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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 P62799, P06897, P84233, Q28D68 -
1 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 P06899, P04908, P62805, P68431 -
2 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 P06899, P04908, P62805, P68431 -
3 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Telomere-associated, Transcription-associated, Euchromatin-associated, Ubiquitin Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, P0CG47, Q6CRQ4 P84233, Q92133, Q6AZJ8, P02281, P62799 0.372
4 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 P04908, P62805, O60814, P68431 -
5 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 P06899, P04908, P62805, P68431 -
6 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, Euchromatin-associated, Histone PTM writers O96028 P06899, P62805, P0C0S8, P68431 0.556
7 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 Q9NRC8 P06899, Q6FI13, P62805, Q71DI3 0.24
8 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 Histone_ubiquitination_H2AK119_writer, Polycomb, Histone PTM writers, Heterochromatin-associated, Transcription-associated, E3 ubiquitin-protein ligation, Histone_methylation_H3K27_writer P35226, Q99496 P02299, P84051, P02283, P84040 0.511
9 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P62807, P62805, P0C0S8, Q71DI3 0.265
10 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 P62799, P06897, P84233, P02281 -
11 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 Transcription-associated, Histone_methylation_H3K9_reader, Heterochromatin-associated, Histone PTM readers P45973 P62799, P02281, P84233, P0C0S6 0.143
12 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 P06899, P04908, P62805, P68431 0.196
13 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 Chromatin remodelers, DNA repair, CHD Q86WJ1 P62799, P06897, P84233, P02281 0.625
14 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 P06899, P04908, P62805, P68431 -
15 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, Histone_acetylation_H3K27_writer, Transcription-associated, Histone PTM writers Q92793 P06899, P04908, P62805, P68431 0.195
16 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 Chromatin remodelers, Histone chaperones, INO80, Histone PTM readers, SRCAP (INO80), Transcription-associated, Euchromatin-associated, Cell cycle, Histone_acetylation_reader Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, P62807, Q93077, P68431 0.218
17 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, Euchromatin-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P16403, P68431, P04908, P62805 0.228
18 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 P62799, P06897, P02281, P02302 -
19 2F8N X-ray 2.90 2006-05-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A,macroH2A 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 P84233, O75367, Q9D2U9, Q8CGP6, P02281, P62799 -
20 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 P06899, P04908, P62805, P68431 -
21 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 P06899, P04908, P62805, P68431 -
22 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 P06899, P04908, P62805, P68431 -
23 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 P06899, P04908, P62805, P68431 -
24 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 P62799, Q6AZJ8, P84233, P02281 -
25 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 P62799, Q6AZJ8, P84233, P02281 -
26 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 P62799, P06897, P84233, P02281 -
27 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 P06899, P04908, P62805, P68431 -
28 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 P62799, P06897, P84233, P02281 0.256
29 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 P06899, P04908, P62805, P68431 -
30 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 P62799, P06897, P84233, P02281 -
31 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 Histone PTM writers, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, E3 ubiquitin-protein ligation Q07457 P62799, P06897, P84233, P02281 0.52
32 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 P62799, P06897, P84233, P02281 0.424
33 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer P61077, Q8IYW5 P04908, P62805, O60814, Q71DI3 0.423
34 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 P06899, Q92522, P68431, P04908, P62805 -
35 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 P62799, P04911, P02293, P61830 0.424
36 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 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.36
37 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 P06746 P62807, P62805, P0C0S8, Q71DI3 0.364
38 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 P62807, P62805, P0C0S8, Q71DI3 0.453
39 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 P06746 P62807, P62805, P0C0S8, Q71DI3 0.31
40 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.616
41 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.586
42 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.578
43 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 P06899, P62805, P0C0S8, Q71DI3 0.083
44 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 P06899, P62805, P0C0S8, Q71DI3 0.145
45 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 P06899, P62805, P0C0S8, Q71DI3 0.068
46 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 P62799, A0A310TTQ1, P06897, P02281 0.445
47 9JC6 EM 3.34 2025-09-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.W 601 132 Human H2BW2 nucleosome Nguyen, A.T.T., Ding, D., Bai, X., Pang, M.Y.H., Deng, M., Liu, Y., Jin, T., Xu, Z., Zhang, Y., Zhai, Y., Yan, Y., Ishibashi, T. 10.1093/nar/gkaf825 40874595 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P04908, P62805, P0C1H6, P68431 0.39
48 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.587
49 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.482
50 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 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.239
51 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 P06899, P62805, P0C0S5, Q71DI3 0.562
52 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 P04908, P62805, O60814, Q71DI3 0.108
53 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 P62799, P06897, P84233, P02281 0.224
54 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 P62799, Q6AZJ8, P02281, P84233 0.343
55 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 P06897, P84233, A0A310TTQ1, P02281, P62799 -
56 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 P62799, P06897, P84233, P02281 -
57 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 P06899, P04908, P62805, P68431 -
58 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 P06899, P04908, P62805, P68431 0.199
59 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 P62799, P06897, P84233, P02281 0.598
60 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, A0A1B8Y854, Q6AZJ8, P62798 0.322
61 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 Q16777, P62805, Q16778, P68431 0.531
62 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 P62799, P06897, P84233, P02281 0.552
63 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 Histone PTM writers, p300, Histone_acetylation_writer, DNA repair, Transcription-associated, Cell cycle Q09472 P06899, P04908, P62805, P68431 0.29
64 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) Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK119_reader, Histone PTM readers Q16385, P0CG47 P04908, P62805, O60814, Q71DI3 0.47
65 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 Transcription-associated, Histone_ubiquitination_H2AK119_reader, Histone PTM readers Q16384 P04908, P62805, O60814, Q71DI3 0.532
66 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 Histone_deacetylation, Histone PTM writers, Telomere-associated, Histone PTM erasers, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P32561, P22579, Q12432, Q04779 P62799, P06897, P84233, P02281 0.378
67 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 P62805, P62807, Q93077, P68431 0.525
68 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-associated, Transcription factors O08785, Q9WTL8 P06899, P04908, P62805, P68431 0.267
69 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-associated, Transcription factors O08785, Q9WTL8 P06899, P04908, P62805, P68431 0.177
70 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 P04908, P62805, O60814, P68431 -
71 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 P04908, P62805, O60814, P68431 -
72 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 Chromatin remodelers, INO80, SRCAP (INO80), SWR1 (INO80), Transcription-associated, Euchromatin-associated Q05471, P38326, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P04911, P02293, P61830 0.324
73 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 ORC, DNA replication, Heterochromatin-associated A0A140UHX1, Q75PQ8 P62799, P06897, P84233, P02281 0.497
74 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 Chromatin remodelers, Heterochromatin-associated Q9XFH4 P06897, A0A8J1LTD2, P84233, P02281 0.458
75 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P06899, P04908, P62805, P68431 0.544
76 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P06899, P04908, P62805, P68431 0.535
77 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P06899, P04908, P62805, P68431 0.434
78 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P06899, P04908, P62805, P68431 0.405
79 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 Polycomb, Heterochromatin-associated, Histone PTM writers, Histone chaperones, Transcription-associated, Histone_methylation_H3K27_writer Q15022, Q15910, O75530, Q09028, Q6ZN18 P62799, P06897, P84233, P02281 0.163
80 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 Heterochromatin-associated, Histone PTM writers, DNA repair, Transcription-associated, Histone_methylation_H4K20_writer Q4FZB7 P62799, P06897, P84233, P02281 0.393
81 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 P62799, P06897, P84233, P02281 0.505
82 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-associated, Transcription factors P55317 P06899, P10412, P68431, P04908, P62805 0.493
83 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 P62807, P62805, P0C0S8, Q71DI3 0.534
84 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q12432, Q04779 P04908, P62805, O60814, P68431 0.263
85 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated, Ubiquitin P61964, Q15291, P0CG47 P62799, P06897, P02281, P02302 0.237
86 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 Heterochromatin-associated, Histone PTM writers, DNA repair, Transcription-associated, Histone_methylation_H4K20_writer Q4FZB7 P62799, P02281, P84233, P0C0S5 0.227
87 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, Q9D2U9, C0HKE1, P68433 -
88 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 P06899, P02259, P68431, P04908, P62805 -
89 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 P06899, P04908, P62805, P68431 -
90 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 P62799, P06897, P84233, P02281 -
91 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 P06897, P84233, P22844, P02281, P62799 -
92 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 P62799, P06897, P84233, P02281 -
93 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 P62799, P06897, P84233, P02281 -
94 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 P06899, P04908, P62805, P68431 -
95 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 P62799, P06897, P84233, P02281 0.551
96 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 UV-DDB complex, DNA repair, DCX complex Q16531, Q92466 P06899, P04908, P62805, P68431 0.313
97 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 UV-DDB complex, DNA repair, DCX complex Q16531, Q92466 P06899, P04908, P62805, P68431 0.307
98 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 Chromatin remodelers, SWI/SNF, Transcription-associated, RSC (SWI/SNF) P22082, P09547, P18480, P32591, P53628, P18888, Q12406, Q05123, P53330 P62799, P06897, P84233, P02281 0.122
99 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 P62799, P06897, P84233, P02281 0.504
100 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 P04908, P62805, O60814, P68431 0.332
101 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-associated, Transcription factors P13393, P32773, P32774 P62799, P06897, P84233, P02281 0.516
102 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 O60814, P10412, Q71DI3, P04908, P62805 0.203
103 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 O60814, P10412, Q71DI3, P04908, P62805 0.101
104 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 O60814, P10412, Q71DI3, P04908, P62805 0.351
105 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 O60814, P10412, Q71DI3, P04908, P62805 0.084
106 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 P62799, P04911, P02293, P84233 0.449
107 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 Chromatin remodelers, Heterochromatin-associated Q9XFH4 Q9FJE8, P62799, P59169, O23629 0.445
108 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 P04908, P62805, O60814, P68431 0.109
109 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 P04908, P62805, O60814, P68431 0.107
110 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 Chromatin remodelers, SWI/SNF, Transcription-associated, Cell cycle, PBAF (SWI/SNF) P51532, O96019, P60709, Q68CP9, Q8WUB8, Q9NPI1, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q86U86 P62799, P06897, P84233, P02281 0.315
111 7X58 EM 3.93 2022-11-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 121 Cryo-EM structure of human subnucleosome (open form) Nozawa, K., Takizawa, Y., Pierrakeas, L., Sogawa-Fujiwara, C., Saikusa, K., Akashi, S., Luk, E., Kurumizaka, H. 10.1073/pnas.2206542119 36322721 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2022 P62805, P68431 0.35
