., Armache, J.-P., Murakami, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2025 P84040, P84051, P02283, P02299 0.442
397 9N6H EM 2.54 2025-06-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex Nodelman, I.M., Folkwein, H.J., Glime, W.S., Armache, J.P., Bowman, G.D. 10.1038/s41594-025-01556-y 40437259 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.518
398 9NH8 EM 3.20 2025-05-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 CHD1-nucleosome complex (anchored state) James, A.M., Farnung, L. 10.1016/j.molcel.2025.04.020 40334658 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Histone H3.2, Chromodomain-helicase-DNA-binding protein 1 CHD, Transcription-associated, Chromatin remodelers P84233, O14646 Q6AZJ8, P84233, P62799, P02281 0.293
399 9OGZ EM 3.05 2025-11-05 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_2R 123 Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v2) Shih, R.M., Arimura, Y., Konishi, H.A., Funabiki, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, P06899, P0C0S5 0.562
400 9SJ5 EM 2.85 2025-10-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class1) Gireesh, A., Abad, M.A., Nozawa, R.S., Sotelo-Parrilla, P., Dury, L.C., Likhodeeva, M., Wear, M., Spanos, C., Peralta, C.C., Rappsilber, J., Hopfner, K.P., Wilson, M.D., Vanderlinden, W., Hirota, T., Jeyaprakash, A.A. 10.1038/s44318-025-00594-y 41145915 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2025 Borealin, Baculoviral IAP repeat-containing protein 5, Inner centromere protein Nuclear division, Centromere-associated, CPC Q53HL2, O15392, Q9NQS7 P06899, P84233, P0C0S8, P62799 0.471
401 9Y46 EM 2.59 2025-10-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Human nucleosome structure on Nickel-NTA lipid affinity grid (C2 refinement) Skrajna, A., Lenger, C., Robinson, E., Cannon, K., Sarsam, R., Ouellette, R.G., Abotsi, A.M., Brennwald, P., McGinty, R.K., Strauss, J.D., Baker, R.W. 10.1016/j.jsb.2025.108253 41083086 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62807, P62805, P0C0S8 0.65
402 6E0P EM 2.60 2019-05-22 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 145 Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 scFv P49450, P04908, P62805, P06899 0.57
403 7CRO EM 3.75 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD2 Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated O96028 P06897, Q92133, P62799, P02281 0.448
404 2PYO X-ray 2.43 2007-11-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Drosophila nucleosome core Clapier, C.R., Chakravarthy, S., Petosa, C., Fernandez-Tornero, C., Luger, K., Muller, C.W. 10.1002/prot.21720 17957772 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2007 P84040, P84051, P02283, P02299 -
405 6YOV EM 3.42 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 OCT4-SOX2-bound nucleosome - SHL+6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription factors, Transcription-associated P42212, P48431 P04908, P68431, P62805, P06899 0.35
406 3MVD X-ray 2.90 2010-08-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle Makde, R.D., England, J.R., Yennawar, H.P., Tan, S. 10.1038/nature09321 20739938 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Regulator of chromosome condensation Nuclear division, Cell cycle P25171 Q6AZJ8, P84233, P62799, P02281 -
407 1KX3 X-ray 2.00 2002-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J. 10.1016/S0022-2836(02)00386-8 12079350 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2002 P06897, P84233, P62799, P02281 -
408 6W5N EM 6.00 2021-03-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Lee, Y.T., Ayoub, A., Park, S.H., Sha, L., Xu, J., Mao, F., Zheng, W., Zhang, Y., Cho, U.S., Dou, Y. 10.1038/s41467-021-23268-9 34012049 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.167
409 6FQ6 EM 4.00 2018-04-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Class 2 : distorted nucleosome Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41467-018-03677-z 29626188 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2018 P06897, P84233, P62799, P02281 0.235
410 9GD0 EM 2.80 2024-09-18 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Engeholm, M., Roske, J.J., Oberbeckmann, E., Dienemann, C., Lidschreiber, M., Cramer, P., Farnung, L. 10.1016/j.molcel.2024.08.022 39270644 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 P06897, P84233, P62799, P02281 0.528
411 7V96 EM 3.92 2022-07-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 275 Telomeric Dinucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, P04908, P68431, P62805 0.4
412 10YD EM 2.80 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nucleosome containing a nick at SHL-6 Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Q71DI3, P62807, P62805, P0C0S8 0.577
413 8OF4 EM 2.94 2023-08-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome Bound human SIRT6 (Composite) Smirnova, E., Bignon, E., Schultz, P., Papai, G., Ben Shem, A. 10.7554/eLife.87989 38415718 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P06897, P84233, P62799, P02281 0.446
414 9E0R EM 3.20 2026-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Cryo-EM structure of a single nucleosome (1) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.345
415 6FQ8 EM 4.80 2018-04-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Class 3 : translocated nucleosome Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41467-018-03677-z 29626188 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2018 P02302, P06897, P62799, P02281 0.196
416 8TXW EM 3.60 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P0CG47 P04908, P68431, P62805, P62807 0.455
417 8OW0 EM 3.40 2023-08-09 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601_modified 121 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Dendooven, T., Zhang, Z., Yang, J., McLaughlin, S.H., Schwab, J., Scheres, S.H.W., Yatskevich, S., Barford, D. 10.1126/sciadv.adg7480 37506202 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2023 Centromere-binding protein 1, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Inner kinetochore subunit CNN1, Inner kinetochore subunit AME1, Inner kinetochore subunit WIP1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2 Transcription-associated, Cell cycle, Centromere-associated, Nuclear division, Kinetochore, CCAN P17106, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P43618, P38313, Q2V2P8, Q12493, Q06162 P02309, P02293, P04911, P36012 0.2
418 6KIU EM 3.20 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Ubiquitin, Euchromatin-associated Q03164, Q15291, P62979, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.461
419 6KXV X-ray 3.63 2020-07-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of a nucleosome containing Leishmania histone H3 Dacher, M., Tachiwana, H., Horikoshi, N., Kujirai, T., Taguchi, H., Kimura, H., Kurumizaka, H. 10.1093/nar/gkz1040 31722422 Leishmania major Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P62805, P06899, Q4QHB5 -
420 6L4A EM 12.30 2019-12-04 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 485 H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Takizawa, Y., Ho, C.H., Tachiwana, H., Matsunami, H., Kobayashi, W., Suzuki, M., Arimura, Y., Hori, T., Fukagawa, T., Ohi, M.D., Wolf, M., Kurumizaka, H. 10.1016/j.str.2019.10.016 31711756 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P04908, P68431, P62805, P06899 0.085
421 9GD2 EM 4.20 2024-09-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 237 Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp. Engeholm, M., Roske, J.J., Oberbeckmann, E., Dienemann, C., Lidschreiber, M., Cramer, P., Farnung, L. 10.1016/j.molcel.2024.08.022 39270644 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 P06897, P84233, P62799, P02281 0.295
422 8VFZ EM 4.10 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 171 Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Hepatocyte nuclear factor 3-alpha Transcription factors, Transcription-associated P55317 P04908, P68431, P62805, P06899 0.27
423 8VG0 EM 3.07 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 159 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4 P0AEX9 P04908, P68431, P62805, P06899 0.482
424 8VMN EM 3.50 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K4me3 nucleosome bound to PRC2_AJ1-450 Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 Q71DI3, Q6AZJ8, P62805, A0A8J1LZU9 0.39
425 8X30 EM 4.30 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 Structure of piccolo NuA4 and H2A.Z nucleosome 2:1 complex Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, Q540A3, P38806, P47128 Q12692, P02309, P02293, P61830 0.165
426 8X32 EM 4.40 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ Complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.114
427 8Y3E EM 5.32 2025-01-29 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Cryo-EM structure of the overlapping di-nucleosome (open form) Shimizu, M., Tanaka, H., Nishimura, M., Sato, N., Nozawa, K., Ehara, H., Sekine, S.I., Morishima, K., Inoue, R., Takizawa, Y., Kurumizaka, H., Sugiyama, M. 10.1093/pnasnexus/pgae484 39539301 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P04908, P68431, P62805, P06899 -
428 8ZJR EM 3.30 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 131 Structure of nucleosome-bound RFX5 complex Xue, W., Han, Y., Tian, Y., Wang, J., Xie, Z., Zheng, X., Yue, X., Dong, S., Li, H., Luo, Z., Zhang, S., Yang, Y., Zou, Z., Li, W., Ma, N., Zhu, F., Chen, C., Yin, Y., Zhang, Y., Xu, K. 10.1093/nar/gkaf734 40744500 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-binding protein RFX5 Transcription factors P48382 O60814, Q71DI3, P04908, P62805 0.481
429 9BE6 EM 3.00 2025-04-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.V. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 A0A9J8D176, P0C0S8, Q71DI3, P04908, P62805, P06899 0.547
430 9D3Q EM 2.80 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 5S_somatic 109 167-bp 5S rDNA nucleosome - open II Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, Q6FI13, Q99879 0.519
431 9E1M EM 3.25 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Snf2h bound nucleosome complex - ClassA2 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.535
432 9EGX EM 2.90 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A310TTQ1, P06897, P62799, P02281 0.25
433 9FGQ EM 2.50 2024-07-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 132 Structure of human APC3loop 375-381 bound to the NCP Cirillo, L., Young, R., Veerapathiran, S., Roberti, A., Martin, M., Abubacar, A., Perosa, C., Coates, C., Muhammad, R., Roumeliotis, T.I., Choudhary, J.S., Alfieri, C., Pines, J. 10.1038/s44318-024-00194-2 39143240 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Cell division cycle protein 27 homolog APC/C, Cell cycle, Histone PTM writers P30260 P68431, P62805, Q6FI13, P33778 0.651
434 9GER EM 3.58 2025-08-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Native dimeric Myeloperoxidase bound to nucleosome core particle, intermediate state; composite map Burn, G.L., Raisch, T., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Gimber, N., Raunser, S., Zychlinsky, A. 10.1038/s41586-025-09523-9 40963017 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Myeloperoxidase light chain Neutrophil extracellular traps P05164 P06897, P84233, P62799, P02281 0.454
435 6L9H X-ray 2.60 2020-04-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Soman, A., Liew, C.W., Teo, H.L., Berezhnoy, N.V., Olieric, V., Korolev, N., Rhodes, D., Nordenskiold, L. 10.1093/nar/gkaa289 32374876 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 O60814, P04908, P68431, P62805 -
436 9K46 EM 2.85 2025-11-12 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 145 Cryo-EM structure of Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Wang, Y., Dong, A. 0 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2025 Q9FJE8, Q9LQQ4, P59259, P59169 0.493
437 9KQO EM 3.48 2025-12-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deng, Z., Tao, S., Du, Y., Li, Y., Zhang, L., Shi, Q., Du, X., Sun, M., Tong, Z., Pan, M., Liu, L., Ai, H. 10.1038/s41589-025-02109-6 41495224 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 E3 ubiquitin-protein ligase BRE1B, Polyubiquitin-B, E3 ubiquitin-protein ligase BRE1A, Ubiquitin-conjugating enzyme E2 A Transcription-associated, Histone PTM writers, Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2BK120_writer, DNA repair O75150, J3QS39, Q5VTR2, P49459 P62805, O60814, P04908, A0A653DHJ5 0.406
438 9L22 EM 3.00 2025-05-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 172 hDEK-nucleosome complex (conformation 2) Shen, Y., Liu, Y., Guo, M., Mao, S., Chen, R., Wang, M., Li, Z., Li, Y., Chen, W., Chen, F., Wu, B., Wang, C., Chen, W., Cui, H., Yuan, K., Huang, H. 10.1038/s41594-025-01559-9 40379883 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Protein DEK P35659 P04908, P62805, P06899, P84243 0.442
439 9N6I EM 2.61 2025-06-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex Nodelman, I.M., Folkwein, H.J., Glime, W.S., Armache, J.P., Bowman, G.D. 10.1038/s41594-025-01556-y 40437259 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.49
440 9OH0 EM 2.78 2025-11-05 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_2R 115 Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v2) Shih, R.M., Arimura, Y., Konishi, H.A., Funabiki, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, P06899, P0C0S5 0.579
441 9Q9F EM 4.54 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 129 DNA-PK bound to a 153 bp H2AX nucleosome model 1 Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.215
442 9SI9 EM 2.86 2025-10-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0) Gireesh, A., Abad, M.A., Nozawa, R.S., Sotelo-Parrilla, P., Dury, L.C., Likhodeeva, M., Wear, M., Spanos, C., Peralta, C.C., Rappsilber, J., Hopfner, K.P., Wilson, M.D., Vanderlinden, W., Hirota, T., Jeyaprakash, A.A. 10.1038/s44318-025-00594-y 41145915 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2025 Borealin, Baculoviral IAP repeat-containing protein 5, Inner centromere protein Nuclear division, Centromere-associated, CPC Q53HL2, O15392, Q9NQS7 S4RAZ3, P62799, P84233, P0C0S8, P06899 0.476
443 9U5U EM 3.12 2026-01-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Zhang, T., Zheng, J., Tong, Z., Deng, Z., He, Z., Wu, X., Wang, M., Du, Y., Xu, Z., Tao, S., Tian, X., Deng, H., Pan, M., Ai, H., Liu, L. 10.1101/2025.04.25.650627 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Ubiquitin carboxyl-terminal hydrolase BAP1, Ubiquitin, Polycomb group protein ASXL1 Transcription-associated, Heterochromatin-associated, Polycomb, Ubiquitin, Histone PTM erasers, Histone_deubiquitination_H2AK119 Q92560, P62979, Q8IXJ9 O60814, Q71DI3, P04908, P62805 0.462
444 9WMV EM 4.66 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 168 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.168
445 6DZT EM 2.99 2019-05-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of nucleosome in complex with a single chain antibody fragment Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2019 scFv P84040, P84051, P02283, P02299 0.589
446 10YA EM 2.70 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nucleosome containing a nick at SHL-4 Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Q71DI3, P62807, P62805, P0C0S8 0.589
447 3LZ0 X-ray 2.50 2010-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1) Vasudevan, D., Chua, E.Y., Davey, C.A. 10.1016/j.jmb.2010.08.039 20800598 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P84233, P62799, P02281 -
448 8UBJ EM 2.80 2026-01-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 162 Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 scFv P04908, P68431, P62805, P06899 0.535
449 8TXV EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P0CG47 P04908, P68431, P62805, P62807 0.432
450 8SMX EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.549
451 8RBX EM 4.10 2024-02-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 161 Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Fianu, I., Ochmann, M., Walshe, J.L., Dybkov, O., Cruz, J.N., Urlaub, H., Cramer, P. 10.1038/s41586-024-07269-4 38570683 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT5, Integrator complex subunit 1, Integrator complex subunit 2, Integrator complex subunit 4, Integrator complex subunit 5, Integrator complex subunit 6, Integrator complex subunit 7, Integrator complex subunit 8, Integrator complex subunit 9, Integrator complex subunit 10, Integrator complex subunit 11, Integrator complex subunit 13, Integrator complex subunit 14, Integrator complex subunit 15, Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform, Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, DSS1, Negative elongation factor A, NELF-B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B, Negative elongation factor C/D Cell cycle, Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, Q9H0H0, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, O00267, Q8N201, Q96HW7, Q6P9B9, Q9UL03, Q9NVH2, Q75QN2, Q9NV88, Q9NVR2, Q5TA45, Q9NVM9, Q96SY0, Q96N11, P30153, P67775, Q9H3P2, Q8WX92, Q8IXH7 P62805, Q6NXT2, P06899, P0C0S8 0.037
452 6LA2 X-ray 3.89 2021-02-17 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 343 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P68431, P07305, P04908, P62805, P06899 -
453 6LA9 X-ray 3.70 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 349 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A. 10.1038/s41467-020-18533-2 32958761 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P68431, P07305, P04908, P62805, P06899 -
454 6LTJ EM 3.70 2020-02-12 octamer 1 H3.3 canonical_H4 H2A.X canonical_H2B 601 119 Structure of nucleosome-bound human BAF complex He, S., Wu, Z., Tian, Y., Yu, Z., Yu, J., Wang, X., Li, J., Liu, B., Xu, Y. 10.1126/science.aaz9761 32001526 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4 Cell cycle, SWI/SNF, Transcription-associated, Chromatin remodelers P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785 P06897, Q6PI79, P62799, P02281 0.007
455 6OM3 X-ray 3.30 2019-07-10 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle De Ioannes, P., Leon, V.A., Kuang, Z., Wang, M., Boeke, J.D., Hochwagen, A., Armache, K.J. 10.1038/s41467-019-10609-y 31263106 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Origin recognition complex subunit 1 DNA replication, Transcription-associated, ORC P54784 P06897, P84233, P62799, P02281 -
456 6R0C EM 4.20 2019-09-25 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B Human-D02 142 Human-D02 Nucleosome Core Particle with biotin-streptavidin label Wilson, M.D., Renault, L., Maskell, D.P., Ghoneim, M., Pye, V.E., Nans, A., Rueda, D.S., Cherepanov, P., Costa, A. 10.1038/s41467-019-12007-w 31519882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P0C0S8, P62807, P62805, P84243 0.373
457 6SE0 EM 3.80 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class 1 : CENP-A nucleosome Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P49450, P62807, P62805, Q6FI13 0.328
458 6TDA EM 15.00 2020-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Wagner, F.R., Dienemann, C., Wang, H., Stutzer, A., Tegunov, D., Urlaub, H., Cramer, P. 10.1038/s41586-020-2088-0 32188943 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC8, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex protein RSC6, Chromatin structure-remodeling complex protein RSC58, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC4, Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Cell cycle, RSC (SWI/SNF), Transcription-associated, Chromatin remodelers Q06168, P43609, P32832, Q03124, P25632, Q07979, Q9URQ5, Q02206, P32597, Q12406, Q05123, P53330 P06897, P84233, P62799, P02281 0.081
459 6X0N EM 10.00 2020-09-16 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Bilokapic, S., Suskiewicz, M.J., Ahel, I., Halic, M. 10.1038/s41586-020-2725-7 32939087 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2 Histone_PARylation_writer, DNA repair, Histone PTM writers Q9NWY4, Q9UGN5 P06897, P84233, P62799, P02281 0.113
460 7JO9 EM 3.30 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 1:1 cGAS-nucleosome complex Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q. 10.1126/science.abd0609 32913000 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.483
