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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 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 Q71DI3, P06897, P62805, P02281, P22844 -
1 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers P61077, Q8IYW5 O60814, Q71DI3, P62805, P04908 0.423
2 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, Histone chaperones, DNA replication, CAF-1 Q13111, Q13112 P62805, P68431 0.166
3 8J90 EM 4.71 2024-07-03 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 111 Cryo-EM structure of DDM1-nucleosome complex Osakabe, A., Takizawa, Y., Horikoshi, N., Hatazawa, S., Negishi, L., Sato, S., Berger, F., Kakutani, T., Kurumizaka, H. 10.1038/s41467-024-49465-w 38992002 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59259, P59226, Q9FJE8 0.243
4 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 O23629, P59259, P59226, Q9FJE8 0.53
5 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 DNA repair, Transcription-associated, Heterochromatin-associated, Histone_methylation_H4K20_writer, Histone PTM writers Q4FZB7 P0C0S5, P62805, O60814, P68431 0.433
6 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 P62805, P68431, P04908, P06899 0.13
7 8QZ0 EM 3.80 2024-10-02 octamer 1 H3.3 canonical_H4 H2A.Z,H2A.X canonical_H2B 601 113 SWR1-hexasome-dimer complex Jalal, A.S.B., Girvan, P., Chua, E.Y.D., Liu, L., Wang, S., McCormack, E.A., Skehan, M.T., Knight, C.L., Rueda, D.S., Wigley, D.B. 10.1016/j.molcel.2024.08.015 39226902 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Histone H2A.Z-specific chaperone CHZ1, Helicase SWR1, SWR1-complex protein 5, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 Histone chaperones, SWR1 (INO80), INO80, Euchromatin-associated, SRCAP (INO80), Chromatin remodelers, Transcription-associated P40019, Q05471, P38326, Q12509, Q03433, Q03940, Q12464, Q03388 P61830, P02293, Q12692, P04911, P02309 0.293
8 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 A0A310TTQ1, P02281, Q6AZJ8, P84233, P62799 0.618
9 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077, P0CG47 P62805, P68431, P04908, P06899 0.41
10 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 Telomere-associated, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457 P62799, P06897, P02281, P84233 0.52
11 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 repair, DNA modification O15527 P62799, P06897, P02281, P84233 0.424
12 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 P04908, P06899, P62805, Q92522, P68431 -
13 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, P68431, P62807, Q93077 0.525
14 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, P61830, P02293 0.424
15 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 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.36
16 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, Q71DI3, P62805, P0C0S8 0.364
17 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, Q71DI3, P62805, P0C0S8 0.453
18 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, Q71DI3, P62805, P0C0S8 0.31
19 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.616
20 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.586
21 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.578
22 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 Q71DI3, P62805, P06899, P0C0S8 0.083
23 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 Q71DI3, P62805, P06899, P0C0S8 0.145
24 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P22579, P32561, Q04779, Q12432 P62799, P06897, P02281, P84233 0.345
25 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 P62805, P68431, P04908, P06899 0.109
26 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P22579, P32561, Q12432, Q04779 P62799, P06897, P02281, P84233 0.463
27 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 DNA repair, Euchromatin-associated, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R198 P62805, P68431, P04908, P06899 0.105
28 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 Transcription-associated, Cell cycle, RSC (SWI/SNF), Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P62799, P06897, P02281, P84233 0.099
29 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_ubiquitination_H2BK120_reader, Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer Q8TEK3, P0CG48 P62799, P06897, P02281, P84233 0.436
30 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_methylation_H3K36_reader, Euchromatin-associated, Histone PTM erasers, Histone PTM readers, Transcription-associated, Histone_demethylation_H3K4 Q8NB78, Q49A26 P62799, P06897, P02281, P84233 0.198
31 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_methylation_H3K36_reader, Euchromatin-associated, Histone PTM erasers, Histone PTM readers, Transcription-associated, Histone_demethylation_H3K4 Q8NB78, Q49A26 P62799, P06897, P02281, P84233 0.186
32 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 PTM readers, Histone_methylation_H3K36_reader O75475 P62799, P06897, P02281, P84233 0.529
33 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, Telomere-associated, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, Q6CRQ4 P62799, Q92133, P02281, Q6AZJ8 0.385
34 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 Transcription-associated, Histone_demethylation_H3K4, Histone PTM erasers, Histone_demethylation_H3K9 O60341, Q9UKL0 P62799, P06897, P02281, P84233 -
35 7A08 EM 3.11 2020-09-23 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 132 CryoEM Structure of cGAS Nucleosome complex Michalski, S., de Oliveira Mann, C.C., Stafford, C.A., Witte, G., Bartho, J., Lammens, K., Hornung, V., Hopfner, K.P. 10.1038/s41586-020-2748-0 32911480 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Antiviral defense, Synthesis of second messengers Q8C6L5 Q93077, P62805, P62807, P84243 0.533
36 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 Euchromatin-associated, Histone_methylation_H3K4_writer, Histone_methylation_H3K27_writer, Transcription-associated, Histone PTM writers Q9BZ95 P62799, P06897, P02281, Q92133 0.542
37 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 Euchromatin-associated, Transcription-associated, Histone_methylation_H3K36_writer, Histone PTM writers P46995 P62799, P02281, Q6AZJ8, P84233 0.473
38 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 DNA repair, CHD, Chromatin remodelers Q86WJ1 P62799, P06897, P02281, P84233 0.567
39 7PEW EM 4.60 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 176 Nucleosome 1 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P62805, P04908 0.29
40 7U4D EM 8.10 2022-03-30 octamer, octamer 2 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 139 CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and 601 DNA sequence Zhou, K., Gebala, M., Woods, D., Sundararajan, K., Edwards, G., Krzizike, D., Wereszczynski, J., Straight, A.F., Luger, K. 10.1038/s41594-022-00758-y 35422519 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein N Centromere-associated, CENP-A NAC/CAD, Nuclear division, Kinetochore Q96H22 Q93077, P62805, P62807, P49450 0.114
41 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 P04908, P06899, P62805, P07305, P68431 -
42 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, Q71DI3, P62805, P0C0S8 -
43 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 Euchromatin-associated, Transcription-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, P02281, P84233 0.244
44 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, Q57YA3, Q57Z31, Q4GYX7 0.439
45 8EU2 EM 2.93 2023-07-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Class3 of the INO80-Hexasome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.434
46 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, P02281, P84233 0.445
47 8GUJ EM 2.80 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1-nucleosome complex (Model II) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B E3 ubiquitin-protein ligation, Transcription-associated, Histone_ubiquitination_H2BK120_writer, Histone PTM writers Q5VTR2, O75150 P62805, P68431, P06899, P0C0S8 0.532
48 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 P62805, P68431, P06899, P0C0S8 0.588
49 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 Q71DI3, P62805, P06899, P0C0S8 0.068
50 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, P06897, P02281, A0A310TTQ1 0.445
51 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 P0C1H6, P62805, P68431, P04908 0.39
52 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 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers, SWI/SNF P22082, P09547, P18480, P32591, P53628, P18888, Q12406, Q05123, P53330 P62799, P06897, P02281, P84233 0.122
53 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_ubiquitination_H2BK120_reader, Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer Q8TEK3, P62979 P62805, O60814, P68431, P04908 0.332
54 7EA8 EM 3.10 2021-07-14 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 122 Human SETD2 bound to a nucleosome containing oncohistone mutations Liu, Y., Zhang, Y., Xue, H., Cao, M., Bai, G., Mu, Z., Yao, Y., Sun, S., Fang, D., Huang, J. 10.1038/s41421-021-00261-6 33972509 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Histone-lysine N-methyltransferase SETD2 Euchromatin-associated, Transcription-associated, Histone_methylation_H3K36_writer, Histone PTM writers Q9BYW2 P62799, Q6PI79, P20671, P06899 0.509
55 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, P02281, P84233 0.516
56 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, Q71DI3, P04908, P10412, P62805 0.203
57 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, Q71DI3, P04908, P10412, P62805 0.101
58 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, Q71DI3, P04908, P10412, P62805 0.351
59 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, Q71DI3, P04908, P10412, P62805 0.084
60 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
61 7UX9 EM 3.20 2023-08-09 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 141 Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA) Lee, S.C., Adams, D.W., Ipsaro, J.J., Cahn, J., Lynn, J., Kim, H.S., Berube, B., Major, V., Calarco, J.P., LeBlanc, C., Bhattacharjee, S., Ramu, U., Grimanelli, D., Jacob, Y., Voigt, P., Joshua-Tor, L., Martienssen, R.A. 10.1016/j.cell.2023.08.001 37643610 Arabidopsis thaliana Xenopus laevis Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2023 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59169, P62799, Q9FJE8 0.445
62 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 PBAF (SWI/SNF), Cell cycle, SWI/SNF, Chromatin remodelers, Transcription-associated P51532, O96019, P60709, Q68CP9, Q8WUB8, Q9NPI1, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q86U86 P62799, P06897, P02281, P84233 0.315
63 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
64 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, P02281, P84233 0.525
65 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 repair, DNA modification P29372 P62799, P06897, P02281, P84233 0.466
66 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 P04908, P06899, P62805, P02259, P68431 -
67 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, P02281, P84233 0.598
68 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 Ubiquitin, COMPASS, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers P61964, Q15291, P0CG47 P62799, P02302, P06897, P02281 0.237
69 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
70 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, P02281, P84233 0.552
71 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) Ubiquitin, Transcription-associated, Histone_ubiquitination_H2AK119_reader, Histone PTM readers Q16385, P0CG47 O60814, Q71DI3, P62805, P04908 0.47
72 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 O60814, Q71DI3, P62805, P04908 0.532
73 8JH4 EM 3.20 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 178 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P62805, P84243, P04908 0.313
74 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, P02281, P84233 0.504
75 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_ubiquitination_H2BK120_reader, Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer Q8TEK3, P0CG47 P62799, P06897, P02281, P84233 0.551
76 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.587
77 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 P62805, P68431, P04908, P06899 -
78 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.482
79 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 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.239
80 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 O60814, Q71DI3, P62805, P04908 0.108
81 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, P02281, Q6AZJ8, P84233 0.343
82 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 A0A310TTQ1, P06897, P02281, P84233, P62799 -
83 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, P02281, P84233 -
84 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, P02281, P84233 0.256
85 8JH3 EM 3.70 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P62805, P84243, P04908 0.255
86 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 Ubiquitin, COMPASS, Telomere-associated, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, P0CG47, Q6CRQ4 Q92133, P02281, Q6AZJ8, P84233, P62799 0.372
87 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 Euchromatin-associated, Transcription-associated, Histone_methylation_H3K36_writer, Histone PTM writers O96028 P62805, P68431, P06899, P0C0S8 0.556