112 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 P62799, P06897, P84233, P02281 0.525
113 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 P62799, P06897, P84233, P02281 0.466
114 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P06899, P04908, P62805, P68431 0.41
115 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 Q53HL2 P84233, Q6AZJ8, A0A310TTQ1, P02281, P62799 0.618
116 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 P06899, P04908, P62805, P68431 0.13
117 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P06899, P04908, P62805, P68431 0.445
118 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 Heterochromatin-associated, Histone PTM writers, DNA repair, Transcription-associated, Histone_methylation_H4K20_writer Q4FZB7 P62799, P02281, P84233, P0C0S5 0.516
119 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 DNA modification, Ubiquitin Q9Y6K1, P0CG48 P62799, P06897, P02281, P02302 0.443
120 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 P06899, P04908, P62805, P68431 0.506
121 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P06899, P04908, P62805, P68431 0.464
122 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 P62799, P06897, P84233, P02281 0.516
123 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 P06899, P04908, P62805, P68431 0.559
124 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-associated, Transcription factors P55317 P06899, P04908, P62805, P68431 0.463
125 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 A0A8J1LZU9, P62805, Q6AZJ8, Q71DI3 0.402
126 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 P62805, Q6AZJ8, P02281, Q71DI3 0.258
127 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 P62807, P62805, P0C0S8, Q71DI3 0.41
128 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 Chromatin remodelers, Heterochromatin-associated Q9XFH4 O23629, P59226, P59259, Q9LD28 0.403
129 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 P06899, P04908, P62805, P68431 -
130 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 P04908, P62805, O60814, P68431 0.524
131 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 P62799, P04911, P02293, P61830 0.445
132 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 P62799, A0A310TTQ1, P06897, P02281 0.494
133 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 Histone_ubiquitination_H2AK119_writer, Histone_ubiquitination_reader, Polycomb, Histone PTM writers, Heterochromatin-associated, Histone PTM readers, Transcription-associated, Ubiquitin, E3 ubiquitin-protein ligation, Histone_methylation_H3K27_writer P35226, Q99496, Q8N488, P0CG48 P62799, P06897, P84233, P02281 0.39
134 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 Histone_ubiquitination_H2AK119_writer, Polycomb, Histone PTM writers, Heterochromatin-associated, Transcription-associated, E3 ubiquitin-protein ligation, Histone_methylation_H3K27_writer P35226, Q99496 P62799, P06897, P84233, P02281 0.47
135 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.538
136 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 P62799, P06897, P84233, P02281 0.685
137 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 A0A1B8Y854, None, P62805, Q71DI3 0.124
138 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 Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, RNA polymerases, Histone chaperones, Histone PTM writers, Transcription-associated, Euchromatin-associated, Cell cycle, PAF1C A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 P62799, A0A310TTQ1, P06897, P02281 0.261
139 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 Chromatin remodelers, CHD, Transcription-associated P32657 P62799, P06897, P84233, P02281 0.332
140 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.49
141 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
142 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 P04911, P02293, P62798, P61830 0.374
143 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P06899, P04908, P62805, P68431 0.424
144 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P06899, P04908, P62805, P68431 0.439
145 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 Heterochromatin-associated, Histone PTM writers, DNA repair, Transcription-associated, Histone_methylation_H4K20_writer Q4FZB7 O60814, P62805, P0C0S5, P68431 0.433
146 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P06899, P04908, P62805, P68431 0.526
147 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.42
148 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 P04908, P62805, O60814, Q71DI3 0.47
149 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 DNA repair, Histone PTM writers, Histone_PARylation_writer Q9UGN5 P06899, P04908, P62805, P68431 0.092
150 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, COMPASS, Histone PTM writers, Telomere-associated, Transcription-associated, Ubiquitin P0CG48, P38123, P39706, P38827, P43132, Q03323, Q03012 P62799, P06897, P84233, P02281 0.449
151 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 P06899, P04908, P62805, P68431 0.152
152 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 Nuclear division, Heterochromatin-associated, Histone PTM writers, Transcription-associated, Cell cycle, Histone_methylation_H4K20_writer Q9NQR1 P06899, P04908, P62805, P68431 0.514
153 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, Histone PTM writers, Telomere-associated Q04089, P0CG48 P62799, P06897, P84233, P02281 0.489
154 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 Histone_ubiquitination_H2AK129_writer, Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK127_writer, Transcription-associated, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation P38398, Q99728, P61077 P06899, P04908, P62805, P68431 0.458
155 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P84233, P02281 0.198
156 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 Chromatin remodelers, DNA repair, CHD Q86WJ1 P62799, P06897, P84233, P02281 0.282
157 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 Histone PTM writers, p300, Histone_acetylation_writer, DNA repair, Transcription-associated, Cell cycle Q09472 P06899, P04908, P62805, P68431 0.307
158 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 Chromatin remodelers, Transcription-associated, ISWI P43596, P38144 P62799, P06897, P84233, P02281 0.192
159 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 Heterochromatin-associated, Histone PTM writers, DNA repair, Transcription-associated, Histone_methylation_H4K20_writer Q4FZB7 P06899, P62805, P0C0S5, Q71DI3 0.484
160 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, DNA repair, Transcription-associated, 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 P62799, P06897, P84233, P02281 0.34
161 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 factors, RNA polymerases, DNA repair, Transcription-associated, Euchromatin-associated, Cell cycle 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 P62799, P06897, P84233, P02281 0.234
162 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 P62799, P06897, P84233, P02281 0.574
163 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 P62799, P06897, P84233, P02281 0.575
164 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 Histone_ubiquitination_H2AK119_writer, Polycomb, Histone PTM writers, Heterochromatin-associated, Transcription-associated, Ubiquitin, E3 ubiquitin-protein ligation, Histone_methylation_H3K27_writer P35226, Q99496, P0CG47, P62837 P04908, P62805, O60814, P68431 0.516
165 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 Histone PTM writers, p300, Histone_acetylation_writer, DNA repair, Transcription-associated, Cell cycle Q09472 P06899, P04908, P62805, P68431 0.212
166 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 Histone PTM writers, p300, Histone_acetylation_writer, DNA repair, Transcription-associated, Cell cycle Q09472 P06899, P04908, P62805, P68431 0.2
167 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, Histone_acetylation_H3K27_writer, Transcription-associated, Histone PTM writers Q92793 P06899, P04908, P62805, P68431 0.209
168 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 Histone PTM writers, Telomere-associated, DNA repair, Histone_ubiquitination_H2BK123_writer, Transcription-associated, E3 ubiquitin-protein ligation Q07457, P06104 P04908, P62805, O60814, P68431 0.393
169 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 P06899, P04908, P62805, P68431 0.453
170 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 P06899, P04908, P62805, P68431 0.479
171 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 Shelterin, DNA repair, Cell cycle, Telomere-associated P54274 P62805, P62807, Q93077, P68431 0.579
172 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 P06899, P62805, P0C0S5, Q71DI3 0.579
173 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 P84229, P06899, P04908, P62805 0.297
174 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 DNA repair, Transcription-associated, Cell cycle, Transcription factors P04637 P06899, P04908, P62805, P68431 0.192
175 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 Chromatin remodelers, DNA repair, DNA replication, INO80, Transcription-associated, Cell cycle Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q9C086 P06899, P04908, P62805, P68431 0.181
176 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, Transcription-associated, Histone_demethylation_H3K4, Histone PTM erasers O60341, Q9UKL0 P62799, P06897, P84233, P02281 -
177 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 PTM writers, Transcription-associated, Euchromatin-associated, Histone_methylation_H3K27_writer Q9BZ95 P62799, P06897, Q92133, P02281 0.542
178 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, Euchromatin-associated, Histone PTM writers P46995 P62799, Q6AZJ8, P84233, P02281 0.473
179 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 Chromatin remodelers, DNA repair, CHD Q86WJ1 P06897, P62799, P84233, P02281 0.567
180 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 P04908, P62805, O60814, Q71DI3 0.29
181 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 Q16777, P62805, Q16778, P68431 0.531
182 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 Q16777, P62805, Q16778, P68431 0.548
183 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 P04908, P62805, O60814, P68431 0.093
184 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 P06899, P07305, P68431, P04908, P62805 -
185 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 Chromatin remodelers, INO80 G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62807, P62805, P0C0S8, Q71DI3 -
186 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-associated, Euchromatin-associated, Transcription factors, RNA polymerases A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, I3LJZ9, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657 P62799, P06897, P84233, P02281 0.244
187 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 Q389T1, Q57Z31, Q57YA3, Q4GYX7 0.439
188 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 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.434
189 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-associated, Euchromatin-associated, Transcription factors P17433 Q16777, P62805, Q16778, P68431 0.31
190 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 P62799, P06897, P84233, P02281 0.445
191 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 Histone_ubiquitination_H2BK120_writer, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM writers Q5VTR2, O75150 P06899, P62805, P0C0S8, P68431 0.532
192 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 P06899, P62805, P0C0S8, P68431 0.588
193 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 Histone PTM writers, p300, Histone_acetylation_writer, DNA repair, Transcription-associated, Cell cycle Q09472 P06899, P04908, P62805, P68431 0.159
194 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, RNA polymerases, DNA repair, Transcription-associated, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R198 P06899, P04908, P62805, P68431 0.105
195 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q12432, Q04779 P62799, P06897, P84233, P02281 0.463
196 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 P06899, P04908, P62805, P68431 0.109
197 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q04779, Q12432 P62799, P06897, P84233, P02281 0.345
198 8J6T EM 6.60 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 92 Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B DNA repair, DNA replication, Histone chaperones, CAF-1 Q13111, Q13112 P62805, P68431 0.166
199 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 Chromatin remodelers, Heterochromatin-associated Q9XFH4 Q9FJE8, P59226, P59259, O23629 0.243
200 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
201 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 Chromatin remodelers, Transcription-associated, Cell cycle, RSC (SWI/SNF) Q12406, Q05123, Q9URQ5, P38210, P32832, Q06488, Q06639, Q02206, P43609, P25632, Q03124, Q07979, P53330, Q06168, P32597, P38781 P04908, P62805, O60814, P68431 0.053
202 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Telomere-associated, Transcription-associated, Euchromatin-associated Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, Q6CRQ4 P62799, Q92133, Q6AZJ8, P02281 0.385
203 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 Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P62799, P06897, P84233, P02281 0.529
204 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 P04908, P62805, O60814, P68431 0.532
205 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P06899, P04908, P62805, P68431 0.429
206 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 Chromatin remodelers, DNA repair, DNA replication, INO80, Transcription-associated, Cell cycle Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q6PI98, Q9C086 P06899, P04908, P62805, P68431 0.462