461 7JOA EM 3.30 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 2:1 cGAS-nucleosome complex Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q. 10.1126/science.abd0609 32913000 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.474
462 7PFW EM 5.20 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Nucleosome 2 of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.264
463 7U47 EM 7.50 2022-03-16 octamer, octamer 2 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and palindromic alpha satellite DNA sequence Zhou, K., Gebala, M., Woods, D., Sundararajan, K., Edwards, G., Krzizike, D., Wereszczynski, J., Straight, A.F., Luger, K. 10.1038/s41594-022-00758-y 35422519 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q96H22 P49450, P62807, P62805, Q93077 0.179
464 7U51 EM 3.10 2022-09-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Nucleosome core particle with AP-site at SHL-6 Weaver, T.M., Hoitsma, N.M., Spencer, J.J., Gakhar, L., Schnicker, N.J., Freudenthal, B.D. 10.1038/s41467-022-33057-7 36104361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Q71DI3, P62807, P62805, P0C0S8 0.537
465 7VA4 EM 14.00 2022-07-27 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 539 Telomeric tetranucleosome in open state Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, P04908, P68431, P62805 0.043
466 7VVZ EM 8.80 2022-08-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 180 NuA4 bound to the nucleosome Qu, K., Chen, K., Wang, H., Li, X., Chen, Z. 10.1038/s41586-022-05303-x 36198799 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Chromatin modification-related protein EAF1, Actin-related protein 4, Actin, Enhancer of polycomb-like protein 1, SWR1-complex protein 4, Transcription-associated protein 1, Histone acetyltransferase ESA1, Chromatin modification-related protein YNG2, Epl1 arginine anchor, Chromatin modification-related protein EAF6 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Euchromatin-associated Q06337, P80428, P60010, P43572, P53201, P38811, Q08649, P38806, P47128 P06897, P84233, P62799, P02281 0.108
467 7XFJ EM 3.00 2023-11-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-3-methyladenine glycosylase DNA modification, DNA repair P29372 P06897, P84233, P62799, P02281 0.466
468 7XPX EM 3.20 2022-06-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Cryo-EM structure of the histone methyltransferase SET8 bound to H4K20Ecx-nucleosome Shi, L., Huang, L., Long, H., Song, A., Zhou, Z. 10.1096/fj.202101821R 35532550 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 N-lysine methyltransferase KMT5A Transcription-associated, Histone PTM writers, Cell cycle, Heterochromatin-associated, Nuclear division, Histone_methylation_H4K20_writer Q9NQR1 P06897, P84233, P62799, P02281 0.475
469 7XSE EM 3.60 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 134 RNA polymerase II elongation complex transcribing a nucleosome (EC42) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.238
470 8G57 EM 3.07 2023-04-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Structure of nucleosome-bound Sirtuin 6 deacetylase Chio, U.S., Rechiche, O., Bryll, A.R., Zhu, J., Leith, E.M., Feldman, J.L., Peterson, C.L., Tan, S., Armache, J.P. 10.1126/sciadv.adf7586 37058572 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P06899, P04908, P84233, P62799 0.493
471 8IHM EM 3.58 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Eaf3 CHD domain bound to the nucleosome Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. 10.1038/s41422-023-00884-2 37845487 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Rco1-ABR, Chromatin modification-related protein EAF3 Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair Q04779, Q12432 P06897, P84233, P62799, P02281 0.434
472 8JL9 EM 2.65 2023-10-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 155 Cryo-EM structure of the human nucleosome with scFv Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Ehara, H., Sekine, S.I., Hayashi, G., Takizawa, Y., Kurumizaka, H. 10.1093/nar/gkad754 37718728 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 P04908, P68431, P62805, P06899 0.569
473 8JLD EM 2.48 2023-10-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Ehara, H., Sekine, S.I., Hayashi, G., Takizawa, Y., Kurumizaka, H. 10.1093/nar/gkad754 37718728 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Q71DI3, P04908, P62805, P06899 0.579
474 8JNF EM 6.91 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 The cryo-EM structure of the RAD51 filament bound to the nucleosome Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.143
475 8OX0 EM 2.52 2023-08-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 Structure of apo telomeric nucleosome Hu, H., van Roon, A.M., Ghanim, G.E., Ahsan, B., Oluwole, A.O., Peak-Chew, S.Y., Robinson, C.V., Nguyen, T.H.D. 10.1126/sciadv.adi4148 37624885 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 P62807, P68431, P62805, Q93077 0.607
476 8QZM EM 3.10 2024-10-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome Wapenaar, H., Clifford, G., Rolls, W., Pasquier, M., Burdett, H., Zhang, Y., Deak, G., Zou, J., Spanos, C., Taylor, M.R.D., Mills, J., Watson, J.A., Kumar, D., Clark, R., Das, A., Valsakumar, D., Bramham, J., Voigt, P., Sproul, D., Wilson, M.D. 10.1038/s44319-024-00306-3 39528729 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA (cytosine-5)-methyltransferase 3A DNA modification Q9Y6K1 A0A7K7T3V7, P62807, P62805, P0C0S8 0.506
477 7YRD EM 3.20 2023-08-16 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 histone methyltransferase Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. 10.1016/j.molcel.2023.07.001 37536340 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 Q71DI3, P62805, P06899, P0C0S5 0.484
478 8AAG EM 10.00 2022-12-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0-B 601L 185 H1-bound palindromic nucleosome, state 1 Louro, J.A., Boopathi, R., Beinsteiner, B., Mohideen Patel, A.K., Cheng, T.C., Angelov, D., Hamiche, A., Bendar, J., Kale, S., Klaholz, B.P., Dimitrov, S. 10.1016/j.str.2022.12.005 36610392 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P22844, P06897, P02281, Q71DI3, P62805 -
479 7X3T EM 5.40 2023-09-20 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 339 Cryo-EM structure of ISW1a-dinucleosome Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI one complex protein 3, ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P43596, P38144 P06897, P84233, P62799, P02281 0.192
480 6IR9 EM 3.80 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.264
481 5OXV X-ray 6.72 2017-10-11 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 311 Structure of the 4_601_157 tetranucleosome (C2 form) Ekundayo, B., Richmond, T.J., Schalch, T. 10.1016/j.jmb.2017.09.002 28893533 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P06897, P84233, P62799, P02281 -
482 1ZBB X-ray 9.00 2005-07-12 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 347 Structure of the 4_601_167 Tetranucleosome Schalch, T., Duda, S., Sargent, D.F., Richmond, T.J. 10.1038/nature03686 16001076 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2005 P06897, P84233, P62799, P02281 -
483 3AZL X-ray 2.70 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
484 3REK X-ray 2.60 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P06897, P84233, P62799, P02281 -
485 3UTA X-ray 2.07 2012-04-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) Chua, E.Y.D., Vasudevan, D., Davey, G.E., Wu, B., Davey, C.A. 10.1093/nar/gks261 22453276 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P06897, P84233, P62799, P02281 -
486 4J8V X-ray 2.58 2013-05-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P06897, P84233, P62799, P02281 -
487 4J8W X-ray 2.41 2013-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P06897, P84233, P62799, P02281 -
488 4KUD X-ray 3.20 2013-08-07 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B alphasat_146 146 Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle Yang, D., Fang, Q., Wang, M., Ren, R., Wang, H., He, M., Sun, Y., Yang, N., Xu, R.M. 10.1038/nsmb.2637 23934152 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2013 Regulatory protein SIR3 Transcription-associated P06701 P02309, P02293, P04912, P61830 -
489 4LD9 X-ray 3.31 2013-08-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Arnaudo, N., Fernandez, I.S., McLaughlin, S.H., Peak-Chew, S.Y., Rhodes, D., Martino, F. 10.1038/nsmb.2641 23934150 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 Regulatory protein SIR3 Transcription-associated P06701 P06897, P84233, P62799, P02281 -
490 5CP6 X-ray 2.60 2016-06-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] Ma, Z., Palermo, G., Adhireksan, Z., Murray, B.S., von Erlach, T., Dyson, P.J., Rothlisberger, U., Davey, C.A. 10.1002/anie.201602145 27184539 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P06897, P84233, P62799, P02281 -
491 5Y0D X-ray 1.99 2018-07-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of the human nucleosome containing the H2B E76K mutant Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T., Kurumizaka, H. 10.1093/nar/gky661 30053102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 P04908, P68431, P62805, P06899 -
492 6A5L EM 5.60 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P62805, P06899, P84243 0.182
493 6MUO EM 3.60 2019-07-24 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 147 CENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT) Allu, P.K., Dawicki-McKenna, J.M., Van Eeuwen, T., Slavin, M., Braitbard, M., Xu, C., Kalisman, N., Murakami, K., Black, B.E. 10.1016/j.cub.2019.06.062 31353180 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 Centromere protein C, Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188, Q96H22 P49450, Q5QNW6, P62805, Q93077 0.369
494 8PEO EM 2.69 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.548
495 6O1D EM 3.40 2019-05-22 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 145 Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P49450, P04908, P62805, P06899 0.482
496 6PWF EM 4.07 2019-08-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome Chittori, S., Hong, J., Bai, Y., Subramaniam, S. 10.1093/nar/gkz670 31402386 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2019 chromatin remodeling factor ISWI ISWI, Chromatin remodelers G0S9L5 P84040, P84051, P02283, P02299 0.39
497 6PX3 EM 4.10 2019-08-28 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Set2 bound to nucleosome Bilokapic, S., Halic, M. 10.1038/s41467-019-11726-4 31439846 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis Xenopus laevis 2019 Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone-lysine N-methyltransferase Transcription-associated, Histone PTM writers, Histone_methylation_H3K36_writer, Ubiquitin, Euchromatin-associated P0CH09, G0S676 P02302, P0CH09, P62799, P02281 0.261
498 6R1T EM 4.02 2019-04-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 1, free nuclesome Marabelli, C., Marrocco, B., Pilotto, S., Chittori, S., Picaud, S., Marchese, S., Ciossani, G., Forneris, F., Filippakopoulos, P., Schoehn, G., Rhodes, D., Subramaniam, S., Mattevi, A. 10.1016/j.celrep.2019.03.061 30970244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 P06897, P84233, P62799, P02281 0.339
499 7D20 EM 3.00 2021-02-10 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 136 Cryo-EM structure of SET8-CENP-A-nucleosome complex Ho, C.H., Takizawa, Y., Kobayashi, W., Arimura, Y., Kimura, H., Kurumizaka, H. 10.26508/lsa.202000919 33574035 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Isoform 2 of N-lysine methyltransferase KMT5A Transcription-associated, Histone PTM writers, Cell cycle, Heterochromatin-associated, Nuclear division, Histone_methylation_H4K20_writer Q9NQR1 P49450, P04908, P62805, P06899 0.446
500 7DBP EM 4.50 2020-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601 175 Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Wang, S., Vogirala, V.K., Soman, A., Berezhnoy, N.V., Liu, Z.B., Wong, A.S.W., Korolev, N., Su, C.J., Sandin, S., Nordenskiold, L. 10.1038/s41598-020-79654-8 33432055 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P68431, P07305, O60814, P04908, P62805 0.246
501 7E9C EM 3.50 2022-09-07 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 130 Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M. 0 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2022 Origin recognition complex subunit 1 DNA replication, Transcription-associated, ORC P54784 P02294, P02309, P04912, P61830 0.311
502 7PEY EM 4.50 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 171 Nucleosome 3 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P04908, P62805 0.281
503 7VVU EM 3.40 2022-08-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 180 NuA4 HAT module bound to the nucleosome Qu, K., Chen, K., Wang, H., Li, X., Chen, Z. 10.1038/s41586-022-05303-x 36198799 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Histone acetyltransferase ESA1, Enhancer of polycomb-like protein 1, Chromatin modification-related protein YNG2, Chromatin modification-related protein EAF6 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Euchromatin-associated Q08649, P43572, P38806, P47128 P06897, P84233, P62799, P02281 0.314
504 7XFC EM 2.90 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Structure of nucleosome-DI complex (-30I, Apo state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P06897, P84233, P62799, P02281 0.569
505 7XYF EM 3.80 2023-12-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome Nan, Z., Tao, J., Yangao, H. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2023 ATP-dependent helicase fft3 Heterochromatin-associated, Chromatin remodelers O42861 P84040, P84051, P02283, P02299 0.272
506 7YI1 EM 2.80 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, DNA repair Q12432 P06897, P84233, P62799, P02281 0.572
507 6M4H EM 3.90 2020-09-23 octamer 1 canonical_H3 canonical_H4 H2A.B canonical_H2B 601 103 Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Zhou, M., Dai, L., Li, C., Shi, L., Huang, Y., Guo, Z., Wu, F., Zhu, P., Zhou, Z. 10.15252/embj.2020105907 33073403 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P68431, P62805, Q16778, P0C5Z0 0.365
508 6IPU X-ray 1.99 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Human nucleosome core particle containing 145 bp of DNA Sharma, D., De Falco, L., Padavattan, S., Rao, C., Geifman-Shochat, S., Liu, C.F., Davey, C.A. 10.1038/s41467-019-13641-0 31848352 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P68431, P62805, P06899 -
509 8ATF EM 3.45 2022-12-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Nucleosome-bound Ino80 ATPase Kunert, F., Metzner, F.J., Jung, J., Hopfler, M., Woike, S., Schall, K., Kostrewa, D., Moldt, M., Chen, J.X., Bantele, S., Pfander, B., Eustermann, S., Hopfner, K.P. 10.1126/sciadv.add3189 36490333 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Ino80 ATPase, PAPA-1 domain-containing protein INO80, Chromatin remodelers G0RY01 Q71DI3, P62807, P62805, P0C0S8 0.474
510 9MLS EM 3.60 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 107 GammaH2AX containing nucleosome, Extended (Class 3) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.413
511 8WG5 EM 3.05 2023-12-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Ai, H., He, Z., Deng, Z., Chu, G.C., Shi, Q., Tong, Z., Li, J.B., Pan, M., Liu, L. 10.1038/s41594-024-01342-2 38918638 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Ubiquitin carboxyl-terminal hydrolase 16, Ubiquitin B Cell cycle, Transcription-associated, Ubiquitin, Histone PTM erasers, Histone_deubiquitination_H2AK119 Q9Y5T5, P0CG47 O60814, P04908, P68431, P62805 0.306
512 8WH9 EM 3.31 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of DDM1-nucleosome complex in ADP-BeFx state Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9LD28, P59226, P59259, O23629 0.336
513 8X2Y EM 4.10 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class1 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P0AEX9, P08515, P38806 Q12692, P02309, P02293, P61830 0.229
514 8X31 EM 6.20 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.123
515 8X7I EM 3.27 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair P61077, Q8IYW5, P62979 O60814, Q71DI3, P04908, P62805 0.443
516 9D3K EM 2.70 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 94 Two Dsup molecules in complex with the nucleosome open from both sides Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Damage suppressor protein Q71DI3, P62805, Q6FI13, Q99879 0.598
517 9D3P EM 2.50 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 5S_somatic 123 167-bp 5S rDNA nucleosome - open I (open only on the downstream side) Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, Q6FI13, Q99879 0.589
518 9DWH EM 3.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite) Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.384
519 9E1U EM 3.10 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassC1 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.595
520 9EH0 EM 3.60 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 181 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_methylation_H3K36_writer, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 A0A310TTQ1, P06897, P62799, P02281 0.24
521 9GW2 EM 4.84 2025-11-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 125 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16 Transcription-associated, Histone PTM writers, Histone_methylation_H3K36_writer, Histone chaperones, FACT, DNA replication, DNA repair, Euchromatin-associated Q9BYW2, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.359
522 9K40 EM 3.15 2025-05-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 145 Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Wang, Y., Wu, J., Yang, S., Li, X., Wang, J., Lv, Q., Zhu, X., Lu, G., Zhang, J., Shen, W.H., Liu, B., Lin, J., Dong, A. 10.1016/j.str.2025.04.015 40359943 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2025 Q9LD28, P59226, P59259, Q9LQQ4 0.451
523 9Q80 EM 3.39 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 151 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P16104, P68431, P62805, P06899 0.3
524 5ONG X-ray 2.80 2017-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 146 X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Frouws, T.D., Barth, P.D., Richmond, T.J. 10.1016/j.jmb.2017.10.029 29113904 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P06897, P84233, P62799, P02281 -
525 9QAJ EM 2.95 2025-04-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of the nucleosome-bound human BCL7A Martin, F., Kazrani, A.A., Lafouge, J., Diaz-Jimenez, D.M., Siebert, S., Fabbro-Burtschell, L., Maillard, E., Lapouge, K., Mertens, H.D.T., Sauter, C., Leitner, A., Ochsenbein, F., Blais, A., Bergamin, E. 10.1093/nar/gkaf273 40207634 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Isoform 2 of B-cell CLL/lymphoma 7 protein family member A SWI/SNF, Chromatin remodelers Q4VC05 Q6AZJ8, P84233, P62799, P02281 0.493
526 9EOZ EM 3.10 2024-11-06 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 144 Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Ren, M., Gut, F., Fan, Y., Ma, J., Shan, X., Yikilmazsoy, A., Likhodeeva, M., Hopfner, K.P., Zhou, C. 10.1038/s41467-024-53811-3 39477986 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA modification, DNA repair O15527 P62807, P62805, Q93077, P84243 0.465
527 9GEV EM 3.47 2025-08-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Sharma, M., Aggarwal, P., Hopfner, K.P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, INO80 complex subunit B, INO80 complex subunit C, Actin-related protein 5 Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9C086, Q6PI98, Q9H9F9 P04908, P68431, P62805, Q16778 0.4
528 9EGY EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 160 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A310TTQ1, P06897, P62799, P02281 0.256
529 9D3T EM 2.80 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 5S_somatic 100 147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, Q6FI13, Q99879 0.51
530 10YC EM 2.70 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nucleosome containing a nick at SHL-4 Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Q71DI3, P62807, P62805, P0C0S8 0.581
