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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 10YH EM 2.90 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite) Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q96KK5, Q71DI3, P62805, Q99879 0.522
1 10YI EM 2.90 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite) Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q96KK5, Q71DI3, P62805, Q99879 0.524
2 9GCG EM 3.43 2025-08-13 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 152 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Aggarwal, P., Sharma, M., Hopfner, K.P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, INO80 complex subunit B, INO80 complex subunit C, Actin-related protein 5 Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9C086, Q6PI98, Q9H9F9 P68431, P62805, Q16778, P0C0S5 0.424
3 7E8I EM 3.10 2021-06-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Dai, L., Dai, Y., Han, J., Huang, Y., Wang, L., Huang, J., Zhou, Z. 10.1016/j.molcel.2021.05.010 34102105 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 BRCA1-associated RING domain protein 1, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Ubiquitin, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair Q99728, P0CG47 P06897, P84233, P62799, P02281 0.456
4 8KD6 EM 3.07 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.311
5 8F86 EM 3.10 2023-04-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 SIRT6 bound to an H3K9Ac nucleosome Wang, Z.A., Markert, J.W., Whedon, S.D., Yapa Abeywardana, M., Lee, K., Jiang, H., Suarez, C., Lin, H., Farnung, L., Cole, P.A. 10.1021/jacs.2c13512 36930461 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P06897, P84233, P62799, P02281 0.434
6 9RZC EM 3.66 2025-09-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16 Transcription-associated, Histone PTM writers, Histone_methylation_H3K36_writer, Histone chaperones, FACT, DNA replication, DNA repair, Euchromatin-associated Q9BYW2, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.434
7 9Q8X EM 2.94 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 151 Ku70/80 bound to a 153 bp H2AX nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P16104, P68431, P62805, P06899 0.321
8 9IPU EM 4.30 2024-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601L 170 cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Shi, Q., Deng, Z., Zhang, L., Tong, Z., Li, J.B., Chu, G.C., Ai, H., Liu, L. 10.1002/anie.202413651 39363740 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair P61077, Q8IYW5, P62979 P07305, Q71DI3, O60814, P04908, P62805 0.237
9 8XBU EM 4.24 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.171
10 8TOF EM 2.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 176 Rpd3S bound to an H3K36Cme3 modified nucleosome Markert, J.W., Vos, S.M., Farnung, L. 10.1038/s41467-023-43968-8 38065958 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Rco1, histone N-terminal tail Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P02302, P06897, P62799, P02281 0.464
11 8OL1 EM 3.50 2024-02-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Xu, P., Liu, Y., Liu, C., Guey, B., Li, L., Melenec, P., Ricci, J., Ablasser, A. 10.1038/s41586-024-07112-w 38418882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Cyclic GMP-AMP synthase, SPRY domain-containing SOCS box protein 3, Elongin-C, Elongin-B Transcription factors, Transcription-associated, E3 ubiquitin-protein ligation, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884, Q6PJ21, Q15369, Q15370 Q99877, Q96KK5, Q99878, Q71DI3, Q93079, P62805 0.4
12 8HXZ EM 3.40 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Cryo-EM structure of Eaf3 CHD in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, DNA repair Q12432 P06897, P84233, P62799, P02281 0.326
13 7ZSB EM 6.60 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 219 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription factors, RNA polymerases, Transcription-associated, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P06897, P84233, P62799, P02281 0.277
14 7YI5 EM 3.96 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.254
15 7U50 EM 3.40 2022-09-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Weaver, T.M., Hoitsma, N.M., Spencer, J.J., Gakhar, L., Schnicker, N.J., Freudenthal, B.D. 10.1038/s41467-022-33057-7 36104361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-(apurinic or apyrimidinic site) endonuclease DNA repair P27695 Q71DI3, P62807, P62805, P0C0S8 0.415
16 7SCZ EM 3.50 2022-01-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to multiple BRCTs Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 Histone_PARylation_writer, DNA repair, Histone PTM writers P09874 P04908, P68431, P62805, P06899 0.425
17 6ZHY EM 3.00 2020-12-23 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class. Lehmann, L.C., Bacic, L., Hewitt, G., Brackmann, K., Sabantsev, A., Gaullier, G., Pytharopoulou, S., Degliesposti, G., Okkenhaug, H., Tan, S., Costa, A., Skehel, J.M., Boulton, S.J., Deindl, S. 10.1016/j.celrep.2020.108529 33357431 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.516
18 7JZV EM 3.90 2021-02-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Witus, S.R., Burrell, A.L., Farrell, D.P., Kang, J., Wang, M., Hansen, J.M., Pravat, A., Tuttle, L.M., Stewart, M.D., Brzovic, P.S., Chatterjee, C., Zhao, W., DiMaio, F., Kollman, J.M., Klevit, R.E. 10.1038/s41594-020-00556-4 33589814 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 BRCA1,Ubiquitin-conjugating enzyme E2 D3, BRCA1-associated RING domain protein 1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair P38398, Q99728 O60814, Q71DI3, P62805, Q6FI13 0.313
19 7YI4 EM 3.96 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.23
20 9QMS EM 5.00 2026-01-14 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 141 DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.168
21 9R2Q EM 3.20 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Chakraborty, D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.361
22 9Q9F EM 4.54 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 129 DNA-PK bound to a 153 bp H2AX nucleosome model 1 Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.215
23 9KQO EM 3.48 2025-12-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deng, Z., Tao, S., Du, Y., Li, Y., Zhang, L., Shi, Q., Du, X., Sun, M., Tong, Z., Pan, M., Liu, L., Ai, H. 10.1038/s41589-025-02109-6 41495224 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 E3 ubiquitin-protein ligase BRE1B, Polyubiquitin-B, E3 ubiquitin-protein ligase BRE1A, Ubiquitin-conjugating enzyme E2 A Transcription-associated, Histone PTM writers, Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2BK120_writer, DNA repair O75150, J3QS39, Q5VTR2, P49459 P62805, O60814, P04908, A0A653DHJ5 0.406
24 8TXV EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P0CG47 P04908, P68431, P62805, P62807 0.432