207 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 P06899, P04908, P62805, Q71DI3 -
208 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 FACT, Histone chaperones, DNA repair, DNA replication, Transcription-associated Q9Y5B9, Q08945 P62805, P62807, Q93077, P68431 0.173
209 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 FACT, Histone chaperones, DNA repair, DNA replication, Transcription-associated Q9Y5B9, Q08945 P62805, P62807, Q93077, P68431 0.203
210 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 Chromatin remodelers, Histone chaperones, INO80, Histone PTM readers, SRCAP (INO80), Transcription-associated, Euchromatin-associated, Cell cycle, Histone_acetylation_reader Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, P62807, Q93077, P68431 0.297
211 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 Polycomb, Heterochromatin-associated, Histone PTM writers, Histone chaperones, Transcription-associated, Histone_methylation_H3K27_writer Q15022, Q15910, O75530, Q09028, Q6ZN18 P62799, P06897, P84233, P02281 0.259
212 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 None, P62805, Q71DI3 -
213 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 P06897, P62799, P84233, P02281 0.266
214 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 P62799, P06897, P84233, P02281 -
215 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 P02299, P02259, P84051, P84040, P02283 -
216 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 P62799, P06897, P84233, P02281 -
217 6R25 EM 4.61 2019-04-24 octamer 1 canonical_H3,H3.3 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 PTM erasers, Histone PTM readers, Histone_methylation_H3K36_reader, Transcription-associated, Histone_demethylation_H3K4, Euchromatin-associated Q8NB78, Q49A26 P62799, P06897, P84233, P02281 0.186
218 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 P62799, P06897, P84233, P02281 -
219 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 P62799, P06897, P84233, P02281 -
220 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 P62799, Q6AZJ8, P84233, P02281 -
221 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 Chromatin remodelers, CHD, Transcription-associated P32657 P62799, P06897, P84233, P02281 0.018
222 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 P06899, P04908, P62805, P68431 -
223 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 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.132
224 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 P06899, P04908, P62805, P68431 -
225 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 Q9BTM1, P06899, P62805, P68431 -
226 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 Chromatin remodelers, Transcription-associated, Cell cycle, RSC (SWI/SNF) Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P62799, P06897, P84233, P02281 0.099
227 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 P62799, P06897, P84233, P02281 0.436
228 6R1U EM 4.36 2019-04-24 octamer 1 canonical_H3,H3.3 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 PTM erasers, Histone PTM readers, Histone_methylation_H3K36_reader, Transcription-associated, Histone_demethylation_H3K4, Euchromatin-associated Q8NB78, Q49A26 P62799, P06897, P84233, P02281 0.198
229 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 Chromatin remodelers, Heterochromatin-associated Q9XFH4 O23629, P59226, P59259, Q9LD28 0.394
230 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 P06899, P04908, P62805, P68431 -
231 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, P62805, Q96QV6, P68431 -
232 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated, Ubiquitin Q8NEZ4, Q15291, P62979, P61964, Q9UBL3 P62799, P06897, P84233, P02281 0.33
233 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 P06899, P04908, P62805, P68431 -
234 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 P0C5Z0, P62805, Q16778, P68431 0.493
235 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 Chromatin remodelers, NuRD (CHD) Q14839 P62799, P06897, P84233, P02281 0.52
236 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 Chromatin remodelers, DNA repair, CHD Q86WJ1 P62799, P06897, P84233, P02281 0.516
237 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 Polycomb, Heterochromatin-associated, Histone PTM writers, Transcription-associated, Histone_methylation_H3K27_writer Q15910, Q15022 P62799, P06897, P84233, P02281 0.29
238 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 P84229, P04908, P62805, Q16778 0.387
239 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 P06899, P07305, P68431, P04908, P62805 -
240 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 Chromatin remodelers, SWI/SNF, Transcription-associated, RSC (SWI/SNF) P22082, P09547, P18480, P32591, P53628, P18888, P43554, P53330, Q12406, Q05123 P62799, Q6AZJ8, P84233, P02281 0.105
241 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 P06899, P04908, P62805, P68431 0.59
242 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 Chromatin remodelers, Transcription factors, RNA polymerases, Heterochromatin-associated, CHD, Centromere-associated, Transcription-associated, Euchromatin-associated, SPT4-SPT5 complex P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P32657, P32914, P27692 P62799, P06897, P84233, P02281 0.444
243 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 P06899, P04908, P62805, P68431 0.519
244 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-associated, Transcription factors P13393 P62799, P06897, P84233, P02281 0.435
245 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 O60814, P10412, Q71DI3, P04908, P62805 0.138
246 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 O60814, P10412, Q71DI3, P04908, P62805 0.177
247 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 O60814, P10412, Q71DI3, P04908, P62805 0.109
248 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 O60814, P10412, Q71DI3, P04908, P62805 0.268
249 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 DNA repair, Histone PTM writers, Histone_PARylation_writer P09874 P06899, P04908, P62805, P68431 0.425
250 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 P62799, P06897, P84233, P02281 -
251 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, Cell cycle, Histone PTM writers, Histone_phosphorylation_H3T3_writer Q99986 P62807, P62805, P0C0S8, Q71DI3 0.56
252 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 Q16777, P62805, Q16778, P68431 0.568
253 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 P62807, P62805, P0C0S8, Q71DI3 0.415
254 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 Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, RNA polymerases, Histone chaperones, Histone PTM writers, Transcription-associated, Euchromatin-associated, Cell cycle, PAF1C A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P62799, Q6AZJ8, P84233, P02281 0.216
255 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, Histone_demethylation_H3K36, Heterochromatin-associated, Histone PTM erasers Q9Y2K7 P62807, P62805, P0C0S8, Q71DI3 0.42
256 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 P04908, P62805, O60814, P68431 0.558
257 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 P62799, P06897, P84233, P02281 0.55
258 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 P06899, P07305, P68431, P04908, P62805 -
259 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated, Ubiquitin Q03164, Q15291, P62979, P61964, Q9UBL3 P62799, P06897, P84233, P02281 0.343
260 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 P06899, P04908, P62805, P68431 0.454
261 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 Chromatin remodelers, INO80 G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62807, P62805, P0C0S8, Q71DI3 0.33
262 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 O60814, P10412, Q71DI3, P04908, P62805 0.105
263 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 P06899, P04908, P62805, P68431 0.361
264 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 P06899, P62805, P16104, P68431 0.168
265 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 P06899, P04908, P62805, P68431 -
266 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 P06897, P62799, P84233, P02281 0.554
267 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 P06899, P04908, P62805, P68431 -
268 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 P62799, Q6AZJ8, P84233, P02281 -
269 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q12432, Q04779 P62799, P06897, P84233, P02281 0.23
270 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 Histone_ubiquitination_H2AK129_writer, Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK127_writer, Transcription-associated, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation P38398, Q99728 Q6FI13, P62805, O60814, Q71DI3 0.313
271 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, Q9D2U9, A0A8X6EH29, C0HKE1 0.391
272 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 P62799, P06897, P84233, P02281 -
273 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 P62799, P06897, P84233, P02281 -
274 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 P06899, P04908, P62805, P68431 -
275 3WKJ X-ray 2.80 2014-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 145 The nucleosome containing human TSH2B Urahama, T., Horikoshi, N., Osakabe, A., Tachiwana, H., Kurumizaka, H. 10.1107/S2053230X14004695 24699735 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2014 Q96A08, P04908, P62805, P68431 -
276 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 P06899, P04908, P62805, P68431 -
277 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 P62799, P06897, P84233, P02281 -
278 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 P06899, P04908, P62805, P68431 -
279 5B31 X-ray 2.20 2016-08-03 octamer 1 canonical_H3 canonical_H4 H2A.Z,canonical_H2A 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 P06899, P0C0S5, P68431, P04908, P62805 -
280 5GT3 X-ray 2.91 2017-02-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 146 Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b 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 Q96A08, P62805, P20671, P68431 -
281 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 P06899, P04908, P62805, P68431 -
282 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 P62799, P06897, P84233, P02281 -
283 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 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P62799, P06897, P84233, P02281 0.315
284 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 P06899, P04908, P62805, P68431 -
285 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 P06899, P04908, P62805, P68431 -
286 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 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P62799, Q6AZJ8, P84233, P02281 0.372
287 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 P06899, P07305, P68431, P04908, P62805 -
288 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q12432, Q04779 P62799, P06897, P84233, P02281 0.254
289 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 P06899, P04908, P62805, P68431 0.631
290 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 P62799, Q6AZJ8, P84233, P02281 0.422
291 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 P06899, P62805, P16104, P68431 0.321
292 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 P06899, P04908, P62805, P68431 0.141
293 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 P04908, P62805, O60814, Q71DI3 0.434
294 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 P62799, P06899, P0C0S8, P84233 0.397
295 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 P62799, A0A310TTQ1, A0A8J0U496, Q6AZJ8 0.299
296 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 P04908, P62805, O60814, P68431 0.076
297 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P62799, P06897, P84233, P02281 0.435
298 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 Histone_deacetylation, Histone PTM erasers, DNA repair, Transcription-associated, Histone_deacetylation_H3K9 Q8N6T7 P62799, P06897, P84233, P02281 0.434
299 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 P06899, P62805, P0C0S8, Q71DI3 0.167
300 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 Histone_deacetylation, Histone PTM writers, Telomere-associated, Histone PTM erasers, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P32561, P22579, Q12432, Q04779 P62799, P06897, P84233, P02281 0.311
301 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 P62799, P06897, P84233, P02281 0.356
302 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 P06899, Q92522, P68431, P04908, P62805 0.435
303 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 Q16777, P62805, Q16778, P68431 0.535
304 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 Histone_ubiquitination_H2AK129_writer, Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK127_writer, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation Q99728, P0CG47 P62799, P06897, P84233, P02281 0.456
305 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 P62805, Q16778, P0C0S5, P68431 0.424
306 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, Q9D2U9, C0HKE1, P68433 -
307 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P62799, P06897, P84233, P02281 0.489
308 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 P62805, Q99879, Q96KK5, Q71DI3 0.524
309 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 P62799, P06897, P84233, P02281 -
310 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 P62805, Q99879, Q96KK5, Q71DI3 0.522
311 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 P04908, P62805, O60814, P68431 -
312 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 P06899, P04908, P62805, P68431 -
313 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 P06899, P62805, P0C0S5, P68431 -
314 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 P06899, P62805, P16104, P68431 0.552