531 9R04 EM 4.20 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Chakraborty, D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.232
532 7WBX EM 4.00 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 150 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.298
533 7EG6 EM 3.10 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Snf5 Finger Helix bound to the nucleosome He, Z.Y., Chen, K.J., Ye, Y.P., Chen, Z.C. 10.1038/s41421-021-00262-5 33907182 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 SWI/SNF chromatin-remodeling complex subunit SNF5 SWI/SNF, Transcription-associated, Chromatin remodelers P18480 P06897, P84233, P62799, P02281 0.513
534 6T90 EM 3.05 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 141 OCT4-SOX2-bound nucleosome - SHL-6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription factors, Transcription-associated P42212, P48431 P04908, P68431, P62805, P06899 0.451
535 9CAU EM 4.18 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 P62799, P02293, P04911, P61830 0.34
536 7K61 EM 2.85 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 197 Cryo-EM structure of 197bp nucleosome aided by scFv Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 scFv20 P04908, P68431, P62805, P06899 0.529
537 7YQK EM 3.38 2022-08-17 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 145 cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 Ai, H., Chu, G.C., Gong, Q., Tong, Z.B., Deng, Z., Liu, X., Yang, F., Xu, Z., Li, J.B., Tian, C., Liu, L. 10.1021/jacs.2c06156 36166692 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 UDR motif of 53BP1, TP53-binding protein 1, Polyubiquitin-B Histone PTM readers, Histone_methylation_H4K20_reader, Ubiquitin, Histone_ubiquitination_H2AK15_reader, DNA repair, Telomere-associated Q12888, P0CG47 O60814, P16104, P68431, P62805 0.424
538 8EVI EM 2.64 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 143 CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Single-chain variable fragment, Transcription factor PU.1 Transcription factors, Euchromatin-associated, Transcription-associated P17433 P68431, P62805, Q16778, Q16777 0.559
539 8VG1 EM 2.48 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 171 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Hepatocyte nuclear factor 3-alpha, Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4 Transcription factors, Transcription-associated P55317, P0AEX9 P04908, P68431, P62805, P06899 0.541
540 9MU9 EM 7.80 2025-02-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 174 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Venette-Smith, N.L., Vishwakarma, R.K., Dollinger, R., Schultz, J., Venkatakrishnan, V., Babitzke, P., Anand, G., Gilmour, D.S., Armache, J.-P., Murakami, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2025 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB5, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB12 Transcription-associated, RNA polymerases P04052, P08266, O97183, Q7JZF5, Q24320, Q9VNZ3, P36958, Q9VC49, Q9VJE4, Q6IGE3 P84040, P84051, P02283, P02299 0.202
541 9QIK EM 3.03 2026-01-21 octamer 1 canonical_H3,H3.3 canonical_H4 H2A.X canonical_H2B 601 132 M2 nucleosome Shukla, S., Ngubo, M., Paul, S., Kunert, F., Persinger, J., Lee, J., Hopfner, K.P., Bartholomew, B. 10.1016/j.molcel.2025.10.010 41290000 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 P06897, A0A8T2P505, A0A8J1LTD2, P02281 -
542 9R5K EM 4.20 2026-01-28 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 162 Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Hughes, A.L., Sundaramoorthy, R., Owen-Hughes, T. 10.7554/eLife.52513 41439750 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 P06897, P84233, P62799, P02281 0.294
543 9R5W EM 3.80 2026-02-04 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 162 Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Hughes, A.L., Sundaramoorthy, R., Owen-Hughes, T. 10.7554/eLife.52513 41439750 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 P06897, P84233, P62799, P02281 0.351
544 9SI3 EM 2.83 2025-10-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome Gireesh, A., Abad, M.A., Nozawa, R.S., Sotelo-Parrilla, P., Dury, L.C., Likhodeeva, M., Wear, M., Spanos, C., Peralta, C.C., Rappsilber, J., Hopfner, K.P., Wilson, M.D., Vanderlinden, W., Hirota, T., Jeyaprakash, A.A. 10.1038/s44318-025-00594-y 41145915 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2025 Borealin, Baculoviral IAP repeat-containing protein 5, Inner centromere protein Nuclear division, Centromere-associated, CPC Q53HL2, O15392, Q9NQS7 P06899, P84233, P0C0S8, P62799 0.476
545 9T4V EM 6.60 2025-11-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 ALC1/CHD1L in an intermediate conformation, bound to a PARylated nucleosome Bridges, H.R., Bacic, L., Deindl, S., Gaullier, G. 10.1101/2025.11.10.687450 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.188
546 9ZEN EM 3.17 2026-03-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Chakraborty, U., Saccone, E.C., Becerra, G.C., Khan, L.F., Arslanovic, N., Aguilar, R., Gloor, S.L., Hunt, S.R., Folkwein, H.J., Husby, N.L., Maier, K.E., Marunde, M.R., Schomburg, N.K., Vaidya, A., Cowles, M.W., Venters, B.J., Kassavetis, G., Sun, Z.-W., Kadonaga, J.T., Armache, J.-P., Keogh, M.-C., Tyler, J.K. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Single-chain antibody (VHH) 1B2 O60814, Q71DI3, P04908, P62805 0.473
547 6ESH EM 5.10 2017-12-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 137 Nucleosome breathing : Class 3 Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41594-017-0005-5 29323273 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Q6AZJ8, P84233, P62799, P02281 0.209
548 5GSE X-ray 3.14 2017-05-03 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 244 Crystal structure of unusual nucleosome Kato, D., Osakabe, A., Arimura, Y., Mizukami, Y., Horikoshi, N., Saikusa, K., Akashi, S., Nishimura, Y., Park, S.Y., Nogami, J., Maehara, K., Ohkawa, Y., Matsumoto, A., Kono, H., Inoue, R., Sugiyama, M., Kurumizaka, H. 10.1126/science.aak9867 28408607 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P04908, P68431, P62805, P06899 -
549 9E1Q EM 3.10 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassB3 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.614
550 9EIL EM 3.20 2025-07-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 141 SIRT6 bound to an H3K27Ac nucleosome Wang, Z.A., Markert, J., Whedon, S.D., Abeywardana, M.Y., Sheng, X., Nam, E., Lee, K., Chen, M., Waterbury, A., Zhao, Y., Farnung, L., Cole, P.A. 10.1016/j.jbc.2025.108446 40147774 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P06897, P84233, P62799, P02281 0.395
551 7OH9 EM 3.00 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome with TBP and TFIIA bound at SHL -6 Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription factors, Transcription-associated P13393, P32773, P32774 P06897, P84233, P62799, P02281 0.49
552 8RGM EM 4.00 2025-01-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 603 145 Cryo-EM structure of nucleosome containing Widom603 DNA Armeev, G.A., Moiseenko, A.V., Motorin, N.A., Afonin, D.A., Zhao, L., Vasilev, V.A., Oleinikov, P.D., Glukhov, G.S., Peters, G.S., Studitsky, V.M., Feofanov, A.V., Shaytan, A.K., Shi, X., Sokolova, O.S. 10.1016/j.str.2025.02.007 40101710 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P04908, P68431, P62805, P06899 0.352
553 7K63 EM 3.03 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 197 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 scFv20 P68431, P04908, P10412, P62805, P06899 0.492
554 9M77 EM 3.70 2026-03-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 The activated state of human UHRF1 bound to a mononucleosome, with the finger loop ordered and linker 4 disordered. Naschberger, A., Baradaran, R., Sayed, A., Fischle, W. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 E3 ubiquitin-protein ligase UHRF1 Histone PTM readers, Histone PTM writers, E3 ubiquitin-protein ligation Q96T88 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.282
555 9OH1 EM 3.09 2025-11-05 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601L 132 Cryo-EM analysis of human H2A.Z on 601L DNA Shih, R.M., Arimura, Y., Konishi, H.A., Funabiki, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, P06899, P0C0S5 0.532
556 1KX5 X-ray 1.94 2002-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J. 10.1016/S0022-2836(02)00386-8 12079350 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2002 P06897, P84233, P62799, P02281 -
557 7NKY EM 3.20 2021-07-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 148 RNA Polymerase II-Spt4/5-nucleosome-FACT structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, FACT complex subunit POB3, FACT complex subunit SPT16, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, RNA polymerases, Transcription factors, Centromere-associated, Histone chaperones, Heterochromatin-associated, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, Q04636, P32558, P32914, P27692 P06897, P84233, P62799, P02281 0.358
558 6L49 EM 18.90 2019-12-04 octamer, octamer, octamer 3 cenH3,canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 485 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Takizawa, Y., Ho, C.H., Tachiwana, H., Matsunami, H., Kobayashi, W., Suzuki, M., Arimura, Y., Hori, T., Fukagawa, T., Ohi, M.D., Wolf, M., Kurumizaka, H. 10.1016/j.str.2019.10.016 31711756 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P68431, P49450, P04908, P62805, P06899 0.071
559 10XZ EM 2.60 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Non-damaged nucleosome Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Q71DI3, P62807, P62805, P0C0S8 0.603
560 8Y3C EM 5.21 2025-01-29 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Cryo-EM structure of the overlapping di-nucleosome (closed form) Shimizu, M., Tanaka, H., Nishimura, M., Sato, N., Nozawa, K., Ehara, H., Sekine, S.I., Morishima, K., Inoue, R., Takizawa, Y., Kurumizaka, H., Sugiyama, M. 10.1093/pnasnexus/pgae484 39539301 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P04908, P68431, P62805, P06899 -
561 7XNP EM 2.90 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 123 Structure of nucleosome-AAG complex (A-55I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P06897, P84233, P62799, P02281 0.563
562 6I84 EM 4.40 2019-01-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 169 Structure of transcribing RNA polymerase II-nucleosome complex Farnung, L., Vos, S.M., Cramer, P. 10.1038/s41467-018-07870-y 30575770 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4 Transcription-associated, RNA polymerases, Euchromatin-associated P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422 P06897, P84233, P62799, P02281 0.241
563 7W9V EM 3.95 2022-07-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L., Kutateladze, T.G., Kurumizaka, H. 10.1016/j.isci.2022.104563 35754730 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.307
564 3C1C X-ray 3.15 2008-10-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure Lu, X., Simon, M.D., Chodaparambil, J.V., Hansen, J.C., Shokat, K.M., Luger, K. 10.1038/nsmb.1489 18794842 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2008 P06897, Q28D68, P84233, P62799 -
565 9RL4 EM 3.50 2026-02-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Lastname, F.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, N-terminally processed, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4, Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Cell cycle, Transcription factors, Transcription-associated, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785, P42212, P48431 P04908, P68431, P62805, P06899 0.386
566 7OHC EM 2.50 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P06897, P84233, P62799, P02281 0.587
567 9MLR EM 3.10 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 126 GammaH2AX containing nucleosome, Half-wrapped (Class 2) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.511
568 9KQ2 EM 3.90 2025-11-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of RNF168'-RNF168-UbcH5c complex bound to nucleosome Yang, X., Zhu, H., Shi, L., Song, T., Gong, W., He, S., Shan, S., Xu, C., Zhou, Z. 10.1093/nar/gkaf735 40794873 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 E3 ubiquitin-protein ligase RNF168 Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5 A0A310TTQ1, Q6AZJ8, A0A8J0U496, A0A8J1LTD2 0.45
569 8GPN EM 3.20 2023-02-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 Human menin in complex with H3K79Me2 nucleosome Lin, J., Wu, Y., Tian, G., Yu, D., Yang, E., Lam, W.H., Liu, Z., Jing, Y., Dang, S., Bao, X., Wong, J.W.H., Zhai, Y., Li, X.D. 10.1126/science.adc9318 36795828 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Isoform 2 of Menin Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated O00255 P06897, P84233, P62799, P02281 0.459
570 8VX5 EM 3.30 2024-10-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Nucleosome core particle containing an 8-oxoG damage site You, Q., Feng, X., Cai, Y., Baylin, S.B., Li, H. 10.1038/s42003-024-06919-7 39341999 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 P06897, P84233, P62799, P02281 0.493
571 8JHG EM 3.58 2023-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Native SUV420H1 bound to 167-bp nucleosome Lin, F., Zhang, R., Shao, W., Lei, C., Ma, M., Zhang, Y., Wen, Z., Li, W. 10.1038/s41421-023-00620-5 38052811 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 O60814, P04908, P68431, P62805 0.456
572 8KCC EM 3.10 2024-06-26 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 150 Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2 Zhang, H., Gu, Z., Zeng, Y., Zhang, Y. 10.1016/j.str.2024.05.013 38870940 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9FJE8, P59226, P59259, Q9FFC0 0.387
573 8KD1 EM 3.20 2025-03-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 173 Structure of nucleosome complexed with one DEK molecule Kujirai, T., Echigoya, K., Kishi, Y., Saeki, M., Ito, T., Kato, J., Negishi, L., Kimura, H., Masumoto, H., Takizawa, Y., Gotoh, Y., Kurumizaka, H. 10.1038/s41594-025-01493-w 39984731 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Protein DEK P35659 P04908, P68431, P62805, P06899 0.404
574 8KD7 EM 3.09 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.324
575 8PC5 EM 3.02 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.521
576 8QKU EM 3.80 2024-10-02 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 177 SWR1-nucleosome complex in configuration 1 Girvan, P., Jalal, A.S.B., McCormack, E.A., Skehan, M.T., Knight, C.L., Wigley, D.B., Rueda, D.S. 10.1038/s41586-024-08152-y 39506114 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04912, P61830 0.363
577 8RUP EM 2.42 2025-02-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Ruza, R.R., Chung, C.W., Gold, D.B.H., Serena, M., Roberts, E., Gruneberg, U., Barr, F.A. 10.1038/s44319-025-00523-4 40664717 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Baculoviral IAP repeat-containing protein 5, Borealin, Inner centromere protein Nuclear division, Centromere-associated, CPC O15392, Q53HL2, Q9NQS7 P06897, P62799, P02281, A0A310TTQ1, P84233 0.551
578 8SN1 EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.526
579 8SPS EM 3.00 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 P68431, P62805, Q16778, Q16777 0.434
580 8SVF EM 3.20 2023-08-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 BAP1/ASXL1 bound to the H2AK119Ub Nucleosome Thomas, J.F., Valencia-Sanchez, M.I., Tamburri, S., Gloor, S.L., Rustichelli, S., Godinez-Lopez, V., De Ioannes, P., Lee, R., Abini-Agbomson, S., Gretarsson, K., Burg, J.M., Hickman, A.R., Sun, L., Gopinath, S., Taylor, H.F., Sun, Z.W., Ezell, R.J., Vaidya, A., Meiners, M.J., Cheek, M.A., Rice, W.J., Svetlov, V., Nudler, E., Lu, C., Keogh, M.C., Pasini, D., Armache, K.J. 10.1126/sciadv.adg9832 37556531 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Ubiquitin carboxyl-terminal hydrolase BAP1, Polycomb group protein ASXL1, Ubiquitin Transcription-associated, Heterochromatin-associated, Polycomb, Ubiquitin, Histone PTM erasers, Histone_deubiquitination_H2AK119 Q92560, Q8IXJ9, P0CG48 P06897, P84233, P62799, P02281 0.383
581 8V26 EM 3.33 2024-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2BK120ub-modified nucleosome ubiquitin position 2 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P06897, P84233, P62799, P02281 0.515
582 8V6V EM 2.80 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of doubly-bound SNF2h-nucleosome complex Chio, U.S., Palovcak, E., Smith, A.A.A., Autzen, H., Munoz, E.N., Yu, Z., Wang, F., Agard, D.A., Armache, J.P., Narlikar, G.J., Cheng, Y. 10.1038/s41467-024-46178-y 38472177 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.477
583 8W9E EM 3.60 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Wang, C., Chu, C., Guo, Z., Zhan, X. 10.1126/sciadv.adk7678 38598631 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 O60814, P04908, P68431, P62805 0.188
584 9J0O EM 3.30 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 191 Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RPB12, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P04908, P62805, P06899, P84243 0.313
585 8WHA EM 4.05 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2 Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9LD28, P59226, P59259, O23629 0.306
586 8X2X EM 3.80 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P0AEX9, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.261
587 9C9T EM 3.16 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 147 S.c INO80 in complex with S.c 0/40 nucleosome, Class 2 Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62799, P02293, P04911, P61830 0.399
588 9DWI EM 3.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite) Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.405
589 9DWK EM 4.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 105 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5 Weaver, T.M., Ryan, B.J., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.297
590 9DWL EM 3.90 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 Nucleosome containing a 1-nt gap at SHL-5.5 Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62807, P62805, P0C0S8 0.366
591 9E09 EM 3.72 2026-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Cryo-EM structure a single nucleosome (2) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.316
592 9E1L EM 3.15 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Snf2h bound nucleosome complex - ClassA1 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.559
593 9E1P EM 3.25 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassB2 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.576
594 9IGW EM 3.32 2026-01-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 132 Ku70/80 bound to 147 bp nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P04908, P68431, P62805, P06899 0.321
595 9IGX EM 3.56 2026-01-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Ku70/80 bound to 153 bp nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P04908, P68431, P62805, P06899 0.293
596 9IHD EM 2.97 2025-08-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome core particle bound by one molecule of DTT-reduced native monomeric myeloperoxidase Burn, G.L., Raisch, T., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Gimber, N., Raunser, S., Zychlinsky, A. 10.1038/s41586-025-09523-9 40963017 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Myeloperoxidase light chain Neutrophil extracellular traps P05164 P06897, P84233, P62799, P02281 0.581
597 8VWV EM 3.60 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA modification, DNA repair O15527 Q71DI3, P62807, P62805, P0C0S8 0.359
598 8UX1 EM 2.50 2023-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle Huang, S.K., Rubinstein, J.L., Kay, L.E. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2023 GTP-binding nuclear protein Ran, Regulator of chromosome condensation Cell cycle P62826, P18754 P84040, P84051, P02283, P02299 0.609
599 8UW1 EM 2.88 2024-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome Gretarsson, K.H., Abini-Agbomson, S., Gloor, S.L., Weinberg, D.N., McCuiston, J.L., Kumary, V.U.S., Hickman, A.R., Sahu, V., Lee, R., Xu, X., Lipieta, N., Flashner, S., Adeleke, O.A., Popova, I.K., Taylor, H.F., Noll, K., Windham, C.L., Maryanski, D.N., Venters, B.J., Nakagawa, H., Keogh, M.C., Armache, K.J., Lu, C. 10.1126/sciadv.adp0975 39196936 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA (cytosine-5)-methyltransferase 3A DNA modification Q9Y6K1 P06897, P84233, A0A8J1LTD2, P02281 -