88 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 Q71DI3, Q6FI13, P62805, P06899 0.24
89 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 E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer, Polycomb, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers P35226, Q99496 P84040, P84051, P02283, P02299 0.511
90 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, Antiviral defense, Synthesis of second messengers Q8C6L5 P62807, Q71DI3, P62805, P0C0S8 0.265
91 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, Heterochromatin-associated, Histone_methylation_H3K9_reader, Histone PTM readers P45973 P62799, P0C0S6, P02281, P84233 0.143
92 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 P62805, P68431, P04908, P06899 0.196
93 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 DNA repair, CHD, Chromatin remodelers Q86WJ1 P62799, P06897, P02281, P84233 0.625
94 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 Histone chaperones, INO80, Euchromatin-associated, Histone_acetylation_reader, Cell cycle, SRCAP (INO80), Chromatin remodelers, Histone PTM readers, Transcription-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, Q93077, P68431, P62807 0.218
95 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 Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P06899, P62805, P16403, P68431 0.228
96 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, P02281, Q6AZJ8, P84233 -
97 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, P02281, P84233, P62799, P22844 -
98 6A5O EM 9.90 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 178 RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P62805, P84243, P04908 0.083
99 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_ubiquitination_H2BK120_reader, Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer Q8TEK3, P62979 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.132
100 6A5T EM 6.70 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P62805, P84243, P04908 0.151
101 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 Transcription-associated, CHD, Chromatin remodelers P32657 P62799, P06897, P02281, P84233 0.018
102 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 Q5QNW6, Q71DI3, P62805, Q96KK5 0.494
103 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 Ubiquitin, Histone_ubiquitination_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer, Polycomb, Histone PTM readers, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers P35226, Q99496, Q8N488, P0CG48 P06897, P10412, P02281, P84233, P62799 0.456
104 8OW1 EM 3.70 2023-08-09 hexamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601_modified 153 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Dendooven, T., Zhang, Z., Yang, J., McLaughlin, S.H., Schwab, J., Scheres, S.H.W., Yatskevich, S., Barford, D. 10.1126/sciadv.adg7480 37506202 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2023 Centromere-binding protein 1, Centromere DNA-binding protein complex CBF3 subunit B, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Suppressor of kinetochore protein 1, Inner kinetochore subunit CNN1, Inner kinetochore subunit AME1, Inner kinetochore subunit WIP1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2, Histone H2A.1 Cell cycle, Kinetochore, CCAN, Centromere-associated, Transcription-associated, CBF3, Nuclear division P17106, P40969, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P52286, P43618, P38313, Q2V2P8, Q12493, Q06162, P04911 P02309, P04911, P36012, P02293 0.165
105 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 P04908, P06899, P62805, P07305, P68431 -
106 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 Histone chaperones, INO80, Euchromatin-associated, Histone_acetylation_reader, Cell cycle, SRCAP (INO80), Chromatin remodelers, Histone PTM readers, Transcription-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, Q93077, P68431, P62807 0.292
107 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 DNA repair, Euchromatin-associated, RNA polymerases, Transcription-associated, Transcription factors 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, P02281, P84233 0.342
108 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 chaperones, PAF1C, Euchromatin-associated, Histone_methylation_H3K4_writer, Cell cycle, RNA polymerases, Histone_ubiquitination_H2BK120_writer, Transcription-associated, Transcription factors, Histone PTM writers A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, O00267 P62799, P02281, Q6AZJ8, P84233 0.344
109 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 P62805, P68431, P04908, P06899 0.724
110 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, Antiviral defense, Synthesis of second messengers Q8N884 P62805, P68431, P04908, P06899 0.371
111 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, P02281, P84233 -
112 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 Transcription-associated, Cell cycle, RSC (SWI/SNF), Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P62799, P06897, A0A1L8G0X3, P84233 0.062
113 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.42
114 6SEE EM 4.20 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2A : CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 Centromere protein C Centromere-associated, CENP-A NAC/CAD, Nuclear division, Kinetochore Q03188 P62807, Q6FI13, P62805, P49450 0.309
115 6TEM EM 3.90 2020-04-08 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 130 CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM Boopathi, R., Danev, R., Khoshouei, M., Kale, S., Nahata, S., Ramos, L., Angelov, D., Dimitrov, S., Hamiche, A., Petosa, C., Bednar, J. 10.1093/nar/gkaa246 32313946 Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 P62799, P06897, P02281, P49450 -
116 6USJ EM 10.50 2020-10-14 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Structure of two nucleosomes bridged by human PARP2 Gaullier, G., Roberts, G., Muthurajan, U.M., Bowerman, S., Rudolph, J., Mahadevan, J., Jha, A., Rae, P.S., Luger, K. 10.1371/journal.pone.0240932 33141820 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Poly [ADP-ribose] polymerase 2 Histone_PARylation_writer, DNA repair, Histone PTM writers Q9UGN5 P62805, P68431, P04908, P06899 0.092
117 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 COMPASS, Telomere-associated, Histone_methylation_H3K4_writer, Ubiquitin, Histone PTM writers, Transcription-associated P0CG48, P38123, P39706, P38827, P43132, Q03323, Q03012 P62799, P06897, P02281, P84233 0.449
118 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, Antiviral defense, Synthesis of second messengers Q8N884 P62805, P68431, P04908, P06899 0.152
119 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 Cell cycle, Transcription-associated, Heterochromatin-associated, Histone_methylation_H4K20_writer, Histone PTM writers, Nuclear division Q9NQR1 P62805, P68431, P04908, P06899 0.514
120 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 Ubiquitin, Histone PTM writers, Telomere-associated, Histone_methylation_H3K79_writer Q04089, P0CG48 P62799, P06897, P02281, P84233 0.489
121 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_H2AK125_writer, DNA repair, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Transcription-associated, Histone PTM writers P38398, Q99728, P61077 P62805, P68431, P04908, P06899 0.458
122 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P02281, P84233 0.198
123 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 DNA repair, CHD, Chromatin remodelers Q86WJ1 P62799, P06897, P02281, P84233 0.282
124 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, Q71DI3, P62805, P04908 0.602
125 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 PTM erasers, SAGA, Histone_deubiquitination, Ubiquitin, Transcription-associated P50102, Q6WNK7, Q03067, P53165, P0CG48 P62799, P06897, P02281, P84233 0.394
126 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 Transcription-associated, Chromatin remodelers, ISWI P43596, P38144 P62799, P06897, P02281, P84233 0.192
127 7XTD EM 3.90 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p DNA repair, Histone chaperones, Euchromatin-associated, DNA replication, SPT4-SPT5 complex, RNA polymerases, FACT, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P06899, P62805, P84243, P04908 0.221
128 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 Telomere-associated, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457 P62799, P06897, P02281, P84233 0.503
129 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Histone PTM writers Q8IYW5 P62805, P68431, P62807, P04908 0.381
130 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, P59259, Q9LD28, P59226 0.5
131 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, P02281, Q6AZJ8, P84233 0.536
132 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 Q71DI3, P04908, P06899, P0C0S8, A0A9J8D176 0.448
133 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, P61830, P02293 0.288
134 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, P02281, P84233 0.527
135 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 Q71DI3, P62805, P06899, P0C0S8 0.159
136 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 Q71DI3, P62805, P06899, P0C0S8 0.072
137 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, P02281, P68431, Q7L7L0 0.534
138 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, P02281, P84233 0.444
139 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, P02281, P84233 0.506
140 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 P04908, P06899, Q02539, P62805, P68431 0.292
141 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.493
142 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.487
143 9MLL EM 3.70 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 137 GammaH2AX containing nucleosomes, Parallel stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P62805, P68431, P06899 0.26
144 9MMM EM 4.00 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosomes, Parallel stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P62805, P68431, P06899 0.204
145 9MMO EM 3.90 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosomes, Right offset stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P62805, P68431, P06899 0.34
146 9MMT EM 3.40 2025-10-29 hexamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 89 H2AX containing nucleosome, Unwrapped (Class 2) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P62805, P68431, P06899 0.388
147 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 P62805, P68431, P04908, P06899 0.39
148 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, Q71DI3, P62805, P0C0S8 0.555
149 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 DNA repair, Histone_acetylation_writer, Cell cycle, p300, Transcription-associated, Histone PTM writers Q09472 P62805, P68431, P04908, P06899 0.307
150 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 DNA repair, Euchromatin-associated, RNA polymerases, Transcription-associated, Transcription factors 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, P02281, P84233 0.34
151 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, P02281, P84233 -
152 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 Ubiquitin, Histone_ubiquitination_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer, Polycomb, Histone PTM readers, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers P35226, Q99496, Q8N488, P0CG48 P62799, P06897, P02281, P84233 0.39
153 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.538
154 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, P02281, P84233 0.685
155 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 Q71DI3, P62805, A0A1B8Y854, None 0.124
156 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 chaperones, PAF1C, Euchromatin-associated, Histone_methylation_H3K4_writer, Cell cycle, RNA polymerases, Histone_ubiquitination_H2BK120_writer, Histone_methylation_H3K36_writer, Transcription-associated, Transcription factors, Histone PTM writers A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 A0A310TTQ1, P62799, P02281, P06897 0.261
157 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 Transcription-associated, CHD, Chromatin remodelers P32657 P62799, P06897, P02281, P84233 0.332
158 9II7 EM 3.50 2025-06-11 hexamer 1 H3.3 canonical_H4 H2A.B canonical_H2B 601_modified 114 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Akatsu, M., Hirano, R., Kujirai, T., Ogasawara, M., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1038/s44318-025-00473-6 40447801 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P0C5Z0, P62805, P84243, P06899 0.285
159 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.49
160 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, P61830, P62798, P02293 0.374
161 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 P06899, P62805, P84229, P04908 0.297
162 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, Cell cycle, Transcription factors, Transcription-associated P04637 P62805, P68431, P04908, P06899 0.192
163 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 DNA repair, INO80, DNA replication, Cell cycle, Chromatin remodelers, Transcription-associated Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q9C086 P62805, P68431, P04908, P06899 0.181
164 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077, P0CG47 P62805, P68431, P04908, P06899 0.429
165 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 DNA repair, INO80, DNA replication, Cell cycle, Chromatin remodelers, Transcription-associated Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q6PI98, Q9C086 P62805, P68431, P04908, P06899 0.462