315 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P84233, P02281 0.217
316 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 P62799, P06897, P84233, P02281 0.398
317 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 P62799, P06897, P84233, P02281 0.282
318 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, DNA repair, Transcription-associated, 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 P62799, P06897, P84233, P02281 0.277
319 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 P06899, P62805, P16104, P68431 0.189
320 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 P62799, P02281, Q6AZJ8, P02302 0.387
321 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 P62799, P06897, P84233, P02281 0.434
322 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 Histone_ubiquitination_H2BK120_writer, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM writers Q5VTR2, O75150 P06899, P62805, P0C0S8, P68431 0.532
323 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 Histone PTM writers, Histone_acetylation_writer, DNA repair, Transcription-associated, NuA4 Q12432 P62799, P06897, P84233, P02281 0.326
324 8JCC EM 3.42 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.W 601 116 Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence 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, P62805, Q7Z2G1, P68431 0.398
325 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, DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, Transcription-associated, E3 ubiquitin-protein ligation Q8N884, Q6PJ21, Q15369, Q15370 Q99877, Q93079, Q96KK5, Q71DI3, P62805, Q99878 0.4
326 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-associated, Transcription factors O08785, Q9WTL8 P06899, P04908, P62805, P68431 0.219
327 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-associated, Transcription factors P01106, P61244 Q8CGP7, P06899, P68431, P04908, P62805 0.411
328 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 Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P62799, P06897, P84233, P02281 0.484
329 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 Q16777, P62805, Q16778, P68431 0.559
330 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 Polycomb, Heterochromatin-associated, Histone PTM writers, Histone PTM erasers, Histone chaperones, Transcription-associated, Histone_methylation_H3K27_writer Q92833, Q15022, Q15910, O75530, Q09028, Q6ZN18 P06897, P84233, P07305, P02281, P62799 0.261
331 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q12432, Q04779 P62799, P06897, P02281, P02302 0.464
332 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 P62807, P62805, P0C0S8, Q71DI3 0.559
333 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 Histone PTM writers, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4 Q08649, P47128, Q540A3, P38806 P02309, P02293, Q12692, P61830 0.237
334 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 P06899, P04908, P62805, P68431 0.171
335 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 Q8TF76 P62799, P06897, P84233, P02281 0.502
336 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 Q6FI13, P62805, Q99879, Q71DI3 0.466
337 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 Histone_ubiquitination_reader, Polycomb, Heterochromatin-associated, Histone PTM readers, Transcription-associated, Ubiquitin Q8N488, P0CG48 P62799, P06897, P84233, P02281 0.382
338 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 P04908, P62805, Q16778, P68431 0.372
339 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 Q9NRC8 P06899, Q6FI13, P62805, Q71DI3 0.545
340 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer P61077, Q8IYW5, P62979 O60814, P07305, Q71DI3, P04908, P62805 0.237
341 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 O75531, H0YAB0 P06899, P04908, P62805, P68431 0.345
342 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 O75531, P02545 P06899, P04908, P62805, P68431 0.164
343 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 P59226, Q9LQQ4, P59259, Q9LD28 0.424
344 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 P06899, P62805, P16104, P68431 0.419
345 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 P06899, P62805, P0C0S8, Q71DI3 0.153
346 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 P06899, P62805, P0C0S8, Q71DI3 0.216
347 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 P62799, P06897, P84233, P02281 0.371
348 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 P04908, P62805, O60814, P68431 0.4
349 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 Histone_deacetylation, Histone PTM erasers, DNA repair, Transcription-associated, Histone_deacetylation_H3K9 Q8N6T7 P62799, P06897, P84233, P02281 0.446
350 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 P06899, P62805, P0C0S8, Q71DI3 0.345
351 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 P62799, P06897, P02281, P02302 0.196
352 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, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P0CG47 P04908, P62805, P62807, P68431 0.455
353 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-associated, Transcription factors P42212, P48431 P06899, P04908, P62805, P68431 0.35
354 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 P62799, P06897, P02281, P02302 -
355 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 P84229, P0C1H5, P02263, P62801 -
356 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, P02281, P84233, P0C0S5 -
357 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 P02309, P04911, P02294, P61830 -
358 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 P62799, P06897, P84233, P02281 -
359 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 P62799, P06897, P02281, P02302 -
360 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 P62799, P06897, P84233, P02281 -
361 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 P06899, P04908, P62805, Q71DI3 -
362 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 P62799, Q6AZJ8, P84233, P02281 -
363 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 P06899, P04908, P62805, P68431 -
364 3X1T X-ray 2.81 2015-09-23 octamer 1 canonical_H3 canonical_H4 H2A.1 H2B.1 alphasat_146 146 Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba 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 Mus musculus Xenopus laevis 2015 P70696, P62805, Q8CGP4, P68431 -
365 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 P62799, P06897, P84233, P02281 -
366 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 Histone_ubiquitination_H2AK119_writer, Polycomb, Histone PTM writers, Heterochromatin-associated, Transcription-associated, E3 ubiquitin-protein ligation, Histone_methylation_H3K27_writer P35226, Q99496 P62799, P06897, P84233, P02281 -
367 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 P62799, P06897, P84233, P02281 -
368 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 P02299, P84051, P02283, P84040 -
369 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 Histone_deubiquitination, Histone PTM erasers, SAGA, Transcription-associated, Ubiquitin P50102, Q6WNK7, Q03067, P0CG47, P53165 P62799, P06897, P84233, P02281 -
370 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 P62799, P06897, P84233, P02281 -
371 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 P06899, P04908, P62805, P68431 -
372 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 P06899, P62805, P0C0S5, P68431 -
373 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 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P62799, Q6AZJ8, P84233, P02281 0.356
374 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 P62807, P62805, P0C0S8, Q71DI3 0.577
375 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 P62799, P06897, P84233, P02281 0.528
376 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.452
377 8JCD EM 3.14 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.W 601 120 Human H2BFWTH100R nucleosome with 601 DNA 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, P62805, Q7Z2G1, P68431 0.445
378 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 P06899, P04908, P62805, P68431 0.598
379 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 P04908, P62805, O60814, Q71DI3 0.511
380 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 Q6FI13, P62805, Q99879, Q71DI3 0.573
381 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.512
382 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 Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, Histone PTM writers, RNA polymerases, Transcription-associated, Euchromatin-associated, PAF1C A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q96ST2, Q6PD62, Q92541, B7Z4W0, Q9GZS3, A0A2R8YHB3, P63272, Q9BYW2 P62799, A0A310TTQ1, P06897, P02281 0.237
383 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 P62805, Q16778, P0C0S5, P68431 0.448
384 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 P62799, P06897, P84233, P02281 0.608
385 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 P62799, P06897, P84233, P02281 0.578
386 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.496
387 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.497
388 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.476
389 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 Q9LQQ4, P59259, Q9LD28, P59169 0.431
390 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 P02299, P84051, P02283, P84040 0.442
391 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 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.518
392 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 P62799, Q6AZJ8, P84233, P02281 0.293
393 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 P06899, P62805, P0C0S5, Q71DI3 0.562
394 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 P62799, P06899, P0C0S8, P84233 0.471
395 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 P62807, P62805, P0C0S8, Q71DI3 0.65
396 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, Euchromatin-associated, Histone PTM writers O96028 P62799, P06897, Q92133, P02281 0.448
397 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 P06899, P04908, P62805, P68431 0.419
398 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 P02299, P84051, P02283, P84040 -
399 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 P62799, Q6AZJ8, P84233, P02281 -
400 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 P62799, P06897, P84233, P02281 -
401 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P84233, P02281 0.167
402 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 P62799, P06897, P84233, P02281 0.235
403 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 P62799, P06897, P84233, P02281 0.301
404 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 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P62799, P06897, P84233, P02281 0.427
405 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 P06899, P04908, P62805, P68431 -
406 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 P06899, P62805, P16104, P68431 -
407 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-associated, Transcription factors P55317 P06899, P04908, P62805, P68431 0.27
408 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 P06899, P04908, P62805, P68431 0.482
409 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 A0A8J1LZU9, P62805, Q6AZJ8, Q71DI3 0.39
410 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 Histone PTM writers, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4 Q08649, Q540A3, P38806, P47128 P02309, P02293, Q12692, P61830 0.165
411 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 Histone PTM writers, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4 Q08649, P47128, Q540A3, P38806 P02309, P02293, Q12692, P61830 0.114
412 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 P06899, P04908, P62805, P68431 -
413 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 P04908, P62805, O60814, Q71DI3 0.481
414 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, P06899, P0C0S8, Q71DI3, P04908, P62805 0.547
415 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 Q6FI13, P62805, Q99879, Q71DI3 0.519
416 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.535
417 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 Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, RNA polymerases, Histone chaperones, Histone PTM writers, Transcription-associated, Euchromatin-associated, Cell cycle, PAF1C A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P62799, A0A310TTQ1, P06897, P02281 0.25
418 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 Q6FI13, P62805, P33778, P68431 0.651
419 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 Chromatin remodelers, CHD, Transcription-associated P32657 P62799, P06897, P84233, P02281 0.295
420 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 P62799, P06897, P84233, P02281 0.454
421 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
422 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 P04908, P62805, A0A653DHJ5, O60814 0.406
423 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 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.49
424 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 P06899, P62805, P0C0S5, Q71DI3 0.579
425 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 P06899, P62805, P16104, P68431 0.215
426 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 P84233, P06899, S4RAZ3, P0C0S8, P62799 0.476
427 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 P04908, P62805, O60814, Q71DI3 0.462
428 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 P02299, P84051, P02283, P84040 0.589
429 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 P62807, P62805, P0C0S8, Q71DI3 0.589
430 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 P62799, Q6AZJ8, P84233, P02281 -
431 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.42
432 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 P06899, P04908, P62805, P68431 0.535