600 8JND EM 3.66 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.19
601 7WBV EM 4.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.267
602 7WBW EM 7.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.137
603 7XCR EM 2.57 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 O60814, Q71DI3, P04908, P62805 0.571
604 7XCT EM 2.72 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 O60814, Q71DI3, P04908, P62805 0.514
605 7XT7 EM 4.20 2022-10-12 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, F2QPX0, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.207
606 8A3Y EM 3.30 2024-07-31 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 138 Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Farnung, L., Ochmann, M., Garg, G., Vos, S.M., Cramer, P. 10.1016/j.molcel.2022.06.027 35858621 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, SPT6, RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein LEO1, RNA polymerase-associated protein RTF1 homolog, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q6PD62, Q92541, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267 Q6AZJ8, P84233, A0A8J1LZU9, P62799 0.231
607 8ETT EM 6.68 2023-07-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Class1 of the INO80-Hexasome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P06897, P84233, P62799, P02281 0.186
608 8EVH EM 2.85 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 141 CX3CR1 nucleosome and wild type PU.1 complex Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Single-chain variable fragment, Transcription factor PU.1 Transcription factors, Euchromatin-associated, Transcription-associated P17433 P68431, P62805, Q16778, Q16777 0.509
609 8G86 EM 2.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 145 Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome) Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Q6AZJ8, P84233, P62799, P02281 0.606
610 8G8B EM 4.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 168 Nucleosome with human nMatn1 sequence in complex with Human Oct4 Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 Q6AZJ8, P84233, P62799, P02281 0.233
611 8H1T EM 3.00 2023-02-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Ge, W., Yu, C., Li, J., Yu, Z., Li, X., Zhang, Y., Liu, C.P., Li, Y., Tian, C., Zhang, X., Li, G., Zhu, B., Xu, R.M. 10.1038/s41586-023-05841-y 36991118 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Ubiquitin carboxyl-terminal hydrolase BAP1, Ubiquitin, Polycomb group protein ASXL1 Transcription-associated, Heterochromatin-associated, Polycomb, Ubiquitin, Histone PTM erasers, Histone_deubiquitination_H2AK119 Q92560, P0CG47, Q8IXJ9 P20671, P68431, P10412, P62805, Q16778 0.435
612 8HAM EM 4.50 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 165 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Transcription-associated, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P04908, P68431, P62805, P06899 0.242
613 8PEP EM 3.33 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.399
614 7KTQ EM 3.30 2021-02-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Nucleosome from a dimeric PRC2 bound to a nucleosome Grau, D., Zhang, Y., Lee, C.H., Valencia-Sanchez, M., Zhang, J., Wang, M., Holder, M., Svetlov, V., Tan, D., Nudler, E., Reinberg, D., Walz, T., Armache, K.J. 10.1038/s41467-020-20775-z 33514705 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Q6AZJ8, P84233, P62799, P02281 0.494
615 8YNY EM 4.52 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 137 Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Nagamura, R., Kujirai, T., Kato, J., Shuto, Y., Kusakizako, T., Hirano, H., Endo, M., Toki, S., Saika, H., Kurumizaka, H., Nureki, O. 10.1038/s41467-024-54768-z 39737984 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 CRISPR-associated endonuclease Cas9/Csn1 CRISPR/Cas Q99ZW2 P04908, P68431, P62805, P06899 0.218
616 9D3R EM 3.30 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 5S_somatic 145 147-bp 5S rDNA nucleosome - closed Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 O60814, Q71DI3, P62805, Q6FI13 0.393
617 9EAR EM 3.10 2025-05-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 CHD1-nucleosome complex (closed state) James, A.M., Farnung, L. 10.1016/j.molcel.2025.04.020 40334658 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Chromodomain-helicase-DNA-binding protein 1 CHD, Transcription-associated, Chromatin remodelers O14646 A0A310TTQ1, Q6AZJ8, A0A1L8FQA5, P62799 0.424
618 9GEL EM 4.86 2025-08-20 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 113 CryoEM structure of the human INO80-Hexasome complex Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., Hopfner, K.P. 10.1093/nar/gkag138 41775336 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P04908, P68431, P62805, Q16778 0.278
619 9K43 EM 2.87 2025-05-14 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 145 Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA (C2 symmetry) Wang, Y., Wu, J., Yang, S., Li, X., Wang, J., Lv, Q., Zhu, X., Lu, G., Zhang, J., Shen, W.H., Liu, B., Lin, J., Dong, A. 10.1016/j.str.2025.04.015 40359943 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2025 Q9C944, P59226, P59259, Q9LQQ4 0.464
620 9Q7U EM 3.40 2026-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 162 Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 7 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 A0A310TTQ1, P06897, P62799, P02281 -
621 9R1D EM 3.21 2026-01-28 octamer 1 H3.V H4.V canonical_H2A canonical_H2B 601 115 Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei Deak, G., Burdett, H., Watson, J.A., Wilson, M.D. 10.1016/j.str.2026.01.008 41709455 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Xenopus laevis 2026 Q387X7, Q587H6, Q389T1, Q57YA3 0.463
622 7ON1 EM 3.35 2021-07-07 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 123 Cenp-A nucleosome in complex with Cenp-C Yan, K., Yang, J., Zhang, Z., Barford, D. 0 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2021 BJ4_G0006610.mRNA.1.CDS.1 Cell cycle, Centromere-associated, Nuclear division, Kinetochore, CCAN P35201 P02309, P02293, P04911, P36012 0.47
623 5AY8 X-ray 2.80 2016-04-06 octamer 1 H3.Y canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal structure of human nucleosome containing H3.Y Kujirai, T., Horikoshi, N., Sato, K., Maehara, K., Machida, S., Osakabe, A., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1093/nar/gkw202 27016736 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P0DPK2, P04908, P62805, P06899 -
624 8G8G EM 3.20 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 174 Interaction of H3 tail in LIN28B nucleosome with Oct4 Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 Q6AZJ8, P84233, P62799, P02281 0.218
625 7Y8R EM 4.40 2022-12-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 165 The nucleosome-bound human PBAF complex Wang, L., Yu, J., Yu, Z., Wang, Q., Li, W., Ren, Y., Chen, Z., He, S., Xu, Y. 10.1038/s41467-022-34859-5 36496390 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Transcription activator BRG1, ACTB protein (Fragment), Actin-like protein 6A, AT-rich interactive domain-containing protein 2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, PHD finger protein 10, Bromodomain-containing protein 7, Protein polybromo-1 Transcription-associated, Chromatin remodelers, Cell cycle, PBAF (SWI/SNF), SWI/SNF P51532, P60709, O96019, Q68CP9, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q8WUB8, Q9NPI1, Q86U86 P62807, P68431, P62805, Q93077 0.172
626 9FBW EM 4.40 2024-10-02 hexamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 112 SWR1 lacking Swc5 subunit in complex with hexasome Jalal, A.S.B., Girvan, P., Chua, E.Y.D., Liu, L., Wang, S., McCormack, E.A., Skehan, M.T., Knight, C.L., Rueda, D.S., Wigley, D.B. 10.1016/j.molcel.2024.08.015 39226902 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04911, P61830 0.193
627 7PFD EM 4.40 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 172 Nucleosome 1 of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.208
628 7K6P EM 3.20 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1 bound to the unacetylated H4 nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Truong, D.M., Lee, R., Armache, J.P., Boeke, J.D., Armache, K.J. 10.1126/science.abc6663 33479126 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Telomere-associated, Histone PTM writers Q04089, P0CG48 P06897, P84233, P62799, P02281 0.473
629 8UBK EM 2.60 2026-01-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 162 Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 scFv, Achaete-scute homolog 1, Transcription factor E2-alpha Heterochromatin-associated, Transcription factors, Transcription-associated Q02067, P15806 P04908, P68431, P62805, P06899 0.514
630 9WMT EM 3.59 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 121 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.225
631 6GEJ EM 3.60 2018-10-17 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 154 Chromatin remodeller-nucleosome complex at 3.6 A resolution. Willhoft, O., Ghoneim, M., Lin, C.L., Chua, E.Y.D., Wilkinson, M., Chaban, Y., Ayala, R., McCormack, E.A., Ocloo, L., Rueda, D.S., Wigley, D.B. 10.1126/science.aat7716 30309918 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2018 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2 Transcription-associated, Chromatin remodelers, INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P02293, P04911, P61830 0.372
632 6GEN EM 3.60 2018-10-17 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 173 Chromatin remodeller-nucleosome complex at 4.5 A resolution. Willhoft, O., Ghoneim, M., Lin, C.L., Chua, E.Y.D., Wilkinson, M., Chaban, Y., Ayala, R., McCormack, E.A., Ocloo, L., Rueda, D.S., Wigley, D.B. 10.1126/science.aat7716 30309918 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2018 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2 Transcription-associated, Chromatin remodelers, INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P02293, P04911, P61830 0.195
633 6J51 EM 4.20 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.23
634 6Y5E EM 3.15 2020-09-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Pathare, G.R., Decout, A., Gluck, S., Cavadini, S., Makasheva, K., Hovius, R., Kempf, G., Weiss, J., Kozicka, Z., Guey, B., Melenec, P., Fierz, B., Thoma, N.H., Ablasser, A. 10.1038/s41586-020-2750-6 32911482 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 O60814, Q71DI3, P62805, Q16777 0.43
635 8CEO EM 3.60 2023-03-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Schilbach, S., Wang, H., Dienemann, C., Cramer, P. 10.1073/pnas.2220542120 37014863 Xenopus laevis Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPD, TFB1 isoform 1, RNA polymerase II transcription factor B subunit 2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, TOA1 isoform 1, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta, Mediator of RNA polymerase II transcription subunit 6, Mediator of RNA polymerase II transcription subunit 8, Mediator of RNA polymerase II transcription subunit 11, Mediator of RNA polymerase II transcription subunit 17, Mediator of RNA polymerase II transcription subunit 18, Mediator of RNA polymerase II transcription subunit 20, Mediator of RNA polymerase II transcription subunit 22, Mediator of RNA polymerase II transcription subunit 4, Mediator of RNA polymerase II transcription subunit 7, Mediator of RNA polymerase II transcription subunit 9, Mediator of RNA polymerase II transcription subunit 10, Mediator of RNA polymerase II transcription subunit 14, Mediator of RNA polymerase II transcription subunit 19, Mediator of RNA polymerase II transcription subunit 21, Mediator of RNA polymerase II transcription subunit 31, Mediator of RNA polymerase II transcription subunit 1 Transcription factors, RNA polymerases, Transcription-associated, Mediator, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145, P38782, P38304, Q99278, P32569, P32585, P34162, P32570, Q12343, Q08278, P33308, Q06213, P19263, P25046, P47822, P38633, Q12321 P06897, P84233, P62799, P02281 0.222
636 8GRQ EM 3.87 2023-04-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.chempr.2023.01.012 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair P38398, Q99728, P61077 O60814, Q71DI3, P04908, P62805 0.352
637 8OO7 EM 2.80 2023-07-26 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 113 CryoEM Structure INO80core Hexasome complex composite model state1 Zhang, M., Jungblut, A., Kunert, F., Hauptmann, L., Hoffmann, T., Kolesnikova, O., Metzner, F., Moldt, M., Weis, F., DiMaio, F., Hopfner, K.P., Eustermann, S. 10.1126/science.adf6287 37384673 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 RuvB-like protein 1, RuvB-like protein 2, Chromatin-remodeling ATPase Ino80, Ino eighty subunit 2, Chromatin-remodeling complex subunit IES6, Actin-related protein 5 INO80, Chromatin remodelers G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62807, P68431, P62805, Q93077 0.556
638 8UBI EM 2.80 2026-01-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 162 Cryo-EM structure of NRCAM nucleosome aided by scFv (Class_A) Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 scFv L8IQP7, A0A9J8D176, H2PI50, P06899 0.542
639 9B1E EM 4.40 2024-10-09 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 181 Cryo-EM structure of native SWR1 bound to nucleosome (composite structure) Louder, R.K., Park, G., Ye, Z., Cha, J.S., Gardner, A.M., Lei, Q., Ranjan, A., Hollmuller, E., Stengel, F., Pugh, B.F., Wu, C. 10.1016/j.cell.2024.09.007 39357520 Drosophila melanogaster Drosophila melanogaster Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, Vacuolar protein sorting-associated protein 72, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, SWR1-complex protein 3 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q03388, Q12509, Q03433, Q03940, Q12464, P31376 P02293, P04911, A0A0B4KFZ9, P02299 0.191
640 9E1X EM 3.40 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Snf2h bound nucleosome complex - ClassD1 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1038/s41422-025-01103-w 40175616 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 Q6AZJ8, P84233, P62799, P02281 0.499
641 9EH2 EM 3.10 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 65 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_methylation_H3K36_writer, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2, Q9Y5B9, Q08945 A0A310TTQ1, P06897, P62799, P02281 0.252
642 9LRV EM 2.99 2026-02-04 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 144 Cryo-EM structure of Fission yeast centromeric nucleosome Class 1 Xiong, Y., Jian, Y., Zhang, Y., Zhang, M., Zhang, X., Zhang, K., Fu, C., Tian, T., Zang, J. 10.1093/jmcb/mjaf056 41453208 Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Xenopus laevis 2026 P04913, Q9Y812, P04909, P09322 0.508
643 10YG EM 3.40 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite) Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q71DI3, Q99879, P62805, P0C0S8 0.488
644 7K5X EM 2.93 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601 197 Cryo-EM structure of a chromatosome containing human linker histone H1.0 Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 scFv20 P68431, P07305, P04908, P62805, P06899 0.489
645 6XJD EM 6.80 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Two mouse cGAS catalytic domain binding to human assembled nucleosome Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. 10.1038/s41586-020-2749-z 32911481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.196
646 6PWW EM 4.40 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Park, S.H., Ayoub, A., Lee, Y.T., Xu, J., Kim, H., Zheng, W., Zhang, B., Sha, L., An, S., Zhang, Y., Cianfrocco, M.A., Su, M., Dou, Y., Cho, U.S. 10.1038/s41467-019-13550-2 31804488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164 P06897, P84233, P62799, P02281 0.26
647 1P3P X-ray 2.70 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
648 3AZJ X-ray 2.89 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
649 3X1S X-ray 2.80 2015-09-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the nucleosome core particle Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bbrc.2015.07.070 26188507 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P33778 -
650 5AVC X-ray 2.40 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
651 5HQ2 X-ray 4.50 2016-03-23 split_octasome 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 73 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Girish, T.S., McGinty, R.K., Tan, S. 10.1016/j.jmb.2016.02.025 26953260 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 Guanine nucleotide exchange factor SRM1, N-lysine methyltransferase SETD8 Cell cycle, Histone PTM writers, Transcription-associated, Heterochromatin-associated, Nuclear division, Histone_methylation_H4K20_writer P21827, Q9NQR1 P06897, P84233, P62799, P02281 -
652 5KGF EM 4.54 2016-07-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Wilson, M.D., Benlekbir, S., Fradet-Turcotte, A., Sherker, A., Julien, J.P., McEwan, A., Noordermeer, S.M., Sicheri, F., Rubinstein, J.L., Durocher, D. 10.1038/nature18951 27462807 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2016 Tumor suppressor p53-binding protein 1, Ubiquitin Histone PTM readers, Histone_methylation_H4K20_reader, Ubiquitin, Histone_ubiquitination_H2AK15_reader, DNA repair, Telomere-associated Q12888, P0CG47 P62807, P84233, P0C0S8, P62799 0.301
653 5X0X EM 3.97 2017-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome Liu, X., Li, M., Xia, X., Li, X., Chen, Z. 10.1038/nature22036 28424519 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Transcription regulatory protein SNF2 SWI/SNF, Transcription-associated, Chromatin remodelers P22082 P06897, P84233, P62799, P02281 0.372
654 6KIZ EM 4.50 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-NCP complex, binding mode2 Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q03164, Q15291, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.31
655 6M4D EM 4.40 2020-09-23 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 125 Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Zhou, M., Dai, L., Li, C., Shi, L., Huang, Y., Guo, Z., Wu, F., Zhu, P., Zhou, Z. 10.15252/embj.2020105907 33073403 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Q71UI9, P68431, P62805, Q16778 0.311
656 6R94 EM 3.50 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP_THF2(-3) Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P04908, P68431, P62805, P06899 0.363
657 6R93 EM 4.00 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-6-4PP Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P04908, P68431, P62805, P06899 0.352
658 7XYG EM 4.20 2023-12-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome Nan, Z., Tao, J., Yangao, H. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2023 ATP-dependent helicase fft3 Heterochromatin-associated, Chromatin remodelers O42861 P84040, P84051, P02283, P02299 0.219
659 1S32 X-ray 2.05 2004-05-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Molecular Recognition of the Nucleosomal 'Supergroove' Edayathumangalam, R.S., Weyermann, P., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1073/pnas.0401743101 15100411 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
660 7VBM EM 3.40 2022-01-19 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 126 The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv Hirai, S., Tomimatsu, K., Miyawaki-Kuwakado, A., Takizawa, Y., Komatsu, T., Tachibana, T., Fukushima, Y., Takeda, Y., Negishi, L., Kujirai, T., Koyama, M., Ohkawa, Y., Kurumizaka, H. 10.1093/nar/gkab1137 34929737 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2022 P62806, C0HKE1, Q9D2U9, A0A8X6EH29 0.506
661 6PX1 EM 3.30 2019-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Set2 bound to nucleosome Bilokapic, S., Halic, M. 10.1038/s41467-019-11726-4 31439846 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis Xenopus laevis 2019 P02302, P0CH09, P62799, P02281 0.49