166 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 DNA repair, Histone chaperones, DNA replication, FACT, Transcription-associated Q9Y5B9, Q08945 P62805, P68431, P62807, Q93077 0.173
167 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 DNA repair, Histone chaperones, DNA replication, FACT, Transcription-associated Q9Y5B9, Q08945 P62805, P68431, P62807, Q93077 0.203
168 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 Histone chaperones, INO80, Euchromatin-associated, Histone_acetylation_reader, Cell cycle, SRCAP (INO80), Chromatin remodelers, Histone PTM readers, Transcription-associated Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, Q93077, P68431, P62807 0.297
169 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 Histone chaperones, Polycomb, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers Q15022, Q15910, O75530, Q09028, Q6ZN18 P62799, P06897, P02281, P84233 0.259
170 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 Q71DI3, P62805, None -
171 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 P62799, P06897, P02281, P84233 0.266
172 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 P02283, P02299, P84040, P84051, P02259 -
173 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 P62805, O60814, P68431, P04908 0.532
174 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 E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer, Polycomb, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers P35226, Q99496 P62799, P06897, P02281, P84233 0.47
175 9C9X EM 2.83 2025-07-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 A0A310TTQ1, P62799, P02281, P06897 0.494
176 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 DNA repair, Euchromatin-associated, Cell cycle, RNA polymerases, Transcription-associated, Transcription factors 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, P02281, P84233 0.234
177 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, P61830, P02293 0.445
178 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, P02281, P84233 0.574
179 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, P02281, P84233 0.575
180 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 Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer, Polycomb, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers P35226, Q99496, P0CG47, P62837 P62805, O60814, P68431, P04908 0.516
181 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 DNA repair, Telomere-associated, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457, P06104 P62805, O60814, P68431, P04908 0.393
182 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 P62805, P68431, P04908, P06899 0.453
183 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 P62805, P68431, P04908, P06899 0.479
184 8PKJ EM 2.50 2024-02-28 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of the nucleosome containing Nr5a2 motif at SHL+5.5 Kobayashi, W., Sappler, A.H., Bollschweiler, D., Kummecke, M., Basquin, J., Arslantas, E.N., Ruangroengkulrith, S., Hornberger, R., Duderstadt, K., Tachibana, K. 10.1038/s41594-024-01239-0 38409506 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2024 C0HKE1, P62806, P84244, Q6ZWY9 0.6
185 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077 P62805, P68431, P04908, P06899 0.526
186 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077, P0CG47 P62805, P68431, P04908, P06899 0.439
187 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077, P0CG47 P62805, P68431, P04908, P06899 0.445
188 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077, P0CG47 P62805, P68431, P04908, P06899 0.424
189 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 DNA repair, Transcription-associated, Heterochromatin-associated, Histone_methylation_H4K20_writer, Histone PTM writers Q4FZB7 P62799, P0C0S5, P02281, P84233 0.516
190 8U5H EM 3.23 2024-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome Chen, X., Guo, Y., Zhao, T., Lu, J., Fang, J., Wang, Y., Wang, G.G., Song, J. 10.1038/s41467-024-50526-3 39043678 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA (cytosine-5)-methyltransferase 3A, Ubiquitin Ubiquitin, DNA modification Q9Y6K1, P0CG48 P62799, P02302, P06897, P02281 0.443
191 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077 P62805, P68431, P04908, P06899 0.464
192 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, P02281, P84233 0.516
193 8VMJ EM 3.10 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K4me3 nucleosome bound to PRC2_AJ119-450 Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 Q71DI3, P62805, A0A8J1LZU9, Q6AZJ8 0.402
194 8VO0 EM 3.30 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 Q71DI3, P62805, Q6AZJ8, P02281 0.258
195 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 repair, DNA modification O15527 P62807, Q71DI3, P62805, P0C0S8 0.41
196 8WH8 EM 3.60 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 125 Structure of DDM1-nucleosome complex in ADP state Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59259, Q9LD28, P59226 0.403
197 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 P62805, P68431, P04908, P06899 -
198 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 P62805, O60814, P68431, P04908 0.524
199 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P32561, P22579, Q12432, Q04779 P62799, P06897, P02281, P84233 0.378
200 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 P62805, P68431, P04908, P06899 0.267
201 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, A2WKP5, A0A0E0HFN0, A2YMC6 0.441
202 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, Q71DI3, P04908, P10412, P62805 0.177
203 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, P02281, P84233 0.52
204 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 DNA repair, CHD, Chromatin remodelers Q86WJ1 P62799, P06897, P02281, P84233 0.516
205 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, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers Q15910, Q15022 P62799, P06897, P02281, P84233 0.29
206 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 Centromere-associated, Nuclear division, Kinetochore O57392, P0AEX9 Q16778, P62805, P84229, P04908 0.387
207 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 P04908, P06899, P62805, P07305, P68431 -
208 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 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers, SWI/SNF P22082, P09547, P18480, P32591, P53628, P18888, P43554, P53330, Q12406, Q05123 P62799, P02281, Q6AZJ8, P84233 0.105
209 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 P62805, P68431, P04908, P06899 0.59
210 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 Euchromatin-associated, CHD, SPT4-SPT5 complex, RNA polymerases, Chromatin remodelers, Centromere-associated, Transcription-associated, Heterochromatin-associated, Transcription factors P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P32657, P32914, P27692 P62799, P06897, P02281, P84233 0.444
211 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, P02281, P84233 0.435
212 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, Q71DI3, P04908, P10412, P62805 0.138
213 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, Q71DI3, P04908, P10412, P62805 0.109
214 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 SWR1 (INO80), INO80, Euchromatin-associated, SRCAP (INO80), Chromatin remodelers, Transcription-associated Q05471, P38326, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P04911, P61830, P02293 0.324
215 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, Q71DI3, P04908, P10412, P62805 0.268
216 7SCZ EM 3.50 2022-01-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to multiple BRCTs Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 Histone_PARylation_writer, DNA repair, Histone PTM writers P09874 P62805, P68431, P04908, P06899 0.425
217 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, P02281, P84233 -
218 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 Histone_phosphorylation_H3T3_writer, Cell cycle, Histone PTM writers, Nuclear division Q99986 P62807, Q71DI3, P62805, P0C0S8 0.56
219 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, Q71DI3, P62805, P0C0S8 0.415
220 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 chaperones, PAF1C, Euchromatin-associated, Histone_methylation_H3K4_writer, Cell cycle, RNA polymerases, Histone_ubiquitination_H2BK120_writer, Transcription-associated, Transcription factors, Histone PTM writers A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P62799, P02281, Q6AZJ8, P84233 0.216
221 7UV9 EM 3.20 2023-02-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate Spangler, C.J., Skrajna, A., Foley, C.A., Nguyen, A., Budziszewski, G.R., Azzam, D.N., Arteaga, E.C., Simmons, H.C., Smith, C.B., Wesley, N.A., Wilkerson, E.M., McPherson, J.E., Kireev, D., James, L.I., Frye, S.V., Goldfarb, D., McGinty, R.K. 10.1038/s41589-023-01256-y 36797403 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Lysine-specific demethylase 2A Centromere-associated, Heterochromatin-associated, Histone PTM erasers, Histone_demethylation_H3K36 Q9Y2K7 P62807, Q71DI3, P62805, P0C0S8 0.42
222 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 P62805, O60814, P68431, P04908 0.558
223 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, P02281, P84233 0.55
224 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 P04908, P06899, P62805, P07305, P68431 -
225 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 P62805, P0C5Z0, P68431, Q16778 0.493
226 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 P62805, P68431, P04908, P06899 -
227 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 P04908, P06899, P62805, P07305, P68431 -
228 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 Ubiquitin, COMPASS, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q8NEZ4, Q15291, P62979, P61964, Q9UBL3 P62799, P06897, P02281, P84233 0.33
229 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, Q71DI3, P62805, P0C0S8 0.589
230 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, P02281, Q6AZJ8, P84233 -
231 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.42
232 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.452
233 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_ubiquitination_H2BK120_reader, Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer Q8TEK3, F5H388 P62799, P06897, P02281, P84233 0.371
234 9E49 EM 5.93 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 314 Cryo-EM structure of a di-nucleosome with an eight base-pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Q71DI3, P62805, P06899, P0C0S8 0.216
235 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 Q71DI3, P62805, P06899, P0C0S8 0.153
236 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, Q71DI3, P04908, P10412, P62805 0.105
237 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 P62805, P68431, P04908, P06899 0.361
238 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 P16104, P62805, P68431, P06899 0.168
239 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 P62805, P06899, P68431, P04908 -
240 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 P62799, P06897, P02281, P84233 0.554
241 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P22579, P32561, Q12432, Q04779 P62799, P06897, P02281, P84233 0.23
242 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_H2AK125_writer, DNA repair, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Transcription-associated, Histone PTM writers P38398, Q99728 O60814, Q6FI13, P62805, Q71DI3 0.313
243 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 C0HKE1, Q9D2U9, P62806, A0A8X6EH29 0.391
244 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, P02281, P84233 -
245 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 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P62799, P06897, P02281, P84233 0.315
246 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 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P62799, P02281, Q6AZJ8, P84233 0.372
247 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, Q71DI3, P62805, P0C0S8 0.33
248 6J4X EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.233
249 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 Ubiquitin, COMPASS, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q03164, Q15291, P62979, P61964, Q9UBL3 P62799, P06897, P02281, P84233 0.343
250 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 P62805, P68431, P04908, P06899 0.454
251 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P22579, P32561, Q12432, Q04779 P62799, P06897, P02281, P84233 0.254
252 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 DNA repair, Euchromatin-associated, RNA polymerases, Transcription-associated, Transcription factors 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, P02281, P84233 0.277
253 9MMN EM 3.60 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosomes, Left offset stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P62805, P68431, P06899 0.189
254 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, P02281, Q6AZJ8, P84233 0.422
255 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, P02281, P84233 0.398
256 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 P16104, P62805, P68431, P06899 0.321
257 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 P62805, P68431, P04908, P06899 0.141
258 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 O60814, Q71DI3, P62805, P04908 0.434
259 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, P0C0S8, P06899, P84233 0.397