433 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, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P0CG47 P04908, P62805, P62807, P68431 0.432
434 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P06899, P04908, P62805, P68431 0.549
435 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 O60814, P10412, Q71DI3, P04908, P62805 0.264
436 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated, Ubiquitin Q03164, Q15291, P62979, P61964, Q9UBL3 P62799, P06897, P84233, P02281 0.461
437 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 P06899, P04908, P62805, Q4QHB5 -
438 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 P06899, P04908, P62805, P68431 0.085
439 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 P04908, P62805, O60814, P68431 -
440 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 P06899, P07305, P68431, P04908, P62805 -
441 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 P06899, P07305, P68431, P04908, P62805 -
442 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 ORC, Transcription-associated, DNA replication P54784 P62799, P06897, P84233, P02281 -
443 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 Chromatin remodelers, Transcription-associated, Cell cycle, RSC (SWI/SNF) Q06168, P43609, P32832, Q03124, P25632, Q07979, Q9URQ5, Q02206, P32597, Q12406, Q05123, P53330 P62799, P06897, P84233, P02281 0.081
444 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 DNA repair, Histone PTM writers, Histone_PARylation_writer Q9NWY4, Q9UGN5 P62799, P06897, P84233, P02281 0.113
445 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P62807, P62805, P0C0S8, Q71DI3 0.483
446 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P62807, P62805, P0C0S8, Q71DI3 0.474
447 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 P62807, P62805, P0C0S8, Q71DI3 0.537
448 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 Transcription factors, RNA polymerases, Transcription-associated, Euchromatin-associated, Cell cycle A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, O00267, Q8N201, Q9H0H0, Q96HW7, Q6P9B9, Q9UL03, Q9NVH2, Q75QN2, Q9NV88, Q9NVR2, Q5TA45, Q9NVM9, Q96SY0, Q96N11, P30153, P67775, Q9H3P2, Q8WX92, Q8IXH7 P62805, P06899, Q6NXT2, P0C0S8 0.037
449 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 P04908, P62805, O60814, P68431 0.043
450 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 Histone PTM writers, Histone_acetylation_writer, Transcription-associated, Euchromatin-associated, Cell cycle, NuA4 Q06337, P80428, P60010, P43572, P53201, P38811, Q08649, P38806, P47128 P62799, P06897, P84233, P02281 0.108
451 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 P62799, P06897, P84233, P02281 0.466
452 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 Nuclear division, Heterochromatin-associated, Histone PTM writers, Transcription-associated, Cell cycle, Histone_methylation_H4K20_writer Q9NQR1 P62799, P06897, P84233, P02281 0.475
453 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 Histone_deacetylation, Histone PTM erasers, DNA repair, Transcription-associated, Histone_deacetylation_H3K9 Q8N6T7 P62799, P06899, P04908, P84233 0.493
454 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Histone_acetylation_writer, DNA repair, Transcription-associated, NuA4, Rpd3 Q04779, Q12432 P62799, P06897, P84233, P02281 0.434
455 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 P06899, P04908, P62805, P68431 0.569
456 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 P06899, P04908, P62805, Q71DI3 0.579
457 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 P06899, P04908, P62805, P68431 0.143
458 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 P62805, P62807, Q93077, P68431 0.607
459 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 P62805, P0C0S8, A0A7K7T3V7, P62807 0.506
460 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 Chromatin remodelers, Transcription-associated, Cell cycle, RSC (SWI/SNF) Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P06897, P62799, P84233, A0A1L8G0X3 0.062
461 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 P06897, Q71DI3, P22844, P02281, P62805 -
462 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 P06899, P10412, P68431, P04908, P62805 0.492
463 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 -
464 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 P62799, P06897, P84233, P02281 -
465 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 P06899, P04908, P62805, P68431 -
466 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 Chromatin remodelers, ISWI G0S9L5 P02299, P84051, P02283, P84040 0.39
467 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 Histone_methylation_H3K36_writer, Histone PTM writers, Transcription-associated, Ubiquitin, Euchromatin-associated P0CH09, G0S676 P62799, P02281, P02302, P0CH09 0.261
468 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 P62799, P06897, P84233, P02281 0.339
469 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 O60814, P07305, P68431, P04908, P62805 0.246
470 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 ORC, Transcription-associated, DNA replication P54784 P02309, P02294, P04912, P61830 0.311
471 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 P04908, P62805, O60814, Q71DI3 0.281
472 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 Histone PTM writers, Histone_acetylation_writer, Transcription-associated, Euchromatin-associated, Cell cycle, NuA4 Q08649, P43572, P38806, P47128 P62799, P06897, P84233, P02281 0.314
473 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 P62799, P06897, P84233, P02281 0.569
474 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 Chromatin remodelers, Heterochromatin-associated O42861 P02299, P84051, P02283, P84040 0.272
475 7Y5W EM 3.50 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 101 Cryo-EM structure of the left-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 P62805, P68431 0.35
476 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 Histone PTM writers, Histone_acetylation_writer, DNA repair, Transcription-associated, NuA4 Q12432 P62799, P06897, P84233, P02281 0.572
477 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 Telomere-associated, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone_methylation_H4K20_reader, Histone PTM readers, Ubiquitin Q12888, P0CG47 P62805, P16104, O60814, P68431 0.424
478 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 Chromatin remodelers, INO80 G0RY01 P62807, P62805, P0C0S8, Q71DI3 0.474
479 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-associated, Euchromatin-associated, Transcription factors P17433 Q16777, P62805, Q16778, P68431 0.559
480 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, Euchromatin-associated, Histone PTM writers O00255 P62799, P06897, P84233, P02281 0.459
481 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 Heterochromatin-associated, Histone PTM writers, DNA repair, Transcription-associated, Histone_methylation_H4K20_writer Q4FZB7 P04908, P62805, O60814, P68431 0.456
482 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 Chromatin remodelers, Heterochromatin-associated Q9XFH4 Q9FJE8, P59226, Q9FFC0, P59259 0.387
483 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 P06899, P04908, P62805, P68431 0.404
484 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 Histone_deacetylation, Histone PTM writers, Telomere-associated, Histone PTM erasers, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P32561, P22579, Q12432, Q04779 P62799, P06897, P84233, P02281 0.324
485 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 Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P62799, P06897, P84233, P02281 0.521
486 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 Chromatin remodelers, INO80, SRCAP (INO80), SWR1 (INO80), Transcription-associated, Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04912, P61830 0.363
487 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 O15392, Q53HL2, Q9NQS7 P06897, P84233, A0A310TTQ1, P02281, P62799 0.551
488 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P06899, P04908, P62805, P68431 0.526
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 P62799, P06897, P84233, P02281 -
490 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 -
491 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 P62799, P06897, P84233, P02281 -
492 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 Chromatin remodelers, SWI/SNF, Transcription-associated P18480 P62799, P06897, P84233, P02281 0.513
493 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 Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, RNA polymerases, Histone chaperones, Histone PTM writers, Transcription-associated, Euchromatin-associated, Cell cycle, PAF1C A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 P62799, A0A310TTQ1, P06897, P02281 0.24
494 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 P04908, P62805, O60814, Q71DI3 0.359
495 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 P59226, Q9LQQ4, P59259, Q9LD28 0.451
496 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 P06899, P62805, P16104, P68431 0.413
497 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 P06899, P62805, P16104, P68431 0.3
498 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 Q4VC05 P62799, Q6AZJ8, P84233, P02281 0.493
499 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 P04908, P62805, Q16778, P68431 0.4
500 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 Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, RNA polymerases, Histone chaperones, Histone PTM writers, Transcription-associated, Euchromatin-associated, Cell cycle, PAF1C A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P62799, A0A310TTQ1, P06897, P02281 0.256
501 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 Q6FI13, P62805, Q99879, Q71DI3 0.51
502 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 P62807, P62805, P0C0S8, Q71DI3 0.581
503 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 P06899, P04908, P62805, P68431 0.232
504 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-associated, Transcription factors P42212, P48431 P06899, P04908, P62805, P68431 0.451
505 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 P62799, P06897, P84233, P02281 -
506 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, P04911, P02293, P61830 0.34
507 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 P06899, P04908, P62805, P68431 0.529
508 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 P62799, P06897, P84233, P02281 -
509 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 P06899, P04908, P62805, P68431 -
510 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 Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P62799, P06897, P84233, P02281 0.548
511 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 P0C5Z0, P62805, Q16778, P68431 0.365
512 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 P62799, P06897, P84233, P02281 -
513 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 P62799, P06897, P84233, P02281 -
514 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 P06899, P04908, P62805, P68431 -
515 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 P62799, P06897, P84233, P02281 -
516 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 P62799, P06897, P84233, P02281 -
517 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-associated, Euchromatin-associated, Transcription factors Q01860 Q16777, P62805, Q16778, P68431 0.434
518 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 Polycomb, Heterochromatin-associated, Histone PTM erasers, Histone_deubiquitination_H2AK119, Transcription-associated, Ubiquitin Q92560, Q8IXJ9, P0CG48 P62799, P06897, P84233, P02281 0.383
519 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 P62799, P06897, P84233, P02281 0.515
520 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 P06899, P62805, P16104, P68431 -
521 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-associated, Transcription factors P13393, P32773, P32774 P62799, P06897, P84233, P02281 0.49
522 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 P06899, P04908, P62805, P68431 0.352
523 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 P04052, P08266, O97183, Q7JZF5, Q24320, Q9VNZ3, P36958, Q9VC49, Q9VJE4, Q6IGE3 P02299, P84051, P02283, P84040 0.202
524 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 P06899, P62805, P0C0S5, Q71DI3 0.532
525 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 P62799, P06897, P84233, P02281 -
526 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 factors, RNA polymerases, Histone chaperones, FACT, DNA repair, Heterochromatin-associated, DNA replication, Centromere-associated, Transcription-associated, Euchromatin-associated, SPT4-SPT5 complex P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, Q04636, P32558, P32914, P27692 P62799, P06897, P84233, P02281 0.358
527 6L49 EM 18.90 2019-12-04 octamer, octamer, octamer 3 canonical_H3,cenH3 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 P06899, P49450, P68431, P04908, P62805 0.071
528 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 P62807, P62805, P0C0S8, Q71DI3 0.603
529 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 P06899, P04908, P62805, P68431 -
530 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 P62799, P06897, P84233, P02281 0.563
531 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, Euchromatin-associated, RNA polymerases P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422 P62799, P06897, P84233, P02281 0.241
532 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 P62799, P06897, P84233, Q28D68 -
533 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.614
534 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 P06899, P04908, P62805, P68431 0.386
535 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 P62799, P06897, P84233, P02281 0.587
536 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 Chromatin remodelers, CHD, Transcription-associated P32657 P62799, P06897, P84233, P02281 -