662 6SEG EM 3.10 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class1: CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P49450, P62807, P62805, Q6FI13 0.512
663 6T7A EM 3.70 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Transcription factor SOX-11 Transcription factors, Transcription-associated P35716 O60814, Q71DI3, P04908, P62805 0.37
664 6T7D EM 4.40 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 117 Structure of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Transcription factor SOX-11 Transcription factors, Transcription-associated P35716 O60814, Q71DI3, P04908, P62805 0.323
665 6W5I EM 6.90 2021-03-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Lee, Y.T., Ayoub, A., Park, S.H., Sha, L., Xu, J., Mao, F., Zheng, W., Zhang, Y., Cho, U.S., Dou, Y. 10.1038/s41467-021-23268-9 34012049 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.135
666 6Y5D EM 4.10 2020-09-23 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Structure of human cGAS (K394E) bound to the nucleosome Pathare, G.R., Decout, A., Gluck, S., Cavadini, S., Makasheva, K., Hovius, R., Kempf, G., Weiss, J., Kozicka, Z., Guey, B., Melenec, P., Fierz, B., Thoma, N.H., Ablasser, A. 10.1038/s41586-020-2750-6 32911482 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 O60814, Q71DI3, P62805, Q6FI13 0.195
667 7E9F EM 4.00 2022-09-07 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 123 Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M. 0 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2022 Origin recognition complex subunit 1 DNA replication, Transcription-associated, ORC P54784 P02294, P02309, P04912, P61830 0.319
668 7PEV EM 6.00 2022-08-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 347 Nucleosome stack of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P04908, P62805 0.224
669 7PF4 EM 4.00 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 167 Nucleosome 3 of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P04908, P62805 0.274
670 7PF5 EM 3.80 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Nucleosome 2 of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.329
671 7PFU EM 5.00 2022-08-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 354 Nucleosome stack of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.236
672 7PII EM 2.68 2022-05-25 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 122 Structure of the human CCAN CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 P49450, P62807, P62805, Q93077 0.573
673 7WLR EM 3.54 2022-07-13 octamer 1 H3.3 canonical_H4 H2A.X canonical_H2B 601 145 Cryo-EM structure of the nucleosome containing Komagataella pastoris histones Fukushima, Y., Hatazawa, S., Hirai, S., Kujirai, T., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1093/jb/mvac043 35485963 Komagataella pastoris Komagataella pastoris Komagataella pastoris Komagataella pastoris Xenopus laevis 2022 A0A1B2JA70, A0A1B2JB78, A0A1B2JBS1, A0A1B2JD99 0.45
674 9GFB EM 3.55 2025-08-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 CryoEM structure of the human INO80 core-nucleosome complex state N-7 Sharma, M., Aggarwal, P., Hopfner, K.P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, INO80 complex subunit B, INO80 complex subunit C, Actin-related protein 5 Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9C086, Q6PI98, Q9H9F9 P04908, P68431, P62805, Q16778 -
675 7XTI EM 3.90 2022-10-12 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 85 RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.223
676 7XZY EM 3.97 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 165 Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P04908, P68431, P62805, P06899 0.256
677 7Y00 EM 3.96 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P04908, P68431, P62805, P06899 0.32
678 8G88 EM 2.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 168 Human Oct4 bound to nucleosome with human nMatn1 sequence Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 Q6AZJ8, P84233, P62799, P02281 0.199
679 8HAK EM 4.50 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.214
680 8JBX EM 3.35 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Human canonical 601 DNA nucleosome Ding, D., Pang, M.Y.H., Deng, M., Nguyen, T.T., Liu, Y., Sun, X., Xu, Z., Zhang, Y., Zhai, Y., Yan, Y., Ishibashi, T. 10.1093/nar/gkae825 39329259 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P04908, P68431, P62805, P62807 0.43
681 8KCB EM 3.17 2024-06-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 126 Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2 Zhang, H., Gu, Z., Zeng, Y., Zhang, Y. 10.1016/j.str.2024.05.013 38870940 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9LD28, P59226, P59259, Q9FFC0 0.38
682 8OOP EM 2.70 2023-07-26 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 110 CryoEM Structure INO80core Hexasome complex composite model state2 Zhang, M., Jungblut, A., Kunert, F., Hauptmann, L., Hoffmann, T., Kolesnikova, O., Metzner, F., Moldt, M., Weis, F., DiMaio, F., Hopfner, K.P., Eustermann, S. 10.1126/science.adf6287 37384673 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 RuvB-like protein 1, RuvB-like protein 2, Chromatin-remodeling ATPase Ino80, Ino eighty subunit 2, Chromatin-remodeling complex subunit IES6, Actin-related protein 5 INO80, Chromatin remodelers G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62807, P68431, P62805, Q93077 0.554
683 8OOS EM 3.29 2023-07-26 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 110 CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2 Zhang, M., Jungblut, A., Kunert, F., Hauptmann, L., Hoffmann, T., Kolesnikova, O., Metzner, F., Moldt, M., Weis, F., DiMaio, F., Hopfner, K.P., Eustermann, S. 10.1126/science.adf6287 37384673 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Chromatin-remodeling ATPase Ino80 P62807, P68431, P62805, Q93077 0.494
684 8QKV EM 4.70 2024-10-02 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 194 SWR1-nucleosome complex in configuration 2 Girvan, P., Jalal, A.S.B., McCormack, E.A., Skehan, M.T., Knight, C.L., Wigley, D.B., Rueda, D.S. 10.1038/s41586-024-08152-y 39506114 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04912, P61830 0.185
685 8T3T EM 3.21 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state3 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Telomere-associated Q07457 P06897, P84233, P62799, P02281 0.535
686 8TXX EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P0CG47 P04908, P68431, P62805, P62807 0.438
687 6PWX EM 4.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of RbBP5 bound to the nucleosome Park, S.H., Ayoub, A., Lee, Y.T., Xu, J., Kim, H., Zheng, W., Zhang, B., Sha, L., An, S., Zhang, Y., Cianfrocco, M.A., Su, M., Dou, Y., Cho, U.S. 10.1038/s41467-019-13550-2 31804488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Retinoblastoma-binding protein 5 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291 P06897, P84233, P62799, P02281 0.332
688 6PWE EM 3.95 2019-08-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of nucleosome core particle Chittori, S., Hong, J., Bai, Y., Subramaniam, S. 10.1093/nar/gkz670 31402386 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2019 P84040, P84051, P02283, P02299 0.409
689 6LE9 X-ray 2.60 2020-04-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Soman, A., Liew, C.W., Teo, H.L., Berezhnoy, N.V., Olieric, V., Korolev, N., Rhodes, D., Nordenskiold, L. 10.1093/nar/gkaa289 32374876 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 O60814, P04908, P68431, P62805 -
690 6K1K X-ray 2.20 2020-01-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601L 145 Human nucleosome core particle with H2A.X S139E variant Sharma, D., De Falco, L., Padavattan, S., Rao, C., Geifman-Shochat, S., Liu, C.F., Davey, C.A. 10.1038/s41467-019-13641-0 31848352 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P16104, P68431, P62805, P06899 -
691 9CA8 EM 3.92 2025-06-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 Cryo-EM structure of human SRCAP-nucleosome complex in the partially-engaged state (composite structure) Park, G., Patel, A.B., Wu, C., Louder, R.K. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2 Transcription-associated, Chromatin remodelers, Cell cycle, SRCAP (INO80), Histone chaperones, INO80, Euchromatin-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230 P06897, P62799, P84233, P02281 0.368
692 9GE5 EM 3.35 2025-08-20 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 113 CryoEM structure of the human INO80-Hexasome complex Aggarwal, P., Sharma, M., Hopfner, K.P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, INO80 complex subunit B, INO80 complex subunit C, Actin-related protein 5 Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9C086, Q6PI98, Q9H9F9 P04908, P68431, P62805, P33778 -
693 9V33 EM 5.90 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 134 Calypso/Asx/NCP-ub complex Wang, C., Sun, F., Zhao, H., Zhang, N., Guan, J., Zhou, Y., Shuai, W., Zheng, H., He, J. 10.1016/j.isci.2026.114958 41782825 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 Ubiquitin carboxyl-terminal hydrolase calypso, Polycomb group protein Asx, Polyubiquitin-B Transcription-associated, Polycomb, Ubiquitin, Histone PTM erasers, Histone_deubiquitination_H2AK119 Q7K5N4, Q9V727, P0CG47 A0A310TTQ1, Q6AZJ8, A0A8J0U496, P62799 0.241
694 7KBE EM 3.50 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction) Arimura, Y., Shih, R.M., Froom, R., Funabiki, H. 10.1016/j.molcel.2021.08.010 34478647 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P84233, P02281, P62799, Q6DKE3 0.445
695 9S3G EM 6.40 2025-11-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 67 State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Histone-lysine N-methyltransferase SETD2, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A8D1KNW4, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q9BYW2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267, Q9Y5B9, Q08945 O60814, Q71DI3, P04908, P62805 0.187
696 9J0N EM 3.40 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 167 Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RPB12, Transcription elongation factor A protein 1, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, P23193, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P04908, P62805, P06899, P84243 0.316
697 9CAA EM 4.04 2025-06-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Cryo-EM structure of human SRCAP-nucleosome complex in the pre-engaged state (composite structure) Park, G., Patel, A.B., Wu, C., Louder, R.K. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2 Transcription-associated, Chromatin remodelers, Cell cycle, SRCAP (INO80), Histone chaperones, INO80, Euchromatin-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230 P06897, P62799, P84233, P02281 0.303
698 6NOG EM 3.90 2019-02-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C. 10.1016/j.cell.2019.02.002 30765112 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, J3QS39 P06897, P84233, P62799, P02281 0.356
699 7D69 EM 3.57 2021-09-08 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601L 125 Cryo-EM structure of the nucleosome containing Giardia histones Sato, S., Takizawa, Y., Hoshikawa, F., Dacher, M., Tanaka, H., Tachiwana, H., Kujirai, T., Iikura, Y., Ho, C.H., Adachi, N., Patwal, I., Flaus, A., Kurumizaka, H. 10.1093/nar/gkab644 34352093 Giardia intestinalis Giardia intestinalis Giardia intestinalis Giardia intestinalis Xenopus laevis 2021 A8BHS7, A8BI78, A8BUJ9, E2RU29 0.427
700 1M1A X-ray 2.65 2003-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1016/S0022-2836(02)01407-9 12559907 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2003 P02302, P06897, P62799, P02281 -
701 1P3B X-ray 3.00 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
702 2FJ7 X-ray 3.20 2006-09-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_A16 147 Crystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element Bao, Y., White, C.L., Luger, K. 10.1016/j.jmb.2006.06.051 16860337 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2006 P06897, P84233, P62799, P02281 -
703 3REL X-ray 2.70 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Triamminechloroplatinum(II) Chloride Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P06897, P84233, P62799, P02281 -
704 4QLC X-ray 3.50 2015-07-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H5 601 166 Crystal structure of chromatosome at 3.5 angstrom resolution Zhou, B.R., Jiang, J., Feng, H., Ghirlando, R., Xiao, T.S., Bai, Y. 10.1016/j.molcel.2015.06.025 26212454 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Gallus gallus 2015 P84040, P02283, P02259, P02299, P84051 -
705 4YM6 X-ray 3.51 2015-12-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 144 Crystal structure of the human nucleosome containing 6-4PP (outside) Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H. 10.1038/srep16330 26573481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
706 5B0Y X-ray 2.56 2016-01-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Suzuki, Y., Horikoshi, N., Kato, D., Kurumizaka, H. 10.1016/j.bbrc.2015.12.041 26694698 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 Q71DI3, P04908, P62805, P06899 -
707 5DNN X-ray 2.80 2016-09-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes Adhireksan, Z., Palermo, G., Riedel, T., Ma, Z., Muhammad, R., Rothlisberger, U., Dyson, P.J., Davey, C.A. 10.1038/ncomms14860 28358030 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P06897, P84233, P62799, P02281 -
708 5GTC X-ray 2.70 2017-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Amamoto, Y., Aoi, Y., Nagashima, N., Suto, H., Yoshidome, D., Arimura, Y., Osakabe, A., Kato, D., Kurumizaka, H., Kawashima, S.A., Yamatsugu, K., Kanai, M. 10.1021/jacs.7b02138 28534629 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 LANA peptide Viral Q9QR71 P04908, P68431, P62805, P06899 -
709 5OMX X-ray 2.32 2017-11-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 X-ray Structure of the H2A-N38C Nucleosome Core Particle Frouws, T.D., Barth, P.D., Richmond, T.J. 10.1016/j.jmb.2017.10.029 29113904 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P06897, P84233, P62799, P02281 -
710 5XM0 X-ray 2.87 2018-03-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4 Harada, A., Maehara, K., Ono, Y., Taguchi, H., Yoshioka, K., Kitajima, Y., Xie, Y., Sato, Y., Iwasaki, T., Nogami, J., Okada, S., Komatsu, T., Semba, Y., Takemoto, T., Kimura, H., Kurumizaka, H., Ohkawa, Y. 10.1038/s41467-018-03845-1 29643389 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2018 P62806, P84244, C0HKE1, Q9D2U9 -
711 5Z3L EM 4.31 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex in apo state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 SWI/SNF, Transcription-associated, Chromatin remodelers P22082 P06897, P84233, P62799, P02281 0.261
712 6ESG EM 5.40 2017-12-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 141 Nucleosome breathing : Class 2 Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41594-017-0005-5 29323273 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Q6AZJ8, P84233, P62799, P02281 0.198
713 6FTX EM 4.50 2018-08-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 159 Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome Sundaramoorthy, R., Hughes, A.L., El-Mkami, H., Norman, D.G., Ferreira, H., Owen-Hughes, T. 10.7554/eLife.35720 30079888 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2018 Polyubiquitin-B, Chromatin-remodeling ATPase CHD, Ubiquitin, Transcription-associated, Chromatin remodelers P0CG47, P32657 P02302, S4RAZ3, Q28D68, P06897, P62799 0.23
714 6J4Y EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.235
715 6J4Z EM 4.10 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Spt5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.244
716 7TN2 EM 2.30 2022-03-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A Cryo-EM maps Nodelman, I.M., Das, S., Faustino, A.M., Fried, S.D., Bowman, G.D., Armache, J.P. 10.1038/s41594-021-00719-x 35173352 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 P06897, P84233, P62799, P02281 -
717 6K1J X-ray 2.85 2020-01-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B alphasat_147 145 Human nucleosome core particle with H2A.X variant Sharma, D., De Falco, L., Padavattan, S., Rao, C., Geifman-Shochat, S., Liu, C.F., Davey, C.A. 10.1038/s41467-019-13641-0 31848352 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P16104, P68431, P62805, P06899 -
718 6KW3 EM 7.13 2019-11-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The ClassA RSC-Nucleosome Complex Ye, Y., Wu, H., Chen, K., Clapier, C.R., Verma, N., Zhang, W., Deng, H., Cairns, B.R., Gao, N., Chen, Z. 10.1126/science.aay0033 31672915 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Chromatin structure-remodeling complex protein RSC58, Chromatin structure-remodeling complex protein RSC30, Chromatin structure-remodeling complex protein RSC8, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC6, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex subunit RSC4, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Cell cycle, RSC (SWI/SNF), Transcription-associated, Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P06897, P84233, P62799, P02281 0.086
719 3B6G X-ray 3.45 2007-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome core particle treated with oxaliplatin Wu, B., Droge, P., Davey, C.A. 10.1038/nchembio.2007.58 18157123 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2007 P06897, P84233, P62799, P02281 -
720 7XZX EM 4.53 2022-10-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 171 Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.146
721 7YWX EM 12.00 2022-05-18 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 162 Structure of the human CCAN CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein S, Centromere protein T, Centromere protein U, Centromere protein W, Centromere protein X, Centromere protein C CENP-A NAC/CAD, Transcription-associated, Cell cycle, Centromere-associated, Fanconi anemia core complex, Nuclear division, Kinetochore, DNA repair Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q8N2Z9, Q96BT3, Q71F23, Q5EE01, A8MT69, Q03188 P49450, P62807, P62805, Q93077 0.054
722 8B0A EM 3.00 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome Bacic, L., Gaullier, G., Mohapatra, J., Mao, G., Brackmann, K., Panfilov, M., Liszczak, G., Sabantsev, A., Deindl, S. 10.1038/s41467-024-45237-8 38307862 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.483
723 8BYQ EM 4.10 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Cell cycle, Transcription factors, RNA polymerases, DNA repair, Euchromatin-associated P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P06897, P84233, P62799, P02281 0.187
724 8CBN EM 3.34 2023-12-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.392
725 8EUE EM 3.48 2023-07-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class1 of the INO80-Nucleosome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus Xenopus Xenopus Xenopus Xenopus laevis 2023 P06897, P84233, P62799, P02281 0.356
726 8H0W EM 4.60 2022-12-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.2 601 196 RNA polymerase II transcribing a chromatosome (type II) Hirano, R., Ehara, H., Kujirai, T., Uejima, T., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1038/s41467-022-35003-z 36435862 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P68431, P06899, P04908, P62805, P16403 0.16
727 8HXY EM 3.10 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.44
728 8IEJ EM 3.12 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 RNF20-RNF40/hRad6A-Ub/nucleosome complex Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.molcel.2023.08.001 37633270 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1B, E3 ubiquitin-protein ligase BRE1A, Ubiquitin-conjugating enzyme E2 A Transcription-associated, Histone PTM writers, E3 ubiquitin-protein ligation, DNA repair, Histone_ubiquitination_H2BK120_writer O75150, Q5VTR2, P49459 O60814, P04908, P68431, P62805 0.461
729 8KD4 EM 2.93 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.373