260 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 A0A310TTQ1, A0A8J0U496, P62799, Q6AZJ8 0.299
261 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 Transcription-associated, Chromatin remodelers, ISWI P38144 P62799, P06897, P02281, P84233 0.435
262 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 DNA repair, Histone PTM erasers, Histone_deacetylation, Histone_deacetylation_H3K9, Transcription-associated Q8N6T7 P62799, P06897, P02281, P84233 0.434
263 9E2F EM 5.90 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 318 Cryo-EM structure of a di-nucleosome with a five base pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Q71DI3, P62805, P06899, P0C0S8 0.167
264 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P32561, P22579, Q12432, Q04779 P62799, P06897, P02281, P84233 0.311
265 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, P02281, P84233 0.356
266 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 P04908, P06899, P62805, Q92522, P68431 0.435
267 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_H2AK125_writer, DNA repair, Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Transcription-associated, Histone PTM writers Q99728, P0CG47 P62799, P06897, P02281, P84233 0.456
268 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 P0C0S5, P62805, P68431, Q16778 0.424
269 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 Transcription-associated, Chromatin remodelers, ISWI P38144 P62799, P06897, P02281, P84233 0.489
270 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 Q71DI3, Q99879, P62805, Q96KK5 0.524
271 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 Q71DI3, Q99879, P62805, Q96KK5 0.522
272 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 P62805, P68431, P04908, P06899 -
273 9MMK EM 3.20 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosome, Canonical (Class 1) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P62805, P68431, P06899 0.552
274 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P02281, P84233 0.217
275 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, P02281, P84233 0.282
276 9MLN EM 3.30 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 GammaH2AX containing nucleosome, Canonical (Class 1) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P62805, P68431, P06899 0.419
277 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, P02302, P02281, Q6AZJ8 0.387
278 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 P59259, Q9LD28, P59226, Q9LQQ4 0.424
279 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, P02281, P84233 0.434
280 8GUI EM 2.81 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1-nucleosome complex (Model I) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B E3 ubiquitin-protein ligation, Transcription-associated, Histone_ubiquitination_H2BK120_writer, Histone PTM writers Q5VTR2, O75150 P62805, P68431, P06899, P0C0S8 0.532
281 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 DNA repair, Histone_acetylation_writer, NuA4, Transcription-associated, Histone PTM writers Q12432 P62799, P06897, P02281, P84233 0.326
282 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 Q7Z2G1, P62805, P68431, P04908 0.398
283 8JH2 EM 5.70 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.145
284 8KB5 EM 2.26 2023-10-18 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Cryo-EM structure of the human nucleosome containing H3.8 Hirai, S., Kujirai, T., Akatsu, M., Ogasawara, M., Ehara, H., Sekine, S.I., Ohkawa, Y., Takizawa, Y., Kurumizaka, H. 10.1093/jb/mvad069 37757444 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 P06899, P62805, P84243, P04908 0.655
285 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 DNA repair, E3 ubiquitin-protein ligation, 2'3'-cGAMP, Antiviral defense, Synthesis of second messengers, Transcription-associated, Transcription factors Q8N884, Q6PJ21, Q15369, Q15370 Q71DI3, Q99877, P62805, Q96KK5, Q93079, Q99878 0.4
286 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 P62805, P68431, P04908, P06899 0.219
287 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 P04908, P06899, P62805, P68431, Q8CGP7 0.411
288 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 PTM readers, Histone_methylation_H3K36_reader O75475 P62799, P06897, P02281, P84233 0.484
289 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 Histone chaperones, Histone PTM erasers, Polycomb, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers Q92833, Q15022, Q15910, O75530, Q09028, Q6ZN18 P06897, P07305, P02281, P84233, P62799 0.261
290 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P22579, P32561, Q12432, Q04779 P62799, P02302, P06897, P02281 0.464
291 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, Q71DI3, P62805, P0C0S8 0.559
292 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 P62805, P68431, P04908, P06899 0.171
293 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, P02281, P84233 0.502
294 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 Ubiquitin, Histone_ubiquitination_reader, Polycomb, Histone PTM readers, Transcription-associated, Heterochromatin-associated Q8N488, P0CG48 P62799, P06897, P02281, P84233 0.382
295 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 P62805, Q16778, P68431, P04908 0.372
296 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 Q71DI3, Q6FI13, P62805, P06899 0.545
297 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers P61077, Q8IYW5, P62979 O60814, Q71DI3, P04908, P62805, P07305 0.237
298 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 P62805, P68431, P04908, P06899 0.345
299 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 P62805, P68431, P04908, P06899 0.164
300 6DZT EM 2.99 2019-05-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of nucleosome in complex with a single chain antibody fragment Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2019 scFv P84040, P84051, P02283, P02299 0.589
301 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 O60814, Q71DI3, P62805, P04908 0.462
302 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 P06899, S4RAZ3, P84233, P0C0S8, P62799 0.476
303 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.497
304 9K9L EM 3.66 2025-04-30 H3_H4_tetramer, H3_H4_tetramer 2 cenH3 canonical_H4 601 121 Cryo-EM structure of the human CENP-A-H4 octasome. Kawasaki, O., Takizawa, Y., Kiyokawa, I., Kurumizaka, H., Nozawa, K. 10.1111/gtc.70016 40129080 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 P62805, P49450 0.364
305 9L1X EM 2.69 2025-05-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 162 hDEK-nucleosome complex (conformation 1) Shen, Y., Liu, Y., Guo, M., Mao, S., Chen, R., Wang, M., Li, Z., Li, Y., Chen, W., Chen, F., Wu, B., Wang, C., Chen, W., Cui, H., Yuan, K., Huang, H. 10.1038/s41594-025-01559-9 40379883 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P06899, P62805, P84243, P04908 0.541
306 9LRW EM 3.04 2026-02-04 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 140 Cryo-EM structure of Fission yeast centromeric nucleosome Class 2 Xiong, Y., Jian, Y., Zhang, Y., Zhang, M., Zhang, X., Zhang, K., Fu, C., Tian, T., Zang, J. 10.1093/jmcb/mjaf056 41453208 Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Xenopus laevis 2026 Q9Y812, P09322, P04909, P04913 0.436
307 9MU4 EM 3.29 2025-02-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Structure of a native Drosophila melanogaster octameric nucleosome Venette-Smith, N.L., Vishwakarma, R.K., Dollinger, R., Schultz, J., Venkatakrishnan, V., Babitzke, P., Anand, G., Gilmour, D.S., Armache, J.-P., Murakami, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2025 P84040, P84051, P02283, P02299 0.442
308 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 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.518
309 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, P02281, Q6AZJ8, P84233 0.293
310 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, P0C0S8, P06899, P84233 0.471
311 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, Q71DI3, P62805, P0C0S8 0.65
312 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 Euchromatin-associated, Transcription-associated, Histone_methylation_H3K36_writer, Histone PTM writers O96028 P62799, P06897, P02281, Q92133 0.448
313 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 P62805, P68431, P04908, P06899 0.419
314 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 Cell cycle, Nuclear division P25171 P62799, P02281, Q6AZJ8, P84233 -
315 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P02281, P84233 0.167
316 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, P02281, P84233 0.235
317 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 Q7Z2G1, P62805, P68431, P04908 0.445
318 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, P02281, P84233 0.528
319 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, Q71DI3, P62805, P0C0S8 0.577
320 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 DNA repair, Histone PTM erasers, Histone_deacetylation, Histone_deacetylation_H3K9, Transcription-associated Q8N6T7 P62799, P06897, P02281, P84233 0.446
321 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 Q71DI3, P62805, P06899, P0C0S8 0.345
322 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, P02302, P06897, P02281 0.196
323 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Ubiquitin, Histone PTM writers Q8IYW5, P0CG47 P62805, P68431, P62807, P04908 0.455
324 8OW0 EM 3.40 2023-08-09 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601_modified 121 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Dendooven, T., Zhang, Z., Yang, J., McLaughlin, S.H., Schwab, J., Scheres, S.H.W., Yatskevich, S., Barford, D. 10.1126/sciadv.adg7480 37506202 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2023 Centromere-binding protein 1, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Inner kinetochore subunit CNN1, Inner kinetochore subunit AME1, Inner kinetochore subunit WIP1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2 Cell cycle, Kinetochore, CCAN, Centromere-associated, Transcription-associated, Nuclear division P17106, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P43618, P38313, Q2V2P8, Q12493, Q06162 P02309, P04911, P36012, P02293 0.2
325 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.476
326 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.496
327 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 E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer, Polycomb, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers P35226, Q99496 P62799, P06897, P02281, P84233 -
328 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, P02281, P84233 0.578
329 8SIY EM 2.90 2023-08-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome Sahu, S., Ekundayo, B.E., Kumar, A., Bleichert, F. 10.15252/embj.2023114654 37551430 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Leucine-rich repeat and WD repeat-containing protein 1, Origin recognition complex subunit 2 Heterochromatin-associated, DNA replication, ORC A0A140UHX1, Q75PQ8 P62799, P06897, P02281, P84233 0.497
330 8SKZ EM 3.50 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome Nartey, W., Williams, G.J. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera Heterochromatin-associated, Chromatin remodelers Q9XFH4 A0A8J1LTD2, P06897, P02281, P84233 0.458
331 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077 P62805, P68431, P04908, P06899 0.544
332 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077 P62805, P68431, P04908, P06899 0.535
333 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077, P0CG47 P62805, P68431, P04908, P06899 0.434
334 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077, P0CG47 P62805, P68431, P04908, P06899 0.405
335 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 Histone chaperones, Polycomb, Histone_methylation_H3K27_writer, Transcription-associated, Heterochromatin-associated, Histone PTM writers Q15022, Q15910, O75530, Q09028, Q6ZN18 P62799, P06897, P02281, P84233 0.163
336 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 DNA repair, Transcription-associated, Heterochromatin-associated, Histone_methylation_H4K20_writer, Histone PTM writers Q4FZB7 P62799, P06897, P02281, P84233 0.393
337 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, P02281, P84233 0.505
338 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 P04908, P06899, P10412, P62805, P68431 0.493
339 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, Q71DI3, P62805, P0C0S8 0.534
340 8WH5 EM 3.58 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Structure of DDM1-nucleosome complex in the apo state Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59259, Q9LD28, P59226 0.394
341 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 P62805, P68431, P04908, P06899 0.199
342 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 P62805, P68431, P04908, P06899 -
343 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 P62805, P68431, P04908, P06899 0.631
344 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 P62805, P68431, P04908, P06899 0.598
345 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 Q71DI3, Q6FI13, P62805, Q99879 0.573
346 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.512
347 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 PAF1C, Euchromatin-associated, Histone_methylation_H3K4_writer, RNA polymerases, Histone_ubiquitination_H2BK120_writer, Histone_methylation_H3K36_writer, Transcription-associated, Transcription factors, Histone PTM writers A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q96ST2, Q6PD62, Q92541, B7Z4W0, Q9GZS3, A0A2R8YHB3, P63272, Q9BYW2 A0A310TTQ1, P62799, P02281, P06897 0.237