537 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-associated, Transcription factors P55317, P0AEX9 P06899, P04908, P62805, P68431 0.541
538 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 Chromatin remodelers, Transcription-associated, Cell cycle, RSC (SWI/SNF) Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P62799, P06897, P84233, P02281 0.086
539 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 P62799, P06897, P84233, P02281 0.515
540 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 P62799, None, P06897, P02281 0.329
541 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 P06899, P04908, P62805, P68431 0.227
542 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 Histone_ubiquitination_H2AK129_writer, Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK127_writer, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation P0CG47, Q99728 P06899, P04908, P62805, P68431 0.566
543 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 P06899, P04908, P62805, P68431 -
544 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 Q99879, P62805, P0C0S8, Q71DI3 0.57
545 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 P62799, P06897, P84233, P02281 0.395
546 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 P06899, P04908, P62805, P68431 -
547 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.477
548 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.576
549 8VLR EM 2.60 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 136 Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Shen, X.Y., Chen, C.X., Wang, Y., Zheng, W., Zheng, J.H., Jones, A.E., Zhu, B., Zhang, H., Lyons, C., Rijal, A., Moley, J.A., Cao, G.S., Liu, K., Winn, R., McGinty, R.K., Zhang, K., Wang, H.B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q96A08, P04908, P62805, P68431 0.602
550 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 P62799, P06897, P84233, P02281 0.493
551 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q12432, Q04779 P04908, P62805, O60814, P68431 0.188
552 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 Chromatin remodelers, Heterochromatin-associated Q9XFH4 O23629, P59226, P59259, Q9LD28 0.306
553 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 Histone PTM writers, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4 Q08649, P0AEX9, Q540A3, P38806 P02309, P02293, Q12692, P61830 0.261
554 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 P62799, P04911, P02293, P61830 0.399
555 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 P06746 P62807, P62805, P0C0S8, Q71DI3 0.405
556 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 P06746 P62807, P62805, P0C0S8, Q71DI3 0.297
557 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 P62807, P62805, P0C0S8, Q71DI3 0.366
558 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 P06899, P62805, P0C0S8, Q71DI3 0.316
559 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.559
560 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 P06899, P04908, P62805, P68431 0.321
561 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 P62799, Q6AZJ8, P84233, P02281 0.209
562 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 P06899, P04908, P62805, P68431 0.293
563 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 P62799, P06897, P84233, P02281 0.581
564 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 A0A310TTQ1, A0A8J0U496, A0A8J1LTD2, Q6AZJ8 0.45
565 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 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.282
566 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 P06899, P62805, P16104, P68431 0.511
567 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, A0A8J1LTD2, P02281, A0A8T2P505 -
568 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 P62799, P06897, P84233, P02281 0.294
569 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 P62799, P06897, P84233, P02281 0.351
570 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 P62799, P06899, P0C0S8, P84233 0.476
571 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 P62799, P06897, P84233, P02281 0.188
572 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 P04908, P62805, O60814, Q71DI3 0.473
573 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.595
574 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 P06746 P62807, P62805, P0C0S8, Q71DI3 0.384
575 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 Q6FI13, P62805, Q99879, Q71DI3 0.589
576 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 Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P62799, P06897, P84233, P02281 0.399
577 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 P04908, P62805, O60814, Q71DI3 0.514
578 7Y61 EM 5.60 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 92 Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B DNA repair, DNA replication, Histone chaperones, CAF-1 Q13111, Q13112 P62805, P68431 0.189
579 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 Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, RNA polymerases, Histone chaperones, Histone PTM writers, Transcription-associated, Euchromatin-associated, Cell cycle, PAF1C A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q6PD62, Q92541, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P62799, Q6AZJ8, A0A8J1LZU9, P84233 0.231
580 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 P62799, P06897, P84233, P02281 0.186
581 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-associated, Euchromatin-associated, Transcription factors P17433 Q16777, P62805, Q16778, P68431 0.509
582 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 P62799, Q6AZJ8, P84233, P02281 0.606
583 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-associated, Euchromatin-associated, Transcription factors Q01860 P62799, Q6AZJ8, P84233, P02281 0.233
584 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 Heterochromatin-associated, Histone PTM erasers, Polycomb, Histone_deubiquitination_H2AK119, Transcription-associated, Ubiquitin Q92560, P0CG47, Q8IXJ9 Q16778, P20671, P10412, P68431, P62805 0.435
585 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, Histone_acetylation_H3K27_writer, Transcription-associated, Histone PTM writers Q92793 P06899, P04908, P62805, P68431 0.242
586 8J6S EM 3.80 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 99 Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B DNA repair, DNA replication, Histone chaperones, CAF-1 Q13111, Q13112 P62805, P68431 0.301
587 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 P06899, P04908, P62805, P68431 0.19
588 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 Q99ZW2 P06899, P04908, P62805, P68431 0.218
589 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 O60814, P10412, Q71DI3, P04908, P62805 0.208
590 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 Q6FI13, P62805, O60814, Q71DI3 0.393
591 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 P62799, A0A310TTQ1, A0A1L8FQA5, Q6AZJ8 0.424
592 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, P62805, Q16778, P68431 0.278
593 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
594 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 P62799, A0A310TTQ1, P06897, P02281 -
595 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-associated, Euchromatin-associated, Transcription factors Q01860 P62799, Q6AZJ8, P84233, P02281 0.218
596 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 Chromatin remodelers, SWI/SNF, Transcription-associated, Cell cycle, PBAF (SWI/SNF) P51532, P60709, O96019, Q68CP9, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q8WUB8, Q9NPI1, Q86U86 P62805, P62807, Q93077, P68431 0.172
597 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 Chromatin remodelers, INO80, SRCAP (INO80), SWR1 (INO80), Transcription-associated, Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P04911, P02293, P61830 0.193
598 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 P06899, P04908, P62805, P68431 0.352
599 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 Chromatin remodelers, Heterochromatin-associated O42861 P02299, P84051, P02283, P84040 0.219
600 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 P62799, P06897, P84233, P02281 -
601 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 P04908, P62805, O60814, Q71DI3 0.571
602 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 P62799, Q6AZJ8, P84233, P02281 0.494
603 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 P06897, P62799, P84233, P02281 0.368
604 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P62807, P62805, P0C0S8, Q71DI3 0.196
605 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 Chromatin remodelers, INO80, SWR1 (INO80), Transcription-associated, Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P04911, P02293, P61830 0.372
606 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 Chromatin remodelers, INO80, SWR1 (INO80), Transcription-associated, Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P04911, P02293, P61830 0.195
607 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 Q16777, P62805, O60814, Q71DI3 0.43
608 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, DNA repair, Transcription-associated, Euchromatin-associated, Mediator 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 P62799, P06897, P84233, P02281 0.222
609 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 Histone_ubiquitination_H2AK129_writer, Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK127_writer, Transcription-associated, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation P38398, Q99728, P61077 P04908, P62805, O60814, Q71DI3 0.352
610 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 Chromatin remodelers, INO80 G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62805, P62807, Q93077, P68431 0.556
611 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 P06899, H2PI50, A0A9J8D176, L8IQP7 0.542
612 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 Chromatin remodelers, INO80, SRCAP (INO80), SWR1 (INO80), Transcription-associated, Euchromatin-associated Q05471, Q03388, Q12509, Q03433, Q03940, Q12464, P31376 P04911, P02293, P02299, A0A0B4KFZ9 0.191
613 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, Q6AZJ8, P84233, P02281 0.499
614 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 Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, RNA polymerases, Histone chaperones, Histone PTM writers, DNA repair, FACT, DNA replication, Transcription-associated, Euchromatin-associated, Cell cycle, PAF1C 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 P62799, A0A310TTQ1, P06897, P02281 0.252
615 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 Q99879, P62805, P0C0S8, Q71DI3 0.488
616 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q15291, P61964, Q03164 P62799, P06897, P84233, P02281 0.26
617 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, Histone PTM writers, Telomere-associated Q04089, P0CG48 P62799, P06897, P84233, P02281 0.473
618 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 P62799, P06897, P84233, P02281 -
619 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 P06899, P04908, P62805, P68431 -
620 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, P62805, P33778, P68431 -
621 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 P06899, P04908, P62805, P68431 -
622 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 Nuclear division, Heterochromatin-associated, Histone PTM writers, Transcription-associated, Cell cycle, Histone_methylation_H4K20_writer P21827, Q9NQR1 P62799, P06897, P84233, P02281 -
623 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 Telomere-associated, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone_methylation_H4K20_reader, Histone PTM readers, Ubiquitin Q12888, P0CG47 P62799, P62807, P0C0S8, P84233 0.301
624 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 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P62799, P06897, P84233, P02281 0.372
625 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q03164, Q15291, P61964, Q9UBL3 P62799, P06897, P84233, P02281 0.31
626 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 P62805, Q71UI9, Q16778, P68431 0.311
627 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 P06899, P04908, P62805, P68431 0.363
628 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 P06899, P07305, P68431, P04908, P62805 0.489
629 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 P04908, P62805, Q16778, P68431 -
630 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 P04908, P62805, P33778, P68431 -
631 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 Q6FI13, P62805, Q99879, Q71DI3 0.598
632 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 P62805, P62807, Q93077, P68431 0.494
633 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 P04908, P62805, O60814, Q71DI3 0.224
634 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 P04908, P62805, O60814, Q71DI3 0.274
635 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 O60814, P10412, Q71DI3, P04908, P62805 0.329
636 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 O60814, P10412, Q71DI3, P04908, P62805 0.236
637 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 P06899, P04908, P62805, P68431 0.256
638 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 P06899, P04908, P62805, P68431 0.32
639 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-associated, Euchromatin-associated, Transcription factors Q01860 P62799, Q6AZJ8, P84233, P02281 0.199
640 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 Histone PTM writers, p300, Histone_acetylation_writer, DNA repair, Transcription-associated, Cell cycle Q09472 P06899, P04908, P62805, P68431 0.214
641 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, P62805, P62807, P68431 0.43
642 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 Chromatin remodelers, Heterochromatin-associated Q9XFH4 P59226, Q9FFC0, Q9LD28, P59259 0.38