730 8KE0 EM 4.00 2025-03-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.2 601L 183 Structure of H1.2 bound to the nucleosome Kujirai, T., Echigoya, K., Kishi, Y., Saeki, M., Ito, T., Kato, J., Negishi, L., Kimura, H., Masumoto, H., Takizawa, Y., Gotoh, Y., Kurumizaka, H. 10.1038/s41594-025-01493-w 39984731 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2025 P68431, P06899, P04908, P62805, P16403 0.352
731 8PKI EM 2.58 2024-02-28 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 137 Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 Kobayashi, W., Sappler, A.H., Bollschweiler, D., Kummecke, M., Basquin, J., Arslantas, E.N., Ruangroengkulrith, S., Hornberger, R., Duderstadt, K., Tachibana, K. 10.1038/s41594-024-01239-0 38409506 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2024 Nuclear receptor subfamily 5 group A member 2 Transcription factors, Transcription-associated O00482 P62806, P84244, Q6ZWY9, C0HKE3 0.572
732 8Q15 EM 3.60 2025-02-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 119 CryoEM structure of canonical rice nucleosome core particle Gandhivel, V.H., Sotelo-Parrilla, P., Raju, S., Jha, S., Gireesh, A., Harshith, C.Y., Gut, F., Vinothkumar, K.R., Berger, F., Jeyaprakash, A.A., Shivaprasad, P.V. 10.1038/s41477-025-01974-2 40200022 Oryza Oryza Oryza Oryza Xenopus laevis 2025 A2YMC6, A2Y533, A2WKP5, None 0.401
733 8Q16 EM 3.60 2025-02-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 CryoEM structure of rice nucleosome containing a H4 variant chimera Gandhivel, V.H., Sotelo-Parrilla, P., Raju, S., Jha, S., Gireesh, A., Harshith, C.Y., Gut, F., Vinothkumar, K.R., Berger, F., Jeyaprakash, A.A., Shivaprasad, P.V. 10.1038/s41477-025-01974-2 40200022 Oryza Oryza Oryza Oryza Xenopus laevis 2025 A2YMC6, A2Y533, A2WKP5, A0A0E0HFN0 0.441
734 8Q3M X-ray 2.50 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Batchelor, L.K., De Falco, L., Dyson, P.J., Davey, C.A. 10.1039/d4ra01617c 38495982 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Kaposi sarcoma associated herpesvirus LANA peptide with a methionine to ornithine substitution Viral Q9QR71 O60814, P04908, P68431, P62805 -
735 8Q3X X-ray 2.30 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Batchelor, L.K., De Falco, L., Dyson, P.J., Davey, C.A. 10.1039/d4ra01617c 38495982 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 LANA peptide Viral Q9QR71 O60814, P04908, P68431, P62805 -
736 8SN0 EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.547
737 8T3Y EM 3.47 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state1 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Telomere-associated Q07457 P06897, P84233, P62799, P02281 0.503
738 8U13 EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168 Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5 P04908, P68431, P62805, P62807 0.381
739 8WHB EM 3.17 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 134 Structure of nucleosome core particle of Arabidopsis thaliana Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 Q9LD28, P59226, P59259, O23629 0.5
740 9B2S EM 3.01 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Haspin bound to nucleosome in position 1 Hicks, C.W., Gliech, C.R., Rahman, S., Zhang, X., Eneim, A.S., Vasquez, S.J., Holland, A.J., Wolberger, C. 10.1038/s41594-025-01502-y 39979508 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Serine/threonine-protein kinase haspin Nuclear division, Histone_phosphorylation_H3T3_writer, Histone PTM writers Q8TF76 Q6AZJ8, P84233, P62799, P02281 0.536
741 9BE5 EM 3.30 2025-04-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of Human Nucleosome collected by EPU on Glacios at 3.3 Angstrom resolution Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.V. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 A0A9J8D176, Q71DI3, P04908, P0C0S8, P06899 0.448
742 9CB7 EM 4.04 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers P53115, P40154 P62799, P02293, P04911, P61830 0.288
743 9CG9 EM 2.94 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 154 Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 Saunders, H.S., Chio, U.S., Moore, C.M., Ramani, V., Cheng, Y., Narlikar, G.J. 10.1126/sciadv.ads4473 40815652 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 High mobility group protein B1 P09429 P06897, P84233, P62799, P02281 0.527
744 9E05 EM 8.00 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 321 The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.159
745 9E2R EM 7.71 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 319 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.072
746 9FH9 EM 2.50 2024-07-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of CyclinB1 N-terminus bound to the NCP Cirillo, L., Young, R., Veerapathiran, S., Roberti, A., Martin, M., Abubacar, A., Perosa, C., Coates, C., Muhammad, R., Roumeliotis, T.I., Choudhary, J.S., Alfieri, C., Pines, J. 10.1038/s44318-024-00194-2 39143240 Homo sapiens Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis 2024 G2/mitotic-specific cyclin-B1 APC/C, Cell cycle P14635 P68431, P62805, Q7L7L0, P02281 0.534
747 7XFN EM 2.80 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Structure of nucleosome-DI complex (-55I, Apo state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P06897, P84233, P62799, P02281 0.55
748 7XD0 EM 3.48 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 cryo-EM structure of H2BK34ub nucleosome Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Ubiquitin-60S ribosomal protein L40 Ubiquitin P62987 Q71DI3, P04908, P62805, Q2M2T1 0.457
749 7X3X EM 3.20 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of N1 nucleosome-RA Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 P06897, P84233, P62799, P02281 0.44
750 6PA7 EM 2.94 2020-06-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 166 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Xu, T.H., Liu, M., Zhou, X.E., Liang, G., Zhao, G., Xu, H.E., Melcher, K., Jones, P.A. 10.1038/s41586-020-2747-1 32968275 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 DNA (cytosine-5)-methyltransferase 3A, DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 P06897, P84233, P62799, P02281 0.403
751 3X1U X-ray 3.25 2015-09-23 octamer 1 canonical_H3 canonical_H4 H2A.1 canonical_H2B alphasat_146 146 Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bbrc.2015.07.070 26188507 Homo sapiens Homo sapiens Mus musculus Homo sapiens Xenopus laevis 2015 P68431, P62805, Q8CGP4, P33778 -
752 4JJN X-ray 3.09 2013-05-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome Wang, F., Li, G., Altaf, M., Lu, C., Currie, M.A., Johnson, A., Moazed, D. 10.1073/pnas.1300126110 23650358 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2013 Regulatory protein SIR3 Transcription-associated P06701 P02294, P02309, P04912, P61830 -
753 7XFH EM 2.90 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 132 Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-3-methyladenine glycosylase DNA modification, DNA repair P29372 P06897, P84233, P62799, P02281 0.515
754 4Z66 X-ray 2.50 2015-10-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Chatterjee, N., North, J.A., Dechassa, M.L., Manohar, M., Prasad, R., Luger, K., Ottesen, J.J., Poirier, M.G., Bartholomew, B. 10.1128/MCB.00441-15 26416878 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P06897, P84233, P62799, P02281 -
755 5B24 X-ray 3.60 2016-03-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 144 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Horikoshi, N., Tachiwana, H., Kagawa, W., Osakabe, A., Matsumoto, S., Iwai, S., Sugasawa, K., Kurumizaka, H. 10.1016/j.bbrc.2016.01.170 26837048 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P04908, P68431, P62805, P06899 -
756 5B40 X-ray 3.33 2016-06-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Machida, S., Sekine, S., Nishiyama, Y., Horikoshi, N., Kurumizaka, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 Q71DI3, P04908, P62805, P06899 -
757 5Z3O EM 3.62 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex in ADP state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 SWI/SNF, Transcription-associated, Chromatin remodelers P22082 P06897, P84233, P62799, P02281 0.349
758 6IY3 EM 3.67 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B MMTV 147 Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 SWI/SNF, Transcription-associated, Chromatin remodelers P22082 P06897, P84233, P62799, P02281 0.399
759 6JM9 EM 7.30 2019-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 123 cryo-EM structure of DOT1L bound to unmodified nucleosome Jang, S., Kang, C., Yang, H.S., Jung, T., Hebert, H., Chung, K.Y., Kim, S.J., Hohng, S., Song, J.J. 10.1101/gad.323790.118 30923167 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific Histone_methylation_H3K79_writer, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3 Q6AZJ8, P84233, P62799, P02281 0.132
760 6JOU X-ray 2.17 2020-03-25 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 Crystal structure of the human nucleosome containing H2A.Z.1 S42R Horikoshi, N., Kujirai, T., Sato, K., Kimura, H., Kurumizaka, H. 10.1016/j.bbrc.2019.06.012 31186139 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P68431, P62805, P06899, P0C0S5 -
761 6L9Z X-ray 2.50 2021-02-17 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.10 601_modified 338 338 bp di-nucleosome assembled with linker histone H1.X Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 Q92522, P68431, P04908, P62805, P06899 -
762 6NZO EM 3.80 2019-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Set2 bound to nucleosome Bilokapic, S., Halic, M. 10.1038/s41467-019-11726-4 31439846 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated G0S676 P02302, P0CH09, P62799, P02281 0.364
763 6PWV EM 6.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 core complex bound to the nucleosome Park, S.H., Ayoub, A., Lee, Y.T., Xu, J., Kim, H., Zheng, W., Zhang, B., Sha, L., An, S., Zhang, Y., Cianfrocco, M.A., Su, M., Dou, Y., Cho, U.S. 10.1038/s41467-019-13550-2 31804488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2, Protein dpy-30 homolog Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3, Q9C005 P06897, P84233, P62799, P02281 0.188
764 7VDT EM 2.80 2022-05-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Yuan, J.J., Chen, K.J., Zhang, W.B., Chen, Z.C. 10.1038/s41586-022-04658-5 35477757 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Isoform 2 of Transcription activator BRG1 SWI/SNF, Transcription-associated, Chromatin remodelers P51532 P06897, P84233, P62799, P02281 0.549
765 6R91 EM 4.10 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.212
766 6R92 EM 4.80 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.22
767 6SEF EM 3.70 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2C : CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 P49450, P62807, P62805, Q6FI13 0.372
768 6UPH EM 2.70 2019-11-06 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 119 Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution Migl, D., Kschonsak, M., Arthur, C.P., Khin, Y., Harrison, S.C., Ciferri, C., Dimitrova, Y.N. 10.1016/j.str.2019.12.002 32004465 Saccharomyces cerevisiae Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Xenopus laevis 2019 Q6CMU6, Q6CK60, Q6CK59, P36012 0.623
769 7CRQ EM 3.15 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD3 Histone_methylation_H3K4_writer, Histone_methylation_H3K27_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated Q9BZ95 P06897, Q92133, P62799, P02281 0.507
770 7CRR EM 3.48 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 Native NSD3 bound to 187-bp nucleosome Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD3 Histone_methylation_H3K4_writer, Histone_methylation_H3K27_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated Q9BZ95 P06897, Q92133, P62799, P02281 0.464
771 7M1X EM 3.70 2021-09-29 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 136 Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z Lewis, T.S., Sokolova, V., Jung, H., Ng, H., Tan, D. 10.1093/nar/gkab907 34643712 Xenopus laevis Xenopus laevis Mus musculus Xenopus laevis Xenopus laevis 2021 P02302, P0C0S6, P62799, P02281 0.391
772 7PF6 EM 4.00 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Nucleosome 1 of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.27
773 7U46 EM 2.68 2022-03-16 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with CENP-N Zhou, K., Gebala, M., Woods, D., Sundararajan, K., Edwards, G., Krzizike, D., Wereszczynski, J., Straight, A.F., Luger, K. 10.1038/s41594-022-00758-y 35422519 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q96H22 P49450, P62807, P62805, Q93077 0.559
774 7U52 EM 3.40 2022-09-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 nucleosome core particle with AP-site at SHL-6.5 Weaver, T.M., Hoitsma, N.M., Spencer, J.J., Gakhar, L., Schnicker, N.J., Freudenthal, B.D. 10.1038/s41467-022-33057-7 36104361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Q71DI3, P62807, P62805, P0C0S8 0.454
775 7U53 EM 4.00 2022-09-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Nucleosome core particle with AP-site at SHL0 Weaver, T.M., Hoitsma, N.M., Spencer, J.J., Gakhar, L., Schnicker, N.J., Freudenthal, B.D. 10.1038/s41467-022-33057-7 36104361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Q71DI3, P62807, P62805, P0C0S8 0.385
776 7V90 EM 3.50 2022-07-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 Telomeric mononucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, P04908, P68431, P62805 0.459
777 9GEN EM 3.76 2025-08-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Recombinant Myeloperoxidase bound to nucleosome core particle Burn, G.L., Raisch, T., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Gimber, N., Raunser, S., Zychlinsky, A. 10.1038/s41586-025-09523-9 40963017 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Myeloperoxidase light chain Neutrophil extracellular traps P05164 P06897, P84233, P62799, P02281 0.444
778 9GEP EM 2.89 2025-08-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Native monomeric Myeloperoxidase bound to nucleosome core particle Burn, G.L., Raisch, T., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Gimber, N., Raunser, S., Zychlinsky, A. 10.1038/s41586-025-09523-9 40963017 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Myeloperoxidase light chain Neutrophil extracellular traps P05164 P06897, P84233, P62799, P02281 0.506
779 9J8O EM 4.05 2025-02-26 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.1 601 176 Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Horikoshi, N., Miyake, R., Sogawa-Fujiwara, C., Ogasawara, M., Takizawa, Y., Kurumizaka, H. 10.1038/s41467-025-56823-9 39929866 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2025 Barrier-to-autointegration factor, Lamin-A/C Nuclear division O75531, P02545 P68431, Q02539, P04908, P62805, P06899 0.292
780 5XM1 X-ray 3.45 2018-03-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4 Harada, A., Maehara, K., Ono, Y., Taguchi, H., Yoshioka, K., Kitajima, Y., Xie, Y., Sato, Y., Iwasaki, T., Nogami, J., Okada, S., Komatsu, T., Semba, Y., Takemoto, T., Kimura, H., Kurumizaka, H., Ohkawa, Y. 10.1038/s41467-018-03845-1 29643389 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2018 P62806, P84244, C0HKE1, Q9D2U9 -
781 3AZI X-ray 2.70 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
782 3KUY X-ray 2.90 2010-01-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent Davey, G.E., Wu, B., Dong, Y., Surana, U., Davey, C.A. 10.1093/nar/gkp1174 20026584 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P06897, P84233, P62799, P02281 -
783 3LJA X-ray 2.75 2010-04-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome Wu, B., Davey, C.A. 10.1016/j.jmb.2010.03.038 20350553 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P06897, P84233, P62799, P02281 -
784 3MGQ X-ray 2.65 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Nickel ions to the Nucleosome Core Particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P84233, P62799, P02281 -
785 3TU4 X-ray 3.00 2011-11-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Armache, K.J., Garlick, J.D., Canzio, D., Narlikar, G.J., Kingston, R.E. 10.1126/science.1210915 22096199 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2011 Regulatory protein SIR3 Transcription-associated P06701 P06897, P84233, P62799, P02281 -
786 3WAA X-ray 3.20 2013-12-18 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The nucleosome containing human H2A.Z.2 Horikoshi, N., Sato, K., Shimada, K., Arimura, Y., Osakabe, A., Tachiwana, H., Hayashi-Takanaka, Y., Iwasaki, W., Kagawa, W., Harata, M., Kimura, H., Kurumizaka, H. 10.1107/S090744491302252X 24311584 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 Q71UI9, P68431, P62805, P06899 -
787 4J8U X-ray 2.38 2013-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P06897, P84233, P62799, P02281 -
788 4XZQ X-ray 2.40 2015-10-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Chatterjee, N., North, J.A., Dechassa, M.L., Manohar, M., Prasad, R., Luger, K., Ottesen, J.J., Poirier, M.G., Bartholomew, B. 10.1128/MCB.00441-15 26416878 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P06897, P84233, P62799, P02281 -
789 4Z5T X-ray 2.80 2016-02-10 octamer 1 H3.5 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The nucleosome containing human H3.5 Urahama, T., Harada, A., Maehara, K., Horikoshi, N., Sato, K., Sato, Y., Shiraishi, K., Sugino, N., Osakabe, A., Tachiwana, H., Kagawa, W., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1186/s13072-016-0051-y 26779285 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P62805, P04908, Q6NXT2, P06899 -
790 5CPJ X-ray 3.15 2015-10-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_2R 140 Nucleosome containing methylated Sat2R DNA Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H. 10.1098/rsob.150128 26446621 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
791 5GT0 X-ray 2.82 2017-02-15 octamer 1 canonical_H3 canonical_H4 H2A.1 canonical_H2B alphasat_146 146 Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a Padavattan, S., Thiruselvam, V., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bpc.2016.11.013 27992841 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P62807, P68431, P62805, Q96QV6 -
792 5X7X X-ray 2.18 2017-04-19 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Taguchi, H., Xie, Y., Horikoshi, N., Maehara, K., Harada, A., Nogami, J., Sato, K., Arimura, Y., Osakabe, A., Kujirai, T., Iwasaki, T., Semba, Y., Tachibana, T., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1021/acs.biochem.6b01098 28374988 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P04908, P62805, P06899, P84243 -
793 6KW5 EM 10.13 2020-09-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The ClassC RSC-Nucleosome Complex Ye, Y.P., Wu, H., Chen, K.J., Verma, N., Cairns, B., Gao, N., Chen, Z.C. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromatin structure-remodeling complex protein RSC58, Chromatin structure-remodeling complex protein RSC30, Chromatin structure-remodeling complex protein RSC8, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC6, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex subunit RSC4, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Cell cycle, RSC (SWI/SNF), Transcription-associated, Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P06897, A0A1L8G0X3, P84233, P62799 0.062
794 2NQB X-ray 2.30 2007-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Drosophila Nucleosome Structure Chakravarthy, S., Luger, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2007 P84040, P84051, P02283, P02299 -
795 6NE3 EM 3.90 2019-07-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2 Armache, J.P., Gamarra, N., Johnson, S.L., Leonard, J.D., Wu, S., Narlikar, G.J., Cheng, Y. 10.7554/eLife.46057 31210637 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.42
796 6SEE EM 4.20 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2A : CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 P49450, P62807, P62805, Q6FI13 0.309
797 6T79 EM 3.20 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 145 Structure of a human nucleosome at 3.2 A resolution Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 O60814, Q71DI3, P04908, P62805 0.47
798 6TEM EM 3.90 2020-04-08 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 130 CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM Boopathi, R., Danev, R., Khoshouei, M., Kale, S., Nahata, S., Ramos, L., Angelov, D., Dimitrov, S., Hamiche, A., Petosa, C., Bednar, J. 10.1093/nar/gkaa246 32313946 Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 P49450, P06897, P62799, P02281 -