348 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 P0C0S5, P62805, P68431, Q16778 0.448
349 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, P02281, P84233 0.608
350 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 P62805, P68431, P04908, P06899 0.35
351 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 Centromere-associated, Nuclear division, Kinetochore Q66LH7 P84040, P84051, P02283, P02299 -
352 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 P16104, P62805, P68431, P06899 0.215
353 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 repair, DNA modification P29372 P62799, P06897, P02281, P84233 0.466
354 7XSE EM 3.60 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 134 RNA polymerase II elongation complex transcribing a nucleosome (EC42) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P06899, P62805, P84243, P04908 0.238
355 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 DNA repair, Histone PTM erasers, Histone_deacetylation, Histone_deacetylation_H3K9, Transcription-associated Q8N6T7 P62799, P06899, P04908, P84233 0.493
356 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 DNA repair, Histone_acetylation_writer, Histone PTM erasers, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers Q04779, Q12432 P62799, P06897, P02281, P84233 0.434
357 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 P62805, P68431, P04908, P06899 0.569
358 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, Q71DI3, P62805, P04908 0.579
359 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 P62805, P68431, P04908, P06899 0.143
360 8QZM EM 3.10 2024-10-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome Wapenaar, H., Clifford, G., Rolls, W., Pasquier, M., Burdett, H., Zhang, Y., Deak, G., Zou, J., Spanos, C., Taylor, M.R.D., Mills, J., Watson, J.A., Kumar, D., Clark, R., Das, A., Valsakumar, D., Bramham, J., Voigt, P., Sproul, D., Wilson, M.D. 10.1038/s44319-024-00306-3 39528729 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA (cytosine-5)-methyltransferase 3A DNA modification Q9Y6K1 A0A7K7T3V7, P62805, P62807, P0C0S8 0.506
361 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 Euchromatin-associated, Cell cycle, RNA polymerases, Transcription-associated, Transcription factors 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 Q6NXT2, P62805, P06899, P0C0S8 0.037
362 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077 P62805, P68431, P04908, P06899 0.549
363 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Ubiquitin, Histone PTM writers Q8IYW5, P0CG47 P62805, P68431, P62807, P04908 0.432
364 8VMN EM 3.50 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K4me3 nucleosome bound to PRC2_AJ1-450 Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 Q71DI3, P62805, A0A8J1LZU9, Q6AZJ8 0.39
365 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 P62805, P68431, P04908, P06899 -
366 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 Q71DI3, P06899, P04908, P62805, P0C0S8, A0A9J8D176 0.547
367 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.535
368 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 chaperones, PAF1C, Euchromatin-associated, Histone_methylation_H3K4_writer, Cell cycle, RNA polymerases, Histone_ubiquitination_H2BK120_writer, Transcription-associated, Transcription factors, Histone PTM writers A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A310TTQ1, P62799, P02281, P06897 0.25
369 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, Histone PTM writers, Cell cycle P30260 P62805, Q6FI13, P68431, P33778 0.651
370 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 Transcription-associated, CHD, Chromatin remodelers P32657 P62799, P06897, P02281, P84233 0.295
371 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, P02281, P84233 0.454
372 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 O60814, A0A653DHJ5, P62805, P04908 0.406
373 9L22 EM 3.00 2025-05-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 172 hDEK-nucleosome complex (conformation 2) Shen, Y., Liu, Y., Guo, M., Mao, S., Chen, R., Wang, M., Li, Z., Li, Y., Chen, W., Chen, F., Wu, B., Wang, C., Chen, W., Cui, H., Yuan, K., Huang, H. 10.1038/s41594-025-01559-9 40379883 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P06899, P62805, P84243, P04908 0.442
374 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 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.49
375 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 Cell cycle, Transcription-associated, Heterochromatin-associated, Histone_methylation_H4K20_writer, Histone PTM writers, Nuclear division Q9NQR1 P62799, P06897, P02281, P84233 0.475
376 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_acetylation_writer, Euchromatin-associated, Cell cycle, NuA4, Transcription-associated, Histone PTM writers Q06337, P80428, P60010, P43572, P53201, P38811, Q08649, P38806, P47128 P62799, P06897, P02281, P84233 0.108
377 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 PTM erasers, SAGA, Histone_deubiquitination, Ubiquitin, Transcription-associated P50102, Q6WNK7, Q03067, P0CG47, P53165 P62799, P06897, P02281, P84233 -
378 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, Q71DI3, P62805, P0C0S8 0.537
379 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 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P62799, P02281, Q6AZJ8, P84233 0.356
380 6A5P EM 7.00 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 168 RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P62805, P84243, P04908 0.138
381 6BUZ EM 3.92 2017-12-20 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N Chittori, S., Hong, J., Saunders, H., Feng, H., Ghirlando, R., Kelly, A.E., Bai, Y., Subramaniam, S. 10.1126/science.aar2781 29269420 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 Maltose-binding periplasmic protein, Centromere protein N chimera P0AEX9 P06899, P62805, P04908, P49450 0.372
382 6C0W EM 4.00 2018-01-17 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 139 Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A Pentakota, S., Zhou, K., Smith, C., Maffini, S., Petrovic, A., Morgan, G.P., Weir, J.R., Vetter, I.R., Musacchio, A., Luger, K. 10.7554/eLife.33442 29280735 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 Centromere protein N Centromere-associated, CENP-A NAC/CAD, Nuclear division, Kinetochore Q96H22 Q93077, P62805, P62807, P49450 0.39
383 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, P02281, P84233 0.301
384 6INQ EM 6.90 2019-04-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 125 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P62805, P84243, P04908 0.149
385 6J4W EM 7.90 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 171 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, F2QTN1, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.123
386 6J50 EM 4.70 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.195
387 6K1I X-ray 2.75 2020-01-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601_modified 147 Human nucleosome core particle with gammaH2A.X variant Sharma, D., De Falco, L., Padavattan, S., Rao, C., Geifman-Shochat, S., Liu, C.F., Davey, C.A. 10.1038/s41467-019-13641-0 31848352 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P16104, P62805, P68431, P06899 -
388 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 Ubiquitin, COMPASS, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q03164, Q15291, P62979, P61964, Q9UBL3 P62799, P06897, P02281, P84233 0.461
389 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 P62805, P68431, P04908, P06899 0.085
390 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 P04908, P06899, P62805, P07305, P68431 -
391 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 P04908, P06899, P62805, P07305, P68431 -
392 6LTJ EM 3.70 2020-02-12 octamer 1 H3.3 canonical_H4 H2A.X canonical_H2B 601 119 Structure of nucleosome-bound human BAF complex He, S., Wu, Z., Tian, Y., Yu, Z., Yu, J., Wang, X., Li, J., Liu, B., Xu, Y. 10.1126/science.aaz9761 32001526 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4 Transcription-associated, Cell cycle, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785 P62799, Q6PI79, P02281, P06897 0.007
393 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 Transcription-associated, DNA replication, ORC P54784 P62799, P06897, P02281, P84233 -
394 6SE0 EM 3.80 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class 1 : CENP-A nucleosome Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P62807, Q6FI13, P62805, P49450 0.328
395 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 Transcription-associated, Cell cycle, RSC (SWI/SNF), Chromatin remodelers Q06168, P43609, P32832, Q03124, P25632, Q07979, Q9URQ5, Q02206, P32597, Q12406, Q05123, P53330 P62799, P06897, P02281, P84233 0.081
396 6X0N EM 10.00 2020-09-16 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Bilokapic, S., Suskiewicz, M.J., Ahel, I., Halic, M. 10.1038/s41586-020-2725-7 32939087 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2 Histone_PARylation_writer, DNA repair, Histone PTM writers Q9NWY4, Q9UGN5 P62799, P06897, P02281, P84233 0.113
397 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, Antiviral defense, Synthesis of second messengers Q8C6L5 P62807, Q71DI3, P62805, P0C0S8 0.483
398 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, Antiviral defense, Synthesis of second messengers Q8C6L5 P62807, Q71DI3, P62805, P0C0S8 0.474
399 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, Q71DI3, P04908, P10412, P62805 0.264
400 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077 P62805, P68431, P04908, P06899 0.547
401 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, P02281, Q6AZJ8, P84233 0.378
402 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.576
403 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 DNA repair, Histone chaperones, Euchromatin-associated, DNA replication, SPT4-SPT5 complex, RNA polymerases, FACT, Centromere-associated, Transcription-associated, Heterochromatin-associated, Transcription factors P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, Q04636, P32558, P32914, P27692 P62799, P06897, P02281, P84233 0.358
404 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 Transcription-associated, DNA replication, ORC P54784 P02309, P61830, P02294, P04912 0.319
405 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, Antiviral defense, Synthesis of second messengers Q8N884 O60814, Q71DI3, Q6FI13, P62805 0.195
406 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P02281, P84233 0.135
407 6SEG EM 3.10 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class1: CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P62807, Q6FI13, P62805, P49450 0.512
408 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, P02302, P02281, P0CH09 0.49
409 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q15291 P62799, P06897, P02281, P84233 0.332
410 6PWE EM 3.95 2019-08-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of nucleosome core particle Chittori, S., Hong, J., Bai, Y., Subramaniam, S. 10.1093/nar/gkz670 31402386 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2019 P84040, P84051, P02283, P02299 0.409
411 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, P04908, P62805, P68431, P49450 0.071
412 7PF4 EM 4.00 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 167 Nucleosome 3 of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P62805, P04908 0.274
413 6K1K X-ray 2.20 2020-01-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601L 145 Human nucleosome core particle with H2A.X S139E variant Sharma, D., De Falco, L., Padavattan, S., Rao, C., Geifman-Shochat, S., Liu, C.F., Davey, C.A. 10.1038/s41467-019-13641-0 31848352 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P16104, P62805, P68431, P06899 -
414 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, Q71DI3, P62805, P0C0S8 0.603
415 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 P62805, P68431, P04908, P06899 -
416 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, P02281, P84233 0.563
417 6J4Z EM 4.10 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Spt5 Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.244
418 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 Euchromatin-associated, Transcription-associated, RNA polymerases P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422 P62799, P06897, P02281, P84233 0.241
419 6J4Y EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.235
420 7PEV EM 6.00 2022-08-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 347 Nucleosome stack of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P62805, P04908 0.224
421 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, Q71DI3, P04908, P10412, P62805 0.329
422 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 Ubiquitin, CHD, Chromatin remodelers, Transcription-associated P0CG47, P32657 P02302, P06897, Q28D68, S4RAZ3, P62799 0.23
423 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.614
424 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, P02281, P84233 0.351
425 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, P0C0S8, P06899, P84233 0.476
426 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, P02281, P84233 0.188
427 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 O60814, Q71DI3, P62805, P04908 0.473
428 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, P02281, Q6AZJ8, P84233 0.209
429 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 P62805, P68431, P04908, P06899 0.256