643 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 Chromatin remodelers, INO80 G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62805, P62807, Q93077, P68431 0.554
644 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 Chromatin remodelers, INO80, SRCAP (INO80), SWR1 (INO80), Transcription-associated, Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04912, P61830 0.185
645 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 Q6FI13, P62805, O60814, Q71DI3 0.195
646 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 Histone PTM writers, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, E3 ubiquitin-protein ligation Q07457 P62799, P06897, P84233, P02281 0.535
647 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, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P0CG47 P04908, P62805, P62807, P68431 0.438
648 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 P06899, P04908, P62805, P68431 0.514
649 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, A0A8J1LTD2, P84233, P02281 -
650 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 P02299, P84051, P02283, P84040 0.609
651 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 P62807, P62805, P0C0S8, Q71DI3 0.359
652 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 Histone PTM erasers, Histone_deubiquitination_H2AK119, Transcription-associated, Ubiquitin, Cell cycle Q9Y5T5, P0CG47 P04908, P62805, O60814, P68431 0.306
653 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 Chromatin remodelers, Heterochromatin-associated Q9XFH4 O23629, P59226, P59259, Q9LD28 0.336
654 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 Histone PTM writers, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4 Q08649, P0AEX9, P08515, P38806 P02309, P02293, Q12692, P61830 0.229
655 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 Histone PTM writers, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4 Q08649, P47128, Q540A3, P38806 P02309, P02293, Q12692, P61830 0.123
656 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer P61077, Q8IYW5, P62979 P04908, P62805, O60814, Q71DI3 0.443
657 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 ORC, Transcription-associated, DNA replication P54784 P02309, P02294, P04912, P61830 0.319
658 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P84233, P02281 0.135
659 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 P62799, A0A310TTQ1, A0A8J0U496, Q6AZJ8 0.241
660 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 P06899, P04908, P62805, Q71DI3 -
661 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 P62799, Q6DKE3, P84233, P02281 0.445
662 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 P04908, P62805, O60814, Q71DI3 0.187
663 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 P06897, P62799, P84233, P02281 0.303
664 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 P62799, P06897, P84233, P02281 0.356
665 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, E2RU29, A8BI78, A8BUJ9 0.427
666 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 P62799, P06897, P02281, P02302 -
667 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 P62799, P06897, P84233, P02281 -
668 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 P62799, P06897, P84233, P02281 -
669 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 P62799, P06897, P84233, P02281 -
670 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 P02299, P02259, P84051, P84040, P02283 -
671 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 P06899, P04908, P62805, P68431 -
672 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 P62799, P06897, P84233, P02281 -
673 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-associated, Transcription factors P35716 P04908, P62805, O60814, Q71DI3 0.323
674 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 P06899, P04908, P62805, P68431 -
675 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 P62799, P06897, P84233, P02281 -
676 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 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P62799, P06897, P84233, P02281 0.261
677 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 P62799, Q6AZJ8, P84233, P02281 0.198
678 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 Chromatin remodelers, CHD, Transcription-associated, Ubiquitin P0CG47, P32657 P06897, Q28D68, S4RAZ3, P02302, P62799 0.23
679 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 P06899, P62805, P16104, P68431 -
680 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 P04908, P62805, O60814, P68431 -
681 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 P02299, P84051, P02283, P84040 0.409
682 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q15291 P62799, P06897, P84233, P02281 0.332
683 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 P62799, P02281, P02302, P0CH09 0.49
684 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-associated, Transcription factors P35716 P04908, P62805, O60814, Q71DI3 0.37
685 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 P06899, P04908, P62805, P68431 -
686 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 P62799, Q6AZJ8, P84233, P02281 0.378
687 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 P62799, P06897, P84233, P02281 -
688 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.458
689 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 P62799, P06897, P84233, P02281 -
690 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 P06899, P04908, P62805, P68431 -
691 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 P06899, P04908, P62805, P68431 -
692 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 Histone_deubiquitination, Histone PTM erasers, SAGA, Transcription-associated, Ubiquitin P50102, Q6WNK7, Q03067, P53165, P0CG48 P62799, P06897, P84233, P02281 0.394
693 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 P06899, P04908, P62805, P68431 -
694 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 P62799, P06897, P84233, P02281 -
695 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 P62799, Q6AZJ8, P84233, P02281 -
696 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 P33778, P62805, Q8CGP4, P68431 -
697 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 P02309, P02294, P04912, P61830 -
698 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 P62799, P06897, P84233, P02281 -
699 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 P06899, P04908, P62805, P68431 -
700 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 P06899, P04908, P62805, P68431 -
701 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 P06899, P04908, P62805, Q71DI3 -
702 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 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P62799, P06897, P84233, P02281 0.349
703 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 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P62799, P06897, P84233, P02281 0.399
704 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 P62799, Q6AZJ8, P84233, P02281 0.132
705 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 P06899, P04908, P62805, P68431 -
706 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 P06899, P62805, P0C0S5, P68431 -
707 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 P06899, Q92522, P68431, P04908, P62805 -
708 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 P62807, P62805, P0C0S8, Q71DI3 0.555
709 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 P06899, P04908, P62805, P68431 0.31
710 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 P62799, P06897, P84233, P02281 -
711 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 P62805, Q5QNW6, Q96KK5, Q71DI3 0.494
712 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 P02299, P84051, P02283, P84040 0.206
713 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, Centromere-associated, CBF3, Kinetochore P40969 P02309, P04911, P02293, P61830 0.3
714 5GSU X-ray 3.10 2017-02-15 octamer 1 canonical_H3 canonical_H4 H2A.1 H2B.1 alphasat_146 146 Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B 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 Q96A08, P62805, Q96QV6, P68431 -
715 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, P06899, P0C0S8, Q71DI3, P04908 0.448
716 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 P06899, P07305, P68431, P04908, P62805 -
717 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 P62807, P62805, P0C0S8, Q71DI3 0.47
718 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 P06899, P62805, P0C0S5, Q71DI3 0.506
719 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 P06899, P62805, P16104, P68431 0.234
720 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 P06899, P62805, P16104, P68431 0.185
721 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 P62807, P62805, P0C0S8, Q71DI3 0.628
722 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 P06899, P04908, P62805, P68431 0.242
723 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 P62799, P06897, P84233, P02281 -
724 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 P62799, Q6AZJ8, P84233, P02281 0.167
725 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.532
726 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 P62799, Q6DKE3, P84233, P02281 0.489
727 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 Histone_ubiquitination_H2AK119_writer, Histone_ubiquitination_reader, Polycomb, Histone PTM writers, Heterochromatin-associated, Histone PTM readers, Transcription-associated, Ubiquitin, E3 ubiquitin-protein ligation, Histone_methylation_H3K27_writer P35226, Q99496, Q8N488, P0CG48 P06897, P84233, P10412, P02281, P62799 0.456
728 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.566
729 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 P62805, Q7L7L0, O60814, P68431 0.703
730 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 P62799, Q6AZJ8, P02281, P84233 0.591
731 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 P06899, P10412, P68431, P04908, P62805 0.527
732 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 P06899, P04908, P62805, Q71DI3 0.602
733 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-associated, Transcription factors P48431 P04908, P62805, O60814, Q71DI3 0.217
734 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 P04908, P62805, O60814, Q71DI3 0.068
735 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, Euchromatin-associated, Histone PTM writers G0S676 P62799, P02281, P02302, P0CH09 0.364
736 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 P62799, P06897, P84233, P02281 0.403
737 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3, Q9C005 P62799, P06897, P84233, P02281 0.188
738 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 UV-DDB complex, DNA repair, DCX complex Q16531, Q92466 P06899, P04908, P62805, P68431 0.212
739 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.493
740 9J8O EM 4.05 2025-02-26 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B generic_H1 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 O75531, P02545 P06899, Q02539, P68431, P04908, P62805 0.292
741 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 P62799, P06897, P84233, P02281 0.506
742 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q12432, Q04779 P62799, P06897, P84233, P02281 0.44
743 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 Histone_ubiquitination_H2BK120_writer, Histone PTM writers, DNA repair, Transcription-associated, E3 ubiquitin-protein ligation O75150, Q5VTR2, P49459 P04908, P62805, O60814, P68431 0.461
744 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 Histone_deacetylation, Histone PTM writers, Telomere-associated, Histone PTM erasers, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P32561, P22579, Q12432, Q04779 P62799, P06897, P84233, P02281 0.373
745 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 P62799, P06897, P84233, P02281 0.444
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 P62805, Q7L7L0, P02281, P68431 0.534
747 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 P06899, P16403, P68431, P04908, P62805 0.352
748 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 P06899, P62805, P0C0S8, Q71DI3 0.072
749 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 None, A2Y533, A2WKP5, A2YMC6 0.401
750 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 A2Y533, A0A0E0HFN0, A2WKP5, A2YMC6 0.441
751 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 P04908, P62805, O60814, P68431 -
752 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 P04908, P62805, O60814, P68431 -
753 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P06899, P04908, P62805, P68431 0.547
754 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 P06899, P62805, P0C0S8, Q71DI3 0.159
755 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 Histone PTM writers, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, E3 ubiquitin-protein ligation Q07457 P62799, P06897, P84233, P02281 0.503
756 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, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5 P04908, P62805, P62807, P68431 0.381
757 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 O23629, P59226, P59259, Q9LD28 0.5
758 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 Q8TF76 P62799, Q6AZJ8, P84233, P02281 0.536
759 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 P62799, P06897, P84233, P02281 0.527
760 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, Euchromatin-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P16403, P68431, P04908, P62805 0.16
761 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 P62799, P06897, P84233, P02281 0.356
762 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 Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P62799, P06897, P84233, P02281 0.392
763 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 P06899, P62805, P16104, P68431 0.204
764 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 UV-DDB complex, DNA repair, DCX complex Q16531, Q92466 P06899, P04908, P62805, P68431 0.22