799 6USJ EM 10.50 2020-10-14 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Structure of two nucleosomes bridged by human PARP2 Gaullier, G., Roberts, G., Muthurajan, U.M., Bowerman, S., Rudolph, J., Mahadevan, J., Jha, A., Rae, P.S., Luger, K. 10.1371/journal.pone.0240932 33141820 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Poly [ADP-ribose] polymerase 2 Histone_PARylation_writer, DNA repair, Histone PTM writers Q9UGN5 P04908, P68431, P62805, P06899 0.092
800 6VEN EM 3.37 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Yeast COMPASS in complex with a ubiquitinated nucleosome Worden, E.J., Zhang, X., Wolberger, C. 10.7554/eLife.53199 31922488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Ubiquitin, COMPASS component SWD3, COMPASS component SWD1, Histone-lysine N-methyltransferase, H3 lysine-4 specific, COMPASS component BRE2, COMPASS component SDC1, COMPASS component SPP1 Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers, COMPASS, Ubiquitin, Telomere-associated P0CG48, P38123, P39706, P38827, P43132, Q03323, Q03012 P06897, P84233, P62799, P02281 0.449
801 7CCR EM 4.90 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of the 2:2 cGAS-nucleosome complex Cao, D., Han, X., Fan, X., Xu, R.M., Zhang, X. 10.1038/s41422-020-00422-4 33051594 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 P04908, P68431, P62805, P06899 0.152
802 7D1Z EM 3.15 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of SET8-nucleosome complex Ho, C.H., Takizawa, Y., Kobayashi, W., Arimura, Y., Kimura, H., Kurumizaka, H. 10.26508/lsa.202000919 33574035 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Isoform 2 of N-lysine methyltransferase KMT5A Transcription-associated, Histone PTM writers, Cell cycle, Heterochromatin-associated, Nuclear division, Histone_methylation_H4K20_writer Q9NQR1 P04908, P68431, P62805, P06899 0.514
803 7K6Q EM 3.10 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1 bound to the H4K16ac nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Truong, D.M., Lee, R., Armache, J.P., Boeke, J.D., Armache, K.J. 10.1126/science.abc6663 33479126 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Telomere-associated, Histone PTM writers Q04089, P0CG48 P06897, P84233, P62799, P02281 0.489
804 7LYB EM 3.28 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Isoform 7 of Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair P38398, Q99728, P61077 P04908, P68431, P62805, P06899 0.458
805 7MBM EM 4.76 2021-12-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Ayoub, A., Park, S.H., Lee, Y.T., Cho, U.S., Dou, Y. 10.1021/acs.biochem.1c00603 34928138 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.198
806 7OTQ EM 4.80 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome Bacic, L., Gaullier, G., Sabantsev, A., Lehmann, L.C., Brackmann, K., Dimakou, D., Halic, M., Hewitt, G., Boulton, S., Deindl, S., Workman, J.L. 10.7554/eLife.71420 34486521 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.282
807 3AZE X-ray 3.00 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
808 1P3I X-ray 2.30 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
809 9JNZ EM 3.00 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in Apo state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.493
810 6T9L EM 3.60 2020-01-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 SAGA DUB module bound to a ubiqitinated nucleosome Wang, H., Dienemann, C., Stutzer, A., Urlaub, H., Cheung, A.C.M., Cramer, P. 10.1038/s41586-020-1933-5 31969703 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Ubiquitin carboxyl-terminal hydrolase 8, Transcription and mRNA export factor SUS1, SAGA-associated factor 11, SAGA-associated factor 73, Polyubiquitin-C Transcription-associated, Ubiquitin, Histone PTM erasers, SAGA, Histone_deubiquitination P50102, Q6WNK7, Q03067, P53165, P0CG48 P06897, P84233, P62799, P02281 0.394
811 9LIU EM 2.70 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome double-bound complex in ATP-ATP state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.487
812 9MLL EM 3.70 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 137 GammaH2AX containing nucleosomes, Parallel stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.26
813 9MMM EM 4.00 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosomes, Parallel stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.204
814 9MMO EM 3.90 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosomes, Right offset stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.34
815 9MMT EM 3.40 2025-10-29 hexamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 89 H2AX containing nucleosome, Unwrapped (Class 2) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.388
816 9R2M EM 3.50 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Chakraborty, D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.39
817 9WMS EM 3.40 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 118 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.227
818 9WMU EM 4.28 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 171 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.189
819 8XRJ EM 3.60 2025-05-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Kujirai, T., Kato, J., Yamamoto, K., Hirai, S., Fujii, T., Maehara, K., Harada, A., Negishi, L., Ogasawara, M., Yamaguchi, Y., Ohkawa, Y., Takizawa, Y., Kurumizaka, H. 10.1038/s41467-025-59580-x 40436841 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, DNA-directed RNA polymerases I, II, and III subunit RPABC4 Transcription-associated, RNA polymerases P24928, P30876, P19387, O15514, P19388, P61218, P62487, P52434, P36954, P62875, P52435, P53803 P04908, P68431, P62805, P06899 0.31
820 10YB EM 2.80 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nucleosome containing a nick at SHL-2 Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Q71DI3, P62807, P62805, P0C0S8 0.555
821 3W97 X-ray 3.20 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P04908, P68431, P62805, P06899 -
822 7XTD EM 3.90 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.221
823 10YF EM 3.00 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite) Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q96KK5, Q71DI3, P62805, Q5QNW6 0.494
824 1P3G X-ray 2.70 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
825 8JLB EM 2.36 2023-10-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Ehara, H., Sekine, S.I., Hayashi, G., Takizawa, Y., Kurumizaka, H. 10.1093/nar/gkad754 37718728 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Q71DI3, P04908, P62805, P06899 0.602
826 9DDE EM 3.20 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 162 ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Homo sapiens 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, RING1 and YY1-binding protein, Ubiquitin Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Histone PTM readers, Histone_ubiquitination_reader, Polycomb, Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496, Q8N488, P0CG48 P06897, P62799, P02281, P10412, P84233 0.456
827 8OW1 EM 3.70 2023-08-09 hexamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601_modified 153 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Dendooven, T., Zhang, Z., Yang, J., McLaughlin, S.H., Schwab, J., Scheres, S.H.W., Yatskevich, S., Barford, D. 10.1126/sciadv.adg7480 37506202 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2023 Centromere-binding protein 1, Centromere DNA-binding protein complex CBF3 subunit B, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Suppressor of kinetochore protein 1, Inner kinetochore subunit CNN1, Inner kinetochore subunit AME1, Inner kinetochore subunit WIP1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2 Transcription-associated, Cell cycle, Centromere-associated, Nuclear division, E3 ubiquitin-protein ligation, Kinetochore, CCAN, CBF3 P17106, P40969, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P52286, P43618, P38313, Q2V2P8, Q12493, Q06162 P02309, P02293, P04911, P36012 0.165
828 6LAB X-ray 3.20 2021-02-17 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601L 169 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P68431, P07305, P04908, P62805, P06899 -
829 8X19 EM 3.20 2024-03-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state Yu, J., Sui, F., Gu, F., Li, W., Yu, Z., Wang, Q., He, S., Wang, L., Xu, Y. 10.1038/s41421-023-00640-1 38331872 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2, Actin, cytoplasmic 1, Actin-like protein 6A, DNA methyltransferase 1-associated protein 1, YEATS domain-containing protein 4 Transcription-associated, Chromatin remodelers, Cell cycle, SRCAP (INO80), Histone chaperones, Histone PTM readers, INO80, Histone_acetylation_reader, Euchromatin-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P68431, P62807, P62805, Q93077 0.292
830 7ZSA EM 4.00 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription factors, RNA polymerases, Transcription-associated, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P06897, P84233, P62799, P02281 0.342
831 6IQ4 X-ray 2.25 2019-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Batchelor, L.K., De Falco, L., von Erlach, T., Sharma, D., Adhireksan, Z., Roethlisberger, U., Davey, C.A., Dyson, P.J. 10.1002/anie.201906423 31478581 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P04908, P68431, P62805, P06899 -
832 7UNC EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 155 Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, O00267 Q6AZJ8, P84233, P62799, P02281 0.344
833 7VZ4 EM 1.89 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Takizawa, Y., Ho, C.H., Sato, S., Danev, R., Kurumizaka, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 P04908, P68431, P62805, P06899 0.724
834 7CCQ EM 3.80 2020-10-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of the 1:1 cGAS-nucleosome complex Cao, D., Han, X., Fan, X., Xu, R.M., Zhang, X. 10.1038/s41422-020-00422-4 33051594 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 P04908, P68431, P62805, P06899 0.371
835 1P34 X-ray 2.70 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
836 1P3F X-ray 2.90 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
837 3MGP X-ray 2.44 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Cobalt ions to the Nucleosome Core Particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P84233, P62799, P02281 -
838 4XUJ X-ray 3.18 2016-01-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound Hanif, M., Meier, S.M., Adhireksan, Z., Henke, H., Martic, S., Movassaghi, S., Labib, M., Kandioller, W., Jamieson, S.M.F., Hejl, M., Jakupec, M.A., Kraatz, H.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1002/cplu.201700050 31961568 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P06897, P84233, P62799, P02281 -
839 3AZN X-ray 3.00 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
840 6QLD EM 4.15 2019-10-02 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 124 Structure of inner kinetochore CCAN-Cenp-A complex Yan, K., Yang, J., Zhang, Z., McLaughlin, S.H., Chang, L., Fasci, D., Ehrenhofer-Murray, A.E., Heck, A.J.R., Barford, D. 10.1038/s41586-019-1609-1 31578520 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2019 Inner kinetochore subunit MIF2, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Inner kinetochore subunit AME1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2 Cell cycle, Centromere-associated, Nuclear division, Kinetochore, CCAN P35201, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P38313, Q12493, Q06162 P36012, P02294, P02309, P02293, P04911 0.328
841 6RYU EM 4.00 2020-07-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Nucleosome-CHD4 complex structure (two CHD4 copies) Farnung, L., Ochmann, M., Cramer, P. 10.7554/eLife.56178 32543371 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 4,CHD4,Chromodomain-helicase-DNA-binding protein 4 NuRD (CHD), Chromatin remodelers Q14839 P06897, P84233, P62799, P02281 0.342
842 6SE6 EM 3.50 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2 : CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 P49450, P62807, P62805, Q6FI13 0.416
843 6T7C EM 4.00 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Transcription factor SOX-11 Transcription factors, Transcription-associated P35716 O60814, Q71DI3, P04908, P62805 0.355
844 6VZ4 EM 3.90 2020-12-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state Baker, R.W., Reimer, J.M., Carman, P.J., Turegun, B., Arakawa, T., Dominguez, R., Leschziner, A.E. 10.1038/s41594-020-00528-8 33288924 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Cell cycle, RSC (SWI/SNF), Transcription-associated, Chromatin remodelers P32597, Q12406, Q05123, P53330 P06897, Q92133, P62799, P02281 -
845 6W5M EM 4.60 2021-03-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Lee, Y.T., Ayoub, A., Park, S.H., Sha, L., Xu, J., Mao, F., Zheng, W., Zhang, Y., Cho, U.S., Dou, Y. 10.1038/s41467-021-23268-9 34012049 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.177
846 6WZ9 EM 2.80 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Bilokapic, S., Suskiewicz, M.J., Ahel, I., Halic, M. 10.1038/s41586-020-2725-7 32939087 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 P06897, P84233, P62799, P02281 0.508
847 6X59 EM 2.98 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 The mouse cGAS catalytic domain binding to human assembled nucleosome Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. 10.1038/s41586-020-2749-z 32911481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.54
848 6Z6P EM 4.43 2021-02-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 HDAC-PC-Nuc Lee, J.H., Bollschweiler, D., Schafer, T., Huber, R. 10.1126/sciadv.abd4413 33523989 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone deacetylase HDA1, HDA1 complex subunit 3,HDA1 complex subunit 3, HDA1 complex subunit 2 HDA1, Transcription-associated, Histone PTM erasers, Histone_deacetylation P53973, Q06623, Q06629 P06897, P62799, P02281, Q6AZJ8, P84233 0.189
849 7C0M EM 3.90 2020-09-16 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Human cGAS-nucleosome complex Kujirai, T., Zierhut, C., Takizawa, Y., Kim, R., Negishi, L., Uruma, N., Hirai, S., Funabiki, H., Kurumizaka, H. 10.1126/science.abd0237 32912999 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 P04908, P68431, P62805, P06899 0.225
850 7KBF EM 4.42 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.8 601L 172 H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) Arimura, Y., Shih, R.M., Froom, R., Funabiki, H. 10.1016/j.molcel.2021.08.010 34478647 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P02281, P62799, P15308, Q6DKE3, P84233 0.29
851 7PEX EM 5.10 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 177 Nucleosome 2 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.267
852 7PF2 EM 5.10 2022-08-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 339 Nucleosome stack of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.217
853 7PFE EM 4.40 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 177 Nucleosome 2 of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.302
854 7PFF EM 4.30 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 167 Nucleosome 3 of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P04908, P62805 0.221
855 7PFX EM 4.30 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 177 Nucleosome 3 of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, P10412, O60814, P04908, P62805 0.269
856 7SCY EM 4.10 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to single BRCT Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 Histone_PARylation_writer, DNA repair, Histone PTM writers P09874 P04908, P68431, P62805, P06899 0.273
857 7UD5 EM 4.25 2022-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Rahman, S., Hoffmann, N.A., Worden, E.J., Smith, M.L., Namitz, K.E.W., Knutson, B.A., Cosgrove, M.S., Wolberger, C. 10.1073/pnas.2205691119 36095189 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 cDNA FLJ56846, highly similar to Zinc finger protein HRX, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2, Retinoblastoma-binding protein 5, Polyubiquitin-B, Protein dpy-30 homolog Transcription-associated, COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Ubiquitin, Euchromatin-associated B4DIJ7, P61964, Q9UBL3, Q15291, P0CG47, Q9C005 P06897, P84233, P62799, P02281 0.263
858 7X3V EM 3.09 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of IOC3-N2 nucleosome Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI one complex protein 3 ISWI, Chromatin remodelers P43596 P06897, P84233, P62799, P02281 0.502
859 7XX5 X-ray 3.19 2023-05-31 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.3 601L 169 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P68431, P16402, P04908, P62805, P06899 -
860 3AZG X-ray 2.40 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
861 8J91 EM 2.90 2024-07-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 113 Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones Osakabe, A., Takizawa, Y., Horikoshi, N., Hatazawa, S., Negishi, L., Sato, S., Berger, F., Kakutani, T., Kurumizaka, H. 10.1038/s41467-024-49465-w 38992002 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 P59226, Q9LHQ5, P59259, O23629 0.545
862 8JHO EM 7.60 2023-09-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 340 Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.067
863 8KD2 EM 3.02 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 174 Rpd3S in complex with 187bp nucleosome Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.35
864 8KD3 EM 2.90 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.376
865 8OTS EM 3.30 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 OCT4 and MYC-MAX co-bound to a nucleosome Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Green fluorescent protein,POU domain, class 5, transcription factor 1, Myc proto-oncogene protein, Protein max Transcription factors, Transcription-associated P42212, P01106, P61244 P04908, P68431, P62805, P06899 0.404
866 6R90 EM 4.50 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.278
867 6O96 EM 3.50 2019-04-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Vasilyev, N., Chen, R., Nudler, E., Armache, J.-P., Armache, K.J. 10.1016/j.molcel.2019.03.029 30981630 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Polyubiquitin-B Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P06897, P84233, P62799, P02281 0.38
868 8QKT X-ray 3.26 2023-10-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 167 Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment Ma, Z., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 A0A2Y9FT95, H2QSF5, P68431, A0A8C1JQV0, P06899 -
869 6KIX EM 4.10 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-NCP complex, binding mode1 Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q03164, Q15291, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.338
870 9IGJ EM 3.80 2026-03-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 125 structure of two human ELF2 transcription factors in complex with a nucleosome Xiao, T., Crowe-McAuliffe, C., Ochmann, M., Du, Y., Hou, T., Chen, Y., Zhu, F., Seyednasrollah, F., Osmala, M., Vanharanta, S., Morgunova, E., Cramer, P., Rogerson, C., Dienemann, C., Taipale, J. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 ETS-related transcription factor Elf-2 Transcription factors, Transcription-associated Q15723 P06897, P02281, P62799, None 0.329
871 9RN1 EM 5.90 2026-02-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 134 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Na, N.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, N-terminally processed, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4, Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Cell cycle, Transcription factors, Transcription-associated, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785, P42212, P48431 P04908, P68431, P62805, P06899 0.227
872 7XSX EM 3.80 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 108 RNA polymerase II elongation complex transcribing a nucleosome (EC49) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.227