430 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 P62805, P68431, P04908, P06899 -
431 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, P02281, P84233 0.395
432 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, Q71DI3, P04908, P10412, P62805 0.236
433 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, P02281, P84233 0.49
434 7XTI EM 3.90 2022-10-12 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 85 RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p DNA repair, Histone chaperones, Euchromatin-associated, DNA replication, SPT4-SPT5 complex, RNA polymerases, FACT, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P06899, P62805, P84243, P04908 0.223
435 7WLR EM 3.54 2022-07-13 octamer 1 H3.3 canonical_H4 H2A.X canonical_H2B 601 145 Cryo-EM structure of the nucleosome containing Komagataella pastoris histones Fukushima, Y., Hatazawa, S., Hirai, S., Kujirai, T., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1093/jb/mvac043 35485963 Komagataella pastoris Komagataella pastoris Komagataella pastoris Komagataella pastoris Xenopus laevis 2022 A0A1B2JA70, A0A1B2JD99, A0A1B2JB78, A0A1B2JBS1 0.45
436 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 P84040, P84051, P02283, P02299 0.202
437 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 P04908, P06899, P10412, P62805, P68431 0.492
438 7VBM EM 3.40 2022-01-19 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 126 The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv Hirai, S., Tomimatsu, K., Miyawaki-Kuwakado, A., Takizawa, Y., Komatsu, T., Tachibana, T., Fukushima, Y., Takeda, Y., Negishi, L., Kujirai, T., Koyama, M., Ohkawa, Y., Kurumizaka, H. 10.1093/nar/gkab1137 34929737 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2022 C0HKE1, Q9D2U9, P62806, A0A8X6EH29 0.506
439 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 P0C0S5, Q71DI3, P62805, P06899 0.532
440 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 P62805, P68431, P04908, P06899 0.386
441 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, P02281, P84233 0.587
442 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 P04908, P06899, P62805, P16402, P68431 -
443 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, Q71DI3, P04908, P10412, P62805 0.267
444 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 Transcription-associated, Cell cycle, RSC (SWI/SNF), Chromatin remodelers P32597, Q12406, Q05123, P53330 P62799, Q92133, P02281, P06897 -
445 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P62799, P06897, P02281, P84233 0.177
446 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, P02281, P84233 0.508
447 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, Antiviral defense, Synthesis of second messengers Q8C6L5 P62807, Q71DI3, P62805, P0C0S8 0.54
448 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 PTM erasers, Histone_deacetylation P53973, Q06623, Q06629 P06897, P02281, Q6AZJ8, P84233, P62799 0.189
449 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, Antiviral defense, Synthesis of second messengers Q8N884 P62805, P68431, P04908, P06899 0.225
450 7KBF EM 4.42 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.8 601L 172 H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) Arimura, Y., Shih, R.M., Froom, R., Funabiki, H. 10.1016/j.molcel.2021.08.010 34478647 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P02281, P84233, P62799, P15308, Q6DKE3 0.29
451 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, Q71DI3, P04908, P10412, P62805 0.217
452 6SE6 EM 3.50 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2 : CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 Centromere protein C Centromere-associated, CENP-A NAC/CAD, Nuclear division, Kinetochore Q03188 P62807, Q6FI13, P62805, P49450 0.416
453 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, Q71DI3, P04908, P10412, P62805 0.302
454 7PFF EM 4.30 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 167 Nucleosome 3 of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P62805, P04908 0.221
455 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 A8BUJ9, A8BHS7, A8BI78, E2RU29 0.427
456 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, Q71DI3, P04908, P10412, P62805 0.269
457 7SCY EM 4.10 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to single BRCT Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 Histone_PARylation_writer, DNA repair, Histone PTM writers P09874 P62805, P68431, P04908, P06899 0.273
458 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 Ubiquitin, COMPASS, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers B4DIJ7, P61964, Q9UBL3, Q15291, P0CG47, Q9C005 P62799, P06897, P02281, P84233 0.263
459 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, P02281, P84233 0.502
460 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 P02283, P02299, P84040, P84051, P02259 -
461 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, P02281, P84233 0.342
462 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, P02281, Q6AZJ8, P84233 0.198
463 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_H2AK125_writer, DNA repair, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Ubiquitin, Histone PTM writers, Transcription-associated P0CG47, Q99728 P62805, P68431, P04908, P06899 0.566
464 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 Transcription-associated, CHD, Chromatin remodelers P32657 P62799, P06897, P02281, P84233 -
465 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 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P62799, P06897, P02281, P84233 0.261
466 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 Transcription-associated, Cell cycle, RSC (SWI/SNF), Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P62799, P06897, P02281, P84233 0.086
467 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 repair, DNA modification P29372 P62799, P06897, P02281, P84233 0.515
468 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, P06897, P02281, None 0.329
469 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 P62805, P68431, P04908, P06899 0.227
470 7XSX EM 3.80 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 108 RNA polymerase II elongation complex transcribing a nucleosome (EC49) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p DNA repair, Histone chaperones, Euchromatin-associated, DNA replication, SPT4-SPT5 complex, RNA polymerases, FACT, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P06899, P62805, P84243, P04908 0.227
471 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 P62805, P68431, P04908, P06899 -
472 6QLD EM 4.15 2019-10-02 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 124 Structure of inner kinetochore CCAN-Cenp-A complex Yan, K., Yang, J., Zhang, Z., McLaughlin, S.H., Chang, L., Fasci, D., Ehrenhofer-Murray, A.E., Heck, A.J.R., Barford, D. 10.1038/s41586-019-1609-1 31578520 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2019 Inner kinetochore subunit MIF2, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Inner kinetochore subunit AME1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2 Cell cycle, Kinetochore, Nuclear division, Centromere-associated, CCAN P35201, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P38313, Q12493, Q06162 P02294, P02293, P04911, P36012, P02309 0.328
473 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 Q71DI3, Q99879, P62805, P0C0S8 0.57
474 6A5R EM 8.70 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 136 RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P62805, P84243, P04908 0.11
475 6A5U EM 7.60 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P62805, P84243, P04908 0.14
476 6E0C EM 2.63 2019-05-22 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 scFv P06899, P62805, P04908, P49450 0.59
477 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 Transcription-associated, CHD, Chromatin remodelers P32657 P62799, Q92133, A0A1L8G0X3, P06897 0.095
478 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q03164, Q15291, P61964, Q9UBL3 P62799, P06897, P02281, P84233 0.338
479 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 Transcription-associated, Chromatin remodelers, SWI/SNF P18480 P62799, P06897, P02281, P84233 0.513
480 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, P02281, P84233 0.294
481 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 A0A8T2P505, A0A8J1LTD2, P06897, P02281 -
482 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 P62805, P68431, P04908, P06899 0.32
483 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, P02281, P84233 -
484 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, P02281, P84233 -
485 8WH9 EM 3.31 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of DDM1-nucleosome complex in ADP-BeFx state Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59259, Q9LD28, P59226 0.336
486 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, Cell cycle, Ubiquitin, Histone_deubiquitination_H2AK119, Transcription-associated Q9Y5T5, P0CG47 P62805, O60814, P68431, P04908 0.306
487 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 repair, DNA modification O15527 P62807, Q71DI3, P62805, P0C0S8 0.359
488 6A5L EM 5.60 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P62805, P84243, P04908 0.182
489 6IR9 EM 3.80 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.264
490 8UX1 EM 2.50 2023-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle Huang, S.K., Rubinstein, J.L., Kay, L.E. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2023 GTP-binding nuclear protein Ran, Regulator of chromosome condensation Cell cycle P62826, P18754 P84040, P84051, P02283, P02299 0.609
491 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Ubiquitin, Histone PTM writers Q8IYW5, P0CG47 P62805, P68431, P62807, P04908 0.438
492 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 Q71DI3, Q6FI13, P62805, Q99879 0.598
493 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 P84040, P84051, P02283, P02299 0.39
494 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 Euchromatin-associated, Histone_methylation_H3K36_writer, Ubiquitin, Histone PTM writers, Transcription-associated P0CH09, G0S676 P62799, P02302, P02281, P0CH09 0.261
495 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, P02281, P84233 0.339
496 7D20 EM 3.00 2021-02-10 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 136 Cryo-EM structure of SET8-CENP-A-nucleosome complex Ho, C.H., Takizawa, Y., Kobayashi, W., Arimura, Y., Kimura, H., Kurumizaka, H. 10.26508/lsa.202000919 33574035 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Isoform 2 of N-lysine methyltransferase KMT5A Cell cycle, Transcription-associated, Heterochromatin-associated, Histone_methylation_H4K20_writer, Histone PTM writers, Nuclear division Q9NQR1 P06899, P62805, P04908, P49450 0.446
497 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, P04908, P62805, P07305, P68431 0.246
498 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 Transcription-associated, DNA replication, ORC P54784 P02309, P61830, P02294, P04912 0.311
499 7PEY EM 4.50 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 171 Nucleosome 3 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 O60814, Q71DI3, P62805, P04908 0.281
500 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers P61077, Q8IYW5, P62979 O60814, Q71DI3, P62805, P04908 0.443
501 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, Q71DI3, P62805, P0C0S8 0.384
502 9MLR EM 3.10 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 126 GammaH2AX containing nucleosome, Half-wrapped (Class 2) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P62805, P68431, P06899 0.511
503 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 P62805, Q16778, P68431, P04908 0.4
504 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, P61830, P02293 0.34
505 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 P62805, P68431, P04908, P06899 0.529
506 7WBX EM 4.00 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 150 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.298
507 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 P62805, P68431, P04908, P06899 0.232
508 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, Q71DI3, P62805, P0C0S8 0.581
509 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 PTM readers, Histone_methylation_H3K36_reader O75475 P62799, P06897, P02281, P84233 0.548
510 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 chaperones, PAF1C, Euchromatin-associated, Histone_methylation_H3K4_writer, Cell cycle, RNA polymerases, Histone_ubiquitination_H2BK120_writer, Transcription-associated, Transcription factors, Histone PTM writers A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A310TTQ1, P62799, P02281, P06897 0.256
511 9EOZ EM 3.10 2024-11-06 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 144 Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Ren, M., Gut, F., Fan, Y., Ma, J., Shan, X., Yikilmazsoy, A., Likhodeeva, M., Hopfner, K.P., Zhou, C. 10.1038/s41467-024-53811-3 39477986 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA repair, DNA modification O15527 Q93077, P62805, P84243, P62807 0.465
512 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.595
513 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, P02281, Q6AZJ8, P84233 0.493
514 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 P16104, P62805, P68431, P06899 0.3
515 9MLS EM 3.60 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 107 GammaH2AX containing nucleosome, Extended (Class 3) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P62805, P68431, P06899 0.413