765 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 P06899, P04908, P62805, P68431 0.39
766 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 PTM writers, Transcription-associated, Euchromatin-associated, Histone_methylation_H3K27_writer Q9BZ95 P62799, P06897, Q92133, P02281 0.507
767 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 PTM writers, Transcription-associated, Euchromatin-associated, Histone_methylation_H3K27_writer Q9BZ95 P62799, P06897, Q92133, P02281 0.464
768 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 P62799, P02281, P02302, P0C0S6 0.391
769 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 O60814, P10412, Q71DI3, P04908, P62805 0.27
770 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 P62807, P62805, P0C0S8, Q71DI3 0.454
771 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 P06899, P62805, P16104, P68431 0.388
772 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 P06899, P62805, P16104, P68431 0.34
773 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 P62807, P62805, P0C0S8, Q71DI3 0.385
774 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 factors, RNA polymerases, DNA repair, Transcription-associated, Euchromatin-associated, Cell cycle 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 P62799, P06897, P84233, P02281 0.187
775 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 P04908, P62805, O60814, P68431 0.459
776 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 Chromatin remodelers, SWI/SNF, Transcription-associated P51532 P62799, P06897, P84233, P02281 0.549
777 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P62799, P06897, P84233, P02281 0.44
778 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 Q2M2T1, P04908, P62805, Q71DI3 0.457
779 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 P62799, P06897, P84233, P02281 0.55
780 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 DNA repair, Transcription-associated, Cell cycle, Transcription factors P04637 P06899, P04908, P62805, P68431 0.146
781 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 P06899, P62805, P16104, P68431 0.26
782 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 Chromatin remodelers, Transcription-associated, ISWI P38144 P06897, A0A310TTQ1, A0A8J1LTD2, P02281 0.487
783 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 Chromatin remodelers, DNA repair, CHD Q86WJ1 P62799, P06897, P84233, P02281 0.483
784 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 Chromatin remodelers, Histone chaperones, INO80, Histone PTM readers, SRCAP (INO80), Transcription-associated, Euchromatin-associated, Cell cycle, Histone_acetylation_reader Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, P62807, Q93077, P68431 0.292
785 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 P62799, P04911, P02293, P61830 0.288
786 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 P62799, P06897, P84233, P02281 -
787 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 Histone_deacetylation, Histone PTM writers, Telomere-associated, Histone PTM erasers, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P32561, P22579, Q12432, Q04779 P62799, P06897, P84233, P02281 0.35
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 P62799, P06897, P84233, P02281 -
789 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 P06899, P04908, P62805, P68431 -
790 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 P06899, P04908, P62805, P68431 -
791 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 O60814, P10412, Q71DI3, P04908, P62805 0.302
792 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 P04908, P62805, O60814, Q71DI3 0.221
793 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 O60814, P10412, Q71DI3, P04908, P62805 0.269
794 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 DNA repair, Histone PTM writers, Histone_PARylation_writer P09874 P06899, P04908, P62805, P68431 0.273
795 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 P06899, P04908, P62805, P68431 -
796 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated, Ubiquitin B4DIJ7, P61964, Q9UBL3, Q15291, P0CG47, Q9C005 P62799, P06897, P84233, P02281 0.263
797 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 P62799, P06897, P84233, P02281 -
798 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 P02299, P84051, P02283, P84040 -
799 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 Chromatin remodelers, ISWI P43596 P62799, P06897, P84233, P02281 0.502
800 7X57 EM 3.63 2022-11-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 121 Cryo-EM structure of human subnucleosome (closed form) Nozawa, K., Takizawa, Y., Pierrakeas, L., Sogawa-Fujiwara, C., Saikusa, K., Akashi, S., Luk, E., Kurumizaka, H. 10.1073/pnas.2206542119 36322721 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2022 P62805, P68431 0.37
801 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 P06899, P16402, P68431, P04908, P62805 -
802 7Y60 EM 3.80 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 108 Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B DNA repair, DNA replication, Histone chaperones, CAF-1 Q13111, Q13112 P62805, P68431 0.304
803 7YOZ EM 4.30 2022-11-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 121 Cryo-EM structure of human subnucleosome (intermediate form) Nozawa, K., Takizawa, Y., Pierrakeas, L., Sogawa-Fujiwara, C., Saikusa, K., Akashi, S., Luk, E., Kurumizaka, H. 10.1073/pnas.2206542119 36322721 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2022 P62805, P68431 0.246
804 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 Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P62799, P06897, P84233, P02281 0.304
805 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 Q9LHQ5, P59226, P59259, O23629 0.545
806 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q12432, Q04779 P62799, P06897, P84233, P02281 0.067
807 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 P62799, P06897, P84233, P02281 -
808 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 O60814, P10412, Q71DI3, P04908, P62805 0.217
809 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 O60814, P10412, Q71DI3, P04908, P62805 0.267
810 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-associated, Transcription factors P35716 P04908, P62805, O60814, Q71DI3 0.355
811 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 P62799, P06897, P84233, P02281 0.38
812 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 P06899, P62805, Q71UI9, P68431 -
813 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 UV-DDB complex, DNA repair, DCX complex Q16531, Q92466 P06899, P04908, P62805, P68431 0.278
814 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 Chromatin remodelers, NuRD (CHD) Q14839 P62799, P06897, P84233, P02281 0.342
815 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 P62799, P06897, P84233, P02281 -
816 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 P62799, Q6AZJ8, P84233, P02281 -
817 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 Chromatin remodelers, CHD, Transcription-associated P32657 P62799, Q92133, P06897, A0A1L8G0X3 0.095
818 3X1V X-ray 2.92 2015-09-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 146 Crystal structure of nucleosome core particle in the presence of histone variant 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 Homo sapiens Mus musculus Xenopus laevis 2015 P70696, P04908, P62805, P68431 -
819 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 Chromatin remodelers, Transcription-associated, Cell cycle, RSC (SWI/SNF) P32597, Q12406, Q05123, P53330 P62799, Q92133, P06897, P02281 -
820 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 Q6DKE3, P84233, P15308, P02281, P62799 0.29
821 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P84233, P02281 0.177
822 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 P62799, P06897, P84233, P02281 0.508
823 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P62807, P62805, P0C0S8, Q71DI3 0.54
824 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 Transcription-associated, HDA1, Histone_deacetylation, Histone PTM erasers P53973, Q06623, Q06629 P06897, P84233, Q6AZJ8, P02281, P62799 0.189
825 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 P62799, P06897, P84233, P02281 -
826 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 P62799, P06897, P84233, P02281 -
827 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 P06899, P04908, P62805, P68431 -
828 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 P06899, P04908, P62805, P68431 0.225
829 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 P62799, Q6AZJ8, P84233, P02281 0.144
830 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 COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Transcription-associated, Euchromatin-associated Q03164, Q15291, P61964, Q9UBL3 P62799, P06897, P84233, P02281 0.338
831 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 Histone_deacetylation, Histone PTM writers, Telomere-associated, Histone PTM erasers, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P32561, P22579, Q12432, Q04779 P62799, A0A310TTQ1, Q6AZJ8, P02281 0.376
832 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-associated, Transcription factors P42212, P01106, P61244 P06899, P04908, P62805, P68431 0.404
833 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 P62807, P62805, P0C0S8, Q71DI3 0.526
834 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 P62799, P06897, P84233, P02281 0.643
835 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 Chromatin remodelers, CHD, Transcription-associated P32657 P62799, P06897, P84233, P02281 0.465
836 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 P62799, P06897, P84233, P02281 0.554
837 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 P04908, P62805, Q16778, P68431 0.388
838 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 P62799, P06897, P84233, P02281 -
839 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 P62799, P06897, P84233, P02281 -
840 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 P62799, P06897, P84233, P02281 -
841 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 P06899, P04908, P62805, P68431 -
842 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 P62799, P06897, P84233, P02281 0.536
843 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 DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 P06899, P04908, P62805, P68431 0.371
844 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 P06899, P04908, P62805, P68431 0.724
845 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 Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, RNA polymerases, Histone chaperones, Histone PTM writers, Transcription-associated, Euchromatin-associated, Cell cycle, PAF1C A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, O00267 P62799, Q6AZJ8, P84233, P02281 0.344
846 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 P06899, P04908, P62805, P68431 -
847 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 P06899, P04908, P62805, P68431 0.397
848 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, DNA repair, Transcription-associated, 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 P62799, P06897, P84233, P02281 0.342
849 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 P62799, P06897, P84233, P02281 -
850 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
851 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
852 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 Q6FI13, P62805, Q99879, Q71DI3 0.465
853 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 Q6FI13, P62805, Q99879, Q71DI3 0.495
854 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 Q6FI13, P62805, Q99879, Q71DI3 0.53
855 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 P62799, P06897, P84233, P02281 -
856 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) Histone_ubiquitination_reader, Polycomb, Heterochromatin-associated, Histone PTM readers, Transcription-associated, Ubiquitin Q8N488, P0CG47 P02299, P84051, P02283, P84040 0.465
857 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 P68431, A0A8C1JQV0, A0A2Y9FT95, P06899, H2QSF5 -
858 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P06899, P04908, P62805, P68431 0.452
859 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P06899, P04908, P62805, P68431 0.443
860 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 P62799, P06897, P84233, P02281 -
861 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-associated, Euchromatin-associated, Transcription factors Q01860 Q16777, P62805, Q16778, P68431 0.496
862 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 P62799, P02281, P84233, P0C0S5 0.508
863 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P06899, P04908, P62805, P68431 0.352
864 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 P06899, P04908, P62805, P68431 0.575
865 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 P62799, P06897, P84233, P02281 0.519
866 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.53
867 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 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P62799, P06897, P84233, P02281 0.456
868 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 P62805, P0C0S8, P02281, Q71DI3 0.375
869 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 Histone_deacetylation, Histone PTM writers, Histone PTM erasers, Telomere-associated, DNA repair, Histone_acetylation_writer, Transcription-associated, Cell cycle, NuA4, Rpd3 P22579, P32561, Q12432, Q04779 P04908, P62805, O60814, P68431 0.156
870 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 Histone PTM writers, DNA repair, Histone_ubiquitination_H2AK15_reader, Histone PTM readers, Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer P61077, Q8IYW5, P62979 P04908, P62805, O60814, Q71DI3 0.391
871 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 P62799, Q6AZJ8, P84233, P02281 -
872 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 P06899, P04908, P62805, P68431 0.24