873 7LYC EM 2.94 2021-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Ubiquitin, BRCA1-associated RING domain protein 1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Ubiquitin, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair P0CG47, Q99728 P04908, P68431, P62805, P06899 0.566
874 6M3V X-ray 4.60 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 355 355 bp di-nucleosome harboring cohesive DNA termini Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A. 10.1038/s41467-020-18533-2 32958761 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P68431, P62805, P06899 -
875 9WMW EM 3.62 2025-12-24 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 75 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.229
876 10YE EM 2.50 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q71DI3, Q99879, P62805, P0C0S8 0.57
877 3W99 X-ray 3.00 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P04908, P68431, P62805, P06899 -
878 1U35 X-ray 3.00 2005-09-27 octamer 1 canonical_H3 canonical_H4 macroH2A canonical_H2B alphasat_146 145 Crystal structure of the nucleosome core particle containing the histone domain of macroH2A Chakravarthy, S., Gundimella, S.K., Caron, C., Perche, P.Y., Pehrson, J.R., Khochbin, S., Luger, K. 10.1128/MCB.25.17.7616-7624.2005 16107708 Mus musculus Mus musculus Homo sapiens Mus musculus Xenopus laevis 2005 P62806, O75367, Q9D2U9, P68433 -
879 3AV2 X-ray 2.80 2011-06-01 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The human nucleosome structure containing the histone variant H3.3 Tachiwana, H., Osakabe, A., Shiga, T., Miya, Y., Kimura, H., Kagawa, W., Kurumizaka, H. 10.1107/S0907444911014818 21636898 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P62805, P06899, P84243 -
880 3AZK X-ray 3.20 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
881 3B6F X-ray 3.45 2007-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome core particle treated with cisplatin Wu, B., Droge, P., Davey, C.A. 10.1038/nchembio.2007.58 18157123 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2007 P06897, P84233, P62799, P02281 -
882 3KWQ X-ray 3.50 2010-05-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Watanabe, S., Resch, M., Lilyestrom, W., Clark, N., Hansen, J.C., Peterson, C., Luger, K. 10.1016/j.bbagrm.2010.01.009 20100606 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P06897, P84233, P62799, P02281 -
883 3LEL X-ray 2.95 2010-05-19 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 147 Structural Insight into the Sequence-Dependence of Nucleosome Positioning Wu, B., Mohideen, K., Vasudevan, D., Davey, C.A. 10.1016/j.str.2010.01.015 20399189 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P84233, P62799, P02281 -
884 3REH X-ray 2.50 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P06897, P84233, P62799, P02281 -
885 4WU8 X-ray 2.45 2015-09-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of trPtNAP-NCP145 Chua, E.Y., Davey, G.E., Chin, C.F., Droge, P., Ang, W.H., Davey, C.A. 10.1093/nar/gkv356 25916851 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P06897, P84233, P62799, P02281 -
886 5AV6 X-ray 2.20 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P68431, P62805, P06899 -
887 5B33 X-ray 2.92 2016-08-03 octamer 1 H3.3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the H2AZ nucleosome with H3.3. Horikoshi, N., Arimura, Y., Taguchi, H., Kurumizaka, H. 10.1098/rsob.160127 27358293 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P06899, P62805, P0C0S5, P84243 -
888 5GXQ X-ray 2.85 2017-04-19 octamer 1 H3.6 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing H3.6 Taguchi, H., Xie, Y., Horikoshi, N., Maehara, K., Harada, A., Nogami, J., Sato, K., Arimura, Y., Osakabe, A., Kujirai, T., Iwasaki, T., Semba, Y., Tachibana, T., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1021/acs.biochem.6b01098 28374988 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P04908, A0A1X8XL64, P62805, P06899 -
889 5ZBX X-ray 2.58 2019-02-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Arimura, Y., Tachiwana, H., Takagi, H., Hori, T., Kimura, H., Fukagawa, T., Kurumizaka, H. 10.1038/s41467-019-08314-x 30718488 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P04908, P68431, P62805, P06899 -
890 6A5R EM 8.70 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 136 RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P62805, P06899, P84243 0.11
891 6A5U EM 7.60 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P62805, P06899, P84243 0.14
892 6E0C EM 2.63 2019-05-22 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 scFv P49450, P04908, P62805, P06899 0.59
893 6G0L EM 10.00 2018-08-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 176 Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome Sundaramoorthy, R., Hughes, A.L., El-Mkami, H., Norman, D.G., Ferreira, H., Owen-Hughes, T. 10.7554/eLife.35720 30079888 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2018 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 P06897, A0A1L8G0X3, Q92133, P62799 0.095
894 6JMA EM 6.80 2019-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 114 cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Jang, S., Kang, C., Yang, H.S., Jung, T., Hebert, H., Chung, K.Y., Kim, S.J., Hohng, S., Song, J.J. 10.1101/gad.323790.118 30923167 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 Q6AZJ8, P84233, P62799, P02281 0.144
895 8PP6 EM 3.18 2024-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 human RYBP-PRC1 bound to H2AK118ub1 nucleosome Ciapponi, M., Karlukova, E., Schkolziger, S., Benda, C., Muller, J. 10.1038/s41594-024-01258-x 38528151 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2024 RING1 and YY1-binding protein, Ubiquitin-40S ribosomal protein S27a (Fragment) Transcription-associated, Heterochromatin-associated, Histone PTM readers, Histone_ubiquitination_reader, Polycomb, Ubiquitin Q8N488, P0CG47 P84040, P84051, P02283, P02299 0.465
896 8CBQ EM 4.00 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.304
897 8SN2 EM 3.60 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.452
898 9GEQ EM 3.12 2025-08-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Native dimeric Myeloperoxidase bound to nucleosome core particle; composite map Burn, G.L., Raisch, T., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Gimber, N., Raunser, S., Zychlinsky, A. 10.1038/s41586-025-09523-9 40963017 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Myeloperoxidase light chain Neutrophil extracellular traps P05164 P06897, P84233, P62799, P02281 0.554
899 9IHF EM 3.16 2025-08-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Nucleosome core particle bound by one monomer and one dimer of of DTT-reduced native myeloperoxidase Burn, G.L., Raisch, T., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Gimber, N., Raunser, S., Zychlinsky, A. 10.1038/s41586-025-09523-9 40963017 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Myeloperoxidase light chain Neutrophil extracellular traps P05164 P06897, P84233, P62799, P02281 0.536
900 9J8W EM 3.38 2025-11-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-UV-DDB complex containing CPD Matsumoto, S., Takizawa, Y., Ogasawara, M., Hashimoto, K., Negishi, L., Xu, W., Tachibana, H., Yamamoto, J., Iwai, S., Sugasawa, K., Kurumizaka, H. 10.1038/s41467-025-65486-5 41219227 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q92466 P04908, P68431, P62805, P06899 0.397
901 9K41 EM 2.81 2025-05-14 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 145 Cryo-EM structure of Arabidopsis thaliana H2A.W-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Wang, Y., Wu, J., Yang, S., Li, X., Wang, J., Lv, Q., Zhu, X., Lu, G., Zhang, J., Shen, W.H., Liu, B., Lin, J., Dong, A. 10.1016/j.str.2025.04.015 40359943 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2025 Q9FJE8, P59226, P59259, Q9LQQ4 0.479
902 9K45 EM 2.71 2025-11-12 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 145 Cryo-EM structure of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Wang, Y., Dong, A. 0 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2025 Q9C944, Q9LQQ4, P59259, P59169 0.521
903 9MU5 EM 6.30 2025-02-19 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Structure of a native Drosophila melanogaster hexameric nucleosome Venette-Smith, N.L., Vishwakarma, R.K., Dollinger, R., Schultz, J., Venkatakrishnan, V., Babitzke, P., Anand, G., Gilmour, D.S., Armache, J.-P., Murakami, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2025 P84040, P84051, P02283, P02299 0.206
904 9NQU EM 3.16 2025-07-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 185 KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate Lin, C.C., Zhao, Y., Foley, C.A., Hawkins, A.T., James, L.I., Frye, S.V., McGinty, R.K. 10.1016/j.molcel.2025.06.025 40683254 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Lysine-specific demethylase 6B Heterochromatin-associated, Histone PTM erasers, Histone_demethylation_H3K27 Q5NCY0 Q71DI3, P62807, P62805, P0C0S8 0.47
905 9OH2 EM 3.14 2025-11-05 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 121 Cryo-EM analysis of human H2A.Z on methylated 601L DNA Shih, R.M., Arimura, Y., Konishi, H.A., Funabiki, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, P06899, P0C0S5 0.506
906 9QCR EM 4.37 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 129 DNA-PK bound to 153 bp H2AX nucleosome model 2 Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.234
907 9QCS EM 4.38 2026-01-14 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 129 Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.185
908 9Y47 EM 2.74 2025-10-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Human nucleosome structure on Nickel-NTA lipid affinity grid (C1 refinement) Skrajna, A., Lenger, C., Robinson, E., Cannon, K., Sarsam, R., Ouellette, R.G., Abotsi, A.M., Brennwald, P., McGinty, R.K., Strauss, J.D., Baker, R.W. 10.1016/j.jsb.2025.108253 41083086 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62807, P62805, P0C0S8 0.628
909 9RMC EM 4.20 2026-02-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Vecchia, L., Weiss, J., Cavadini, S., Kempf, G., Kater, L., Pathare, G., Thoma, N.H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, N-terminally processed, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4, Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Cell cycle, Transcription factors, Transcription-associated, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785, P42212, P48431 P04908, P68431, P62805, P06899 0.242
910 5DNM X-ray 2.81 2016-09-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex Adhireksan, Z., Palermo, G., Riedel, T., Ma, Z., Muhammad, R., Rothlisberger, U., Dyson, P.J., Davey, C.A. 10.1038/ncomms14860 28358030 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P06897, P84233, P62799, P02281 -
911 6ESI EM 6.30 2017-12-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Nucleosome breathing : Class 4 Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41594-017-0005-5 29323273 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Q6AZJ8, P84233, P62799, P02281 0.167
912 9JNT EM 2.70 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP* state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.532
913 7KBD EM 3.38 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) Arimura, Y., Shih, R.M., Froom, R., Funabiki, H. 10.1016/j.molcel.2021.08.010 34478647 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P84233, P02281, P62799, Q6DKE3 0.489
914 3WTP X-ray 2.67 2014-12-03 octamer 1 cenH3,H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Arimura, Y., Shirayama, K., Horikoshi, N., Fujita, R., Taguchi, H., Kagawa, W., Fukagawa, T., Almouzni, G., Kurumizaka, H. 10.1038/srep07115 25408271 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2014 P84243, P49450, P04908, P62805, P06899 -
915 9JNU EM 2.50 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.566
916 9ECP EM 1.91 2025-10-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Structure of the native human NCP purified from HEK293 cells Reid, X.J., Sobti, M., Zeng, Y.C., Zhong, Y., Deshpande, C., Young, P., Brown, S.H.J., Low, J.K.K., Stewart, A.G., Mackay, J.P. 10.1101/2025.10.10.681767 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 O60814, P68431, P62805, Q7L7L0 0.703
917 9WC0 EM 2.40 2026-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 154 The structure of NCP-RA module of ncBAF-nucleosome complex Chen, K., Du, L., Liu, Y., Chen, M., Chen, Z. 10.1038/s41421-025-00858-1 41402274 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 B-cell CLL/lymphoma 7 protein family member A SWI/SNF, Chromatin remodelers Q4VC05 Q6AZJ8, P84233, P62799, P02281 0.591
918 7K5Y EM 2.76 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 197 Cryo-EM structure of a chromatosome containing human linker histone H1.4 Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 scFv20 P68431, P04908, P10412, P62805, P06899 0.527
919 6T7B EM 5.10 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of human Sox2 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Transcription factor SOX-2 Transcription factors, Transcription-associated P48431 O60814, Q71DI3, P04908, P62805 0.217
920 9RZE EM 8.53 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 181 State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Histone-lysine N-methyltransferase SETD2, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit SPT16 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A8D1KNW4, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q9BYW2, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.068
921 7K7G EM 4.20 2021-03-31 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601_modified 123 nucleosome and Gal4 complex Guan, R., Lian, T., Zhou, B.R., He, E., Wu, C., Singleton, M., Bai, Y. 10.1038/s41467-021-21985-9 33741944 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2021 Centromere DNA-binding protein complex CBF3 subunit B Nuclear division, CBF3, Centromere-associated, Kinetochore P40969 P02309, P02293, P04911, P61830 0.3
922 9LJ2 EM 2.98 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 ISWI, Transcription-associated, Chromatin remodelers P38144 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.458
923 1P3K X-ray 2.90 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
924 1P3L X-ray 2.40 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P06897, P84233, P62799, P02281 -
925 3AYW X-ray 2.90 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P04908, P68431, P62805, P06899 -
926 9GF6 EM 3.80 2025-08-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., Hopfner, K.P. 10.1093/nar/gkag138 41775336 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 INO80 complex subunit B INO80, Chromatin remodelers Q9C086 P04908, P68431, P62805, Q16778 0.388
927 9J0P EM 3.30 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 191 Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RPB12, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P04908, P62805, P06899, P84243 0.311
928 9GD3 EM 3.00 2024-09-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. Engeholm, M., Roske, J.J., Oberbeckmann, E., Dienemann, C., Lidschreiber, M., Cramer, P., Farnung, L. 10.1016/j.molcel.2024.08.022 39270644 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 P06897, P84233, P62799, P02281 0.465
929 9B3P EM 3.00 2024-06-12 octamer 1 H3.3 canonical_H4 H2A.Z canonical_H2B 601 128 The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome Jung, H., Sokolova, V., Lee, G., Stevens, V.R., Tan, D. 10.3390/epigenomes8020021 38920622 Homo sapiens Xenopus laevis Mus musculus Xenopus laevis Xenopus laevis 2024 P0C0S6, P02281, P62799, P84243 0.455
930 8SN8 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.443
931 8SPU EM 2.80 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of ESRRB nucleosome bound OCT4 at site c Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 P68431, P62805, Q16778, Q16777 0.496
932 8THU EM 3.10 2023-09-06 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 145 Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. 10.1016/j.molcel.2023.07.020 37595555 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 P84233, P02281, P62799, P0C0S5 0.508
933 8U14 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.352
934 8U9S EM 2.60 2026-01-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 162 Cryo-EM structure of NRCAM nucleosome aided by scFv Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 scFv20 P04908, P68431, P62805, P06899 0.575
935 8V25 EM 3.32 2024-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2BK120ub-modified nucleosome ubiquitin position 1 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P06897, P84233, P62799, P02281 0.519
936 8V4Y EM 2.80 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1) Chio, U.S., Palovcak, E., Smith, A.A.A., Autzen, H., Munoz, E.N., Yu, Z., Wang, F., Agard, D.A., Armache, J.P., Narlikar, G.J., Cheng, Y. 10.1038/s41467-024-46178-y 38472177 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.53
937 8V7L EM 2.90 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 140 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 2) Chio, U.S., Palovcak, E., Smith, A.A.A., Autzen, H., Munoz, E.N., Yu, Z., Wang, F., Agard, D.A., Armache, J.P., Narlikar, G.J., Cheng, Y. 10.1038/s41467-024-46178-y 38472177 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 SWI/SNF, Transcription-associated, Chromatin remodelers O60264 P06897, P84233, P62799, P02281 0.456
938 8VOB EM 3.10 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis 2025 Q71DI3, P62805, P02281, P0C0S8 0.375
939 8W9F EM 4.40 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Wang, C., Chu, C., Guo, Z., Zhan, X. 10.1126/sciadv.adk7678 38598631 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 O60814, P04908, P68431, P62805 0.156
940 8XVS EM 4.10 2025-05-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 163 RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Kujirai, T., Kato, J., Yamamoto, K., Hirai, S., Fujii, T., Maehara, K., Harada, A., Negishi, L., Ogasawara, M., Yamaguchi, Y., Ohkawa, Y., Takizawa, Y., Kurumizaka, H. 10.1038/s41467-025-59580-x 40436841 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, DNA-directed RNA polymerases I, II, and III subunit RPABC4 Transcription-associated, RNA polymerases P24928, P30876, P19387, O15514, P19388, P61218, P62487, P52434, P36954, P62875, P52435, P53803 P04908, P68431, P62805, P06899 0.24
941 8X7J EM 3.39 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair P61077, Q8IYW5, P62979 O60814, Q71DI3, P04908, P62805 0.391
942 6ESF EM 3.70 2017-12-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nucleosome : Class 1 Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41594-017-0005-5 29323273 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Q6AZJ8, P84233, P62799, P02281 0.378
943 9D3S EM 3.10 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 5S_somatic 123 147-bp 5S rDNA nucleosome - open I (open on the downstream side) Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, Q6FI13, Q99879 0.465
944 9F0O EM 2.30 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 The molecular basis and modulation of lamin-specific chromatin interaction Wang, B., Kronenberg-Tenga, R., Rosti, V., Di Patrizio Soldateschi, E., Luo, Q., Iannacchero, U.M., Pinet, L., Eibauer, M., Boujemaa-Paterski, R., Schuler, B., Lanzuolo, C., Medalia, O. 10.1038/s41594-025-01622-5 40750945 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 laminA_peptide P06897, P84233, P62799, P02281 0.643
945 9D3M EM 2.90 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 5S_somatic 101 Two HMGN2s in complex with the nucleosome Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Non-histone chromosomal protein HMG-17 Q71DI3, P62805, Q6FI13, Q99879 0.53
946 9DWF EM 3.10 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 Nucleosome containing a 1-nt gap at SHL-4.5 Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62807, P62805, P0C0S8 0.526
947 9D3O EM 3.00 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 5S_somatic 145 167-bp 5S rDNA nucleosome - closed Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A., Kadonaga, J.T., Leschziner, A.E. 10.1101/gad.352720.125 40721296 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q71DI3, P62805, Q6FI13, Q99879 0.495