516 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 O60814, Q71DI3, P62805, P04908 0.359
517 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 chaperones, PAF1C, Euchromatin-associated, Histone_methylation_H3K4_writer, Cell cycle, RNA polymerases, Histone_ubiquitination_H2BK120_writer, Histone_methylation_H3K36_writer, Transcription-associated, Transcription factors, Histone PTM writers A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 A0A310TTQ1, P62799, P02281, P06897 0.24
518 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 P62805, P0C5Z0, P68431, Q16778 0.365
519 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, P02281, P84233 -
520 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_acetylation_writer, Euchromatin-associated, Cell cycle, NuA4, Transcription-associated, Histone PTM writers Q08649, P43572, P38806, P47128 P62799, P06897, P02281, P84233 0.314
521 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, P02281, P84233 0.569
522 7XYF EM 3.80 2023-12-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome Nan, Z., Tao, J., Yangao, H. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2023 ATP-dependent helicase fft3 Heterochromatin-associated, Chromatin remodelers O42861 P84040, P84051, P02283, P02299 0.272
523 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 Q71DI3, P62805, P06899, P0C0S8 0.316
524 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, P02281, P84233 0.493
525 8WHA EM 4.05 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2 Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59259, Q9LD28, P59226 0.306
526 8KCB EM 3.17 2024-06-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 126 Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2 Zhang, H., Gu, Z., Zeng, Y., Zhang, Y. 10.1016/j.str.2024.05.013 38870940 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9FFC0, P59259, Q9LD28, P59226 0.38
527 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, P61830, P02293 0.399
528 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, Q71DI3, P62805, P0C0S8 0.405
529 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, Q71DI3, P62805, P0C0S8 0.297
530 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, Q71DI3, P62805, P0C0S8 0.366
531 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 P62805, P68431, P62807, P04908 0.43
532 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
533 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.559
534 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 P62805, P68431, P04908, P06899 0.321
535 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 P62805, P68431, P04908, P06899 0.293
536 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, P02281, P84233 0.581
537 9J0O EM 3.30 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 191 Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RPB12, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, Transcription-associated, Transcription factors, RNA polymerases A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P06899, P62805, P84243, P04908 0.313
538 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
539 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 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.282
540 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.477
541 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, P02281, P84233 0.515
542 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 Ubiquitin, Histone PTM erasers, Polycomb, Transcription-associated, Heterochromatin-associated, Histone_deubiquitination_H2AK119 Q92560, Q8IXJ9, P0CG48 P62799, P06897, P02281, P84233 0.383
543 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, P68431, P62807, Q93077 0.554
544 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 DNA repair, Histone_acetylation_writer, NuA4, Transcription-associated, Histone PTM writers Q12432 P62799, P06897, P02281, P84233 0.572
545 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 Ubiquitin, DNA repair, Telomere-associated, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_methylation_H4K20_reader Q12888, P0CG47 P16104, P62805, O60814, P68431 0.424
546 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, Q71DI3, P62805, P0C0S8 0.474
547 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 Telomere-associated, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457 P62799, P06897, P02281, P84233 0.535
548 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 SWR1 (INO80), INO80, Euchromatin-associated, SRCAP (INO80), Chromatin remodelers, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P61830, P04912, P02293 0.185
549 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 Euchromatin-associated, Transcription-associated, Histone_methylation_H3K4_writer, Histone PTM writers O00255 P62799, P06897, P02281, P84233 0.459
550 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 DNA repair, Transcription-associated, Heterochromatin-associated, Histone_methylation_H4K20_writer, Histone PTM writers Q4FZB7 P62805, O60814, P68431, P04908 0.456
551 8KCC EM 3.10 2024-06-26 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 150 Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2 Zhang, H., Gu, Z., Zeng, Y., Zhang, Y. 10.1016/j.str.2024.05.013 38870940 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9FFC0, P59259, P59226, Q9FJE8 0.387
552 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 P62805, P68431, P04908, P06899 0.404
553 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P32561, P22579, Q12432, Q04779 P62799, P06897, P02281, P84233 0.324
554 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, P68431, P62807, Q93077 0.494
555 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 PTM readers, Histone_methylation_H3K36_reader O75475 P62799, P06897, P02281, P84233 0.521
556 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 SWR1 (INO80), INO80, Euchromatin-associated, SRCAP (INO80), Chromatin remodelers, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P61830, P04912, P02293 0.363
557 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 A0A310TTQ1, P06897, P02281, P84233, P62799 0.551
558 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077 P62805, P68431, P04908, P06899 0.526
559 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
560 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_ubiquitination_H2BK120_reader, Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer Q8TEK3, P0CG47 P62799, P06897, P02281, P84233 0.38
561 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_ubiquitination_H2BK120_reader, Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer Q8TEK3, J3QS39 P62799, P06897, P02281, P84233 0.356
562 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, Antiviral defense, Synthesis of second messengers Q8C6L5 P62807, Q71DI3, P62805, P0C0S8 0.196
563 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, Histone chaperones, DNA replication, CAF-1 Q13111, Q13112 P62805, P68431 0.189
564 7XT7 EM 4.20 2022-10-12 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p DNA repair, Histone chaperones, Euchromatin-associated, DNA replication, SPT4-SPT5 complex, RNA polymerases, FACT, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, F2QPX0, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P06899, P62805, P84243, P04908 0.207
565 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_ubiquitination_H2BK120_reader, Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer Q8TEK3, P0CG47 O60814, Q71DI3, P62805, P04908 0.514
566 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_ubiquitination_H2BK120_reader, Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer Q8TEK3, P0CG47 O60814, Q71DI3, P62805, P04908 0.571
567 7WBW EM 7.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.137
568 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, P61830, P02294, P04912 -
569 7WBV EM 4.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.267
570 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, Q71DI3, P04908, P10412, P62805 0.208
571 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, P02281, Q6AZJ8, P84233 0.494
572 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 Ubiquitin, Histone PTM writers, Telomere-associated, Histone_methylation_H3K79_writer Q04089, P0CG48 P62799, P06897, P02281, P84233 0.473
573 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 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P62799, P06897, P02281, P84233 0.349
574 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 P04908, P06899, P62805, P07305, P68431 0.489
575 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, P68431, Q16778 0.311
576 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q03164, Q15291, P61964, Q9UBL3 P62799, P06897, P02281, P84233 0.31
577 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 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P62799, P06897, P02281, P84233 0.372
578 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 Ubiquitin, DNA repair, Telomere-associated, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_methylation_H4K20_reader Q12888, P0CG47 P62799, P62807, P0C0S8, P84233 0.301
579 5HQ2 X-ray 4.50 2016-03-23 split_octasome 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 73 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Girish, T.S., McGinty, R.K., Tan, S. 10.1016/j.jmb.2016.02.025 26953260 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 Guanine nucleotide exchange factor SRM1, N-lysine methyltransferase SETD8 Cell cycle, Transcription-associated, Heterochromatin-associated, Histone_methylation_H4K20_writer, Histone PTM writers, Nuclear division P21827, Q9NQR1 P62799, P06897, P02281, P84233 -
580 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 chaperones, PAF1C, Euchromatin-associated, Histone_methylation_H3K4_writer, Cell cycle, RNA polymerases, Histone_ubiquitination_H2BK120_writer, Transcription-associated, Transcription factors, Histone PTM writers A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q6PD62, Q92541, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P62799, A0A8J1LZU9, Q6AZJ8, P84233 0.231
581 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, P02281, P84233 0.186
582 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.458
583 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 PTM readers, Histone_methylation_H3K36_reader O75475 P62799, P06897, P02281, P84233 0.399
584 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 P16104, P62805, P68431, P06899 0.185
585 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, Q71DI3, P62805, P0C0S8 0.628
586 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 P62805, P68431, P04908, P06899 0.242
587 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 P62805, P68431, P04908, P06899 0.218
588 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, P02281, Q6AZJ8, P84233 0.167
589 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.532
590 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, P02281, Q6DKE3, P84233 0.489
591 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 Transcription-associated, Chromatin remodelers, ISWI P38144 A0A310TTQ1, P06897, A0A8J1LTD2, P02281 0.566
592 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 Centromere-associated, CBF3, Nuclear division, Kinetochore P40969 P02309, P04911, P61830, P02293 0.3
593 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 P62805, P68431, P04908, P06899 0.19
594 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, O60814, P68431, Q7L7L0 0.703
595 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, P02281, Q6AZJ8, P84233 0.591
596 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 P04908, P06899, P10412, P62805, P68431 0.527
597 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, Histone chaperones, DNA replication, CAF-1 Q13111, Q13112 P62805, P68431 0.301
598 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 Histone PTM erasers, Polycomb, Ubiquitin, Heterochromatin-associated, Histone_deubiquitination_H2AK119, Transcription-associated Q92560, P0CG47, Q8IXJ9 P10412, P62805, P68431, P20671, Q16778 0.435
599 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, Histone chaperones, DNA replication, CAF-1 Q13111, Q13112 P62805, P68431 0.304
600 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q15291, P61964, Q03164 P62799, P06897, P02281, P84233 0.26
601 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 Q71DI3, Q99879, P62805, P0C0S8 0.488
602 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 P62805, Q16778, P68431, P04908 0.278
603 9LRV EM 2.99 2026-02-04 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 144 Cryo-EM structure of Fission yeast centromeric nucleosome Class 1 Xiong, Y., Jian, Y., Zhang, Y., Zhang, M., Zhang, X., Zhang, K., Fu, C., Tian, T., Zang, J. 10.1093/jmcb/mjaf056 41453208 Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Xenopus laevis 2026 Q9Y812, P09322, P04909, P04913 0.508
604 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 Transcription-associated, Chromatin remodelers, SWI/SNF P51532 P62799, P06897, P02281, P84233 0.549
605 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 Transcription-associated, Chromatin remodelers, ISWI P38144 P62799, P06897, P02281, P84233 0.44
606 7XD0 EM 3.48 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 cryo-EM structure of H2BK34ub nucleosome Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Ubiquitin-60S ribosomal protein L40 Ubiquitin P62987 Q71DI3, P62805, P04908, Q2M2T1 0.457
607 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, P02281, P84233 0.55
608 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, Cell cycle, Transcription factors, Transcription-associated P04637 P62805, P68431, P04908, P06899 0.146
609 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 SWR1 (INO80), INO80, Euchromatin-associated, Chromatin remodelers, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P04911, P61830, P02293 0.372
610 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 DNA repair, CHD, Chromatin remodelers Q86WJ1 P62799, P06897, P02281, P84233 0.483
611 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 DNA repair, Euchromatin-associated, Cell cycle, RNA polymerases, Transcription-associated, Transcription factors 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, P02281, P84233 0.187
612 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 PTM readers, Histone_methylation_H3K36_reader O75475 P62799, P06897, P02281, P84233 0.392
613 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, P02281, P84233 0.356
614 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 Euchromatin-associated, Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P04908, P06899, P62805, P16403, P68431 0.16
615 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P22579, P32561, Q12432, Q04779 P62799, P06897, P02281, P84233 0.44
616 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 DNA repair, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2BK120_writer, Transcription-associated, Histone PTM writers O75150, Q5VTR2, P49459 P62805, O60814, P68431, P04908 0.461
617 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P32561, P22579, Q12432, Q04779 P62799, P06897, P02281, P84233 0.373
618 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 P04908, P06899, P62805, P16403, P68431 0.352
619 8PKI EM 2.58 2024-02-28 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 137 Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 Kobayashi, W., Sappler, A.H., Bollschweiler, D., Kummecke, M., Basquin, J., Arslantas, E.N., Ruangroengkulrith, S., Hornberger, R., Duderstadt, K., Tachibana, K. 10.1038/s41594-024-01239-0 38409506 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2024 Nuclear receptor subfamily 5 group A member 2 Transcription-associated, Transcription factors O00482 P62806, P84244, Q6ZWY9, C0HKE3 0.572
620 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 A2Y533, A2WKP5, None, A2YMC6 0.401
621 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 SWR1 (INO80), INO80, Euchromatin-associated, Chromatin remodelers, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P04911, P61830, P02293 0.195
622 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, Q71DI3, P62805, P0C0S8 0.385
623 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, Q71DI3, P62805, P0C0S8 0.454
624 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_H2AK125_writer, DNA repair, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Transcription-associated, Histone PTM writers P38398, Q99728, P61077 O60814, Q71DI3, P62805, P04908 0.352
625 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P02281, Q6AZJ8, P84233 0.499
626 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 SWR1 (INO80), INO80, Euchromatin-associated, SRCAP (INO80), Chromatin remodelers, Transcription-associated Q05471, Q03388, Q12509, Q03433, Q03940, Q12464, P31376 P04911, A0A0B4KFZ9, P02293, P02299 0.191
627 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 P04908, P06899, P62805, Q92522, P68431 -
628 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 Euchromatin-associated, Transcription-associated, Histone_methylation_H3K36_writer, Histone PTM writers G0S676 P62799, P02302, P02281, P0CH09 0.364
629 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, P68431, P62807, Q93077 0.556
630 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 Transcription-associated, DNA modification Q9Y6K1, Q9UBC3 P62799, P06897, P02281, P84233 0.403
631 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, Euchromatin-associated, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3, Q9C005 P62799, P06897, P02281, P84233 0.188
632 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 DNA repair, Euchromatin-associated, RNA polymerases, Mediator, Transcription-associated, Transcription factors 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, P02281, P84233 0.222
633 6J51 EM 4.20 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Euchromatin-associated, SPT4-SPT5 complex, RNA polymerases, Transcription-associated, Transcription factors C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P06899, P62805, P84243, P04908 0.23
634 6SEF EM 3.70 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2C : CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 Centromere protein C Centromere-associated, CENP-A NAC/CAD, Nuclear division, Kinetochore Q03188 P62807, Q6FI13, P62805, P49450 0.372
635 6UPH EM 2.70 2019-11-06 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 119 Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution Migl, D., Kschonsak, M., Arthur, C.P., Khin, Y., Harrison, S.C., Ciferri, C., Dimitrova, Y.N. 10.1016/j.str.2019.12.002 32004465 Saccharomyces cerevisiae Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Xenopus laevis 2019 Q6CK60, Q6CK59, P36012, Q6CMU6 0.623
636 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 Euchromatin-associated, Histone_methylation_H3K4_writer, Histone_methylation_H3K27_writer, Transcription-associated, Histone PTM writers Q9BZ95 P62799, P06897, P02281, Q92133 0.507
637 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 Euchromatin-associated, Histone_methylation_H3K4_writer, Histone_methylation_H3K27_writer, Transcription-associated, Histone PTM writers Q9BZ95 P62799, P06897, P02281, Q92133 0.464
638 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, P02302, P0C0S6, P02281 0.391
639 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, Q71DI3, P04908, P10412, P62805 0.27
640 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, Antiviral defense, Synthesis of second messengers Q8N884 Q16777, Q71DI3, P62805, O60814 0.43
641 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 A0A310TTQ1, A0A1L8FQA5, P62799, Q6AZJ8 0.424
642 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 O60814, Q71DI3, P62805, P04908 0.068
643 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 P62805, P68431, P04908, P06899 0.451
644 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) Ubiquitin, Histone_ubiquitination_reader, Polycomb, Histone PTM readers, Transcription-associated, Heterochromatin-associated Q8N488, P0CG47 P84040, P84051, P02283, P02299 0.465
645 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 P62799, P06897, P02281, P84233 0.303
646 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 P62805, Q16778, P68431, P04908 -
647 9J0N EM 3.40 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 167 Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RPB12, Transcription elongation factor A protein 1, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, Transcription-associated, Transcription factors, RNA polymerases A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, P23193, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P06899, P62805, P84243, P04908 0.316
648 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 PBAF (SWI/SNF), Cell cycle, SWI/SNF, Chromatin remodelers, Transcription-associated P51532, P60709, O96019, Q68CP9, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q8WUB8, Q9NPI1, Q86U86 P62805, P68431, P62807, Q93077 0.172
649 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P32561, P22579, Q12432, Q04779 A0A310TTQ1, P62799, P02281, Q6AZJ8 0.376
650 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 P62805, P68431, P04908, P06899 0.404
651 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077 P62805, P68431, P04908, P06899 0.352
652 9B3P EM 3.00 2024-06-12 octamer 1 H3.3 canonical_H4 H2A.Z canonical_H2B 601 128 The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome Jung, H., Sokolova, V., Lee, G., Stevens, V.R., Tan, D. 10.3390/epigenomes8020021 38920622 Homo sapiens Xenopus laevis Mus musculus Xenopus laevis Xenopus laevis 2024 P62799, P0C0S6, P84243, P02281 0.455
653 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, P0C0S5, P02281, P84233 0.508
654 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 SWR1 (INO80), INO80, Euchromatin-associated, SRCAP (INO80), Chromatin remodelers, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P04911, P61830, P02293 0.193
655 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, P02281, Q6DKE3, P84233 0.445
656 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, Q71DI3, P62805, P0C0S8 0.526
657 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 A0A8C1JQV0, P06899, H2QSF5, A0A2Y9FT95, P68431 -
658 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 P62799, P06897, P02281, P84233 0.368
659 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 P62805, P68431, P04908, P06899 0.24
660 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 A0A310TTQ1, A0A8J0U496, P62799, Q6AZJ8 0.241
661 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers P61077, Q8IYW5, P62979 O60814, Q71DI3, P62805, P04908 0.391
662 7XYG EM 4.20 2023-12-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome Nan, Z., Tao, J., Yangao, H. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2023 ATP-dependent helicase fft3 Heterochromatin-associated, Chromatin remodelers O42861 P84040, P84051, P02283, P02299 0.219
663 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 P62805, P68431, P33778, P04908 -
664 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 Ubiquitin, DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077, P0CG47 P62805, P68431, P04908, P06899 0.443
665 8VOB EM 3.10 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis 2025 Q71DI3, P62805, P02281, P0C0S8 0.375
666 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.456
667 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 DNA repair, Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_writer, Histone PTM readers, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_reader, Transcription-associated, Histone PTM writers Q8IYW5, P61077 P62805, P68431, P04908, P06899 0.452
668 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, P02281, P84233 0.519
669 7ON1 EM 3.35 2021-07-07 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 123 Cenp-A nucleosome in complex with Cenp-C Yan, K., Yang, J., Zhang, Z., Barford, D. 0 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2021 BJ4_G0006610.mRNA.1.CDS.1 Cell cycle, Kinetochore, Nuclear division, Centromere-associated, CCAN P35201 P02309, P04911, P36012, P02293 0.47
670 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 A0A310TTQ1, P62799, P02281, P06897 -
671 9MU5 EM 6.30 2025-02-19 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Structure of a native Drosophila melanogaster hexameric nucleosome Venette-Smith, N.L., Vishwakarma, R.K., Dollinger, R., Schultz, J., Venkatakrishnan, V., Babitzke, P., Anand, G., Gilmour, D.S., Armache, J.-P., Murakami, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2025 P84040, P84051, P02283, P02299 0.206
672 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P22579, P32561, Q12432, Q04779 P62799, P06897, P02281, P84233 0.067
673 9R1D EM 3.21 2026-01-28 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 115 Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei Deak, G., Burdett, H., Watson, J.A., Wilson, M.D. 10.1016/j.str.2026.01.008 41709455 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Xenopus laevis 2026 Q57YA3, Q587H6, Q387X7, Q389T1 0.463
674 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 DNA repair, Telomere-associated, Histone_acetylation_writer, Histone PTM erasers, Cell cycle, Histone_deacetylation, NuA4, Transcription-associated, Rpd3, Histone PTM writers P32561, P22579, Q12432, Q04779 P62799, P06897, P02281, P84233 0.35
675 9J0P EM 3.30 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 191 Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RPB12, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, Transcription-associated, Transcription factors, RNA polymerases A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P06899, P62805, P84243, P04908 0.311
676 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 PTM readers, Histone_methylation_H3K36_reader O75475 P62799, P06897, P02281, P84233 0.304
677 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, P02281, P84233 0.536
678 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
679 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 P62805, Q16778, P68431, P04908 0.388
680 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, Q71DI3, P62805, P0C0S8 0.47
681 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, P02281, P84233 0.554
682 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 Transcription-associated, CHD, Chromatin remodelers P32657 P62799, P06897, P02281, P84233 0.465
683 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 P59259, P59226, Q9C944, Q9LQQ4 0.464
684 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, P02281, P84233 0.643
685 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 P16104, P62805, P68431, P06899 0.234
686 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 Transcription-associated, Chromatin remodelers, SWI/SNF O60264 P62799, P06897, P02281, P84233 0.53
687 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 O23629, P59259, P59226, Q9LHQ5 0.545