25 8SMX EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.549
26 8JNF EM 6.91 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 The cryo-EM structure of the RAD51 filament bound to the nucleosome Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.143
27 8IHM EM 3.58 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Eaf3 CHD domain bound to the nucleosome Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. 10.1038/s41422-023-00884-2 37845487 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Rco1-ABR, Chromatin modification-related protein EAF3 Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair Q04779, Q12432 P06897, P84233, P62799, P02281 0.434
28 8G57 EM 3.07 2023-04-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Structure of nucleosome-bound Sirtuin 6 deacetylase Chio, U.S., Rechiche, O., Bryll, A.R., Zhu, J., Leith, E.M., Feldman, J.L., Peterson, C.L., Tan, S., Armache, J.P. 10.1126/sciadv.adf7586 37058572 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P06899, P04908, P84233, P62799 0.493
29 7XFJ EM 3.00 2023-11-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-3-methyladenine glycosylase DNA modification, DNA repair P29372 P06897, P84233, P62799, P02281 0.466
30 7JOA EM 3.30 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 2:1 cGAS-nucleosome complex Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q. 10.1126/science.abd0609 32913000 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.474
31 7JO9 EM 3.30 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 1:1 cGAS-nucleosome complex Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q. 10.1126/science.abd0609 32913000 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.483
32 6X0N EM 10.00 2020-09-16 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Bilokapic, S., Suskiewicz, M.J., Ahel, I., Halic, M. 10.1038/s41586-020-2725-7 32939087 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2 Histone_PARylation_writer, DNA repair, Histone PTM writers Q9NWY4, Q9UGN5 P06897, P84233, P62799, P02281 0.113
33 8TXW EM 3.60 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P0CG47 P04908, P68431, P62805, P62807 0.455
34 8OF4 EM 2.94 2023-08-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome Bound human SIRT6 (Composite) Smirnova, E., Bignon, E., Schultz, P., Papai, G., Ben Shem, A. 10.7554/eLife.87989 38415718 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P06897, P84233, P62799, P02281 0.446
35 8XBT EM 4.12 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.199
36 8W9D EM 3.90 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Wang, C., Chu, C., Guo, Z., Zhan, X. 10.1126/sciadv.adk7678 38598631 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Unclear peptide Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 O60814, P04908, P68431, P62805 0.263
37 8T9H EM 3.37 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 99 Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. 10.1016/j.molcel.2023.07.020 37595555 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 P06897, P84233, P62799, P02281 0.393
38 8SNA EM 4.00 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.405
39 8SN6 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.434
40 8SMZ EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.535
41 8SMY EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.544
42 8KD5 EM 2.90 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.378
43 8HAG EM 3.20 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.29
44 7YRG EM 4.20 2023-12-13 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 histone methyltransferase Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. 10.1016/j.molcel.2023.07.001 37536340 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 P84233, P02281, P62799, P0C0S5 0.227
45 7XFM EM 3.10 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-3-methyladenine glycosylase DNA modification, DNA repair P29372 P06897, P84233, P62799, P02281 0.466
46 6R8Z EM 3.90 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP_THF2(-1)-UV-DDB Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.307
47 6R8Y EM 4.30 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.313
48 6ZHX EM 2.50 2020-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class. Lehmann, L.C., Bacic, L., Hewitt, G., Brackmann, K., Sabantsev, A., Gaullier, G., Pytharopoulou, S., Degliesposti, G., Okkenhaug, H., Tan, S., Costa, A., Skehel, J.M., Boulton, S.J., Deindl, S. 10.1016/j.celrep.2020.108529 33357431 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.625
49 9R2P EM 4.18 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Na, N.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.196
50 6X5A EM 4.36 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. 10.1038/s41586-020-2749-z 32911481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.265
51 9S0U EM 6.72 2025-09-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 175 State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Histone-lysine N-methyltransferase SETD2, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit SPT16 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A8D1KNW4, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q9BYW2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.108
52 9JAO EM 3.10 2025-04-30 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 104 The structure of SMARCAD1 bound to the hexasome in the presence of ADP-BeFx Hu, P., Sun, J., Sun, H., Chen, K., Sia, Y., Xia, X., Xi, Q., Chen, Z. 10.1038/s41586-025-09100-0 40468067 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 Heterochromatin-associated, SWI/SNF, DNA repair, Chromatin remodelers Q9H4L7 A0A310TTQ1, P06897, P62799, P02281 0.445
53 9DWM EM 4.20 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 126 DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.31
54 9DWG EM 3.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite) Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.364
55 9CAN EM 3.30 2025-07-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 S.c INO80 in complex with Xenopus 0/40 nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 A0A310TTQ1, A0A8J1LTD2, P02281, P06897 0.36
56 9C9S EM 3.09 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 147 S.c INO80 in complex with S.c 0/40 nucleosome, Class 1 Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62799, P02293, P04911, P61830 0.424
57 8X7K EM 3.27 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair P61077, Q8IYW5 O60814, Q71DI3, P04908, P62805 0.423
58 8VX6 EM 3.20 2024-10-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Human OGG1 bound at the nucleosomal DNA entry site You, Q., Feng, X., Cai, Y., Baylin, S.B., Li, H. 10.1038/s42003-024-06919-7 39341999 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 N-glycosylase/DNA lyase DNA modification, DNA repair O15527 P06897, P84233, P62799, P02281 0.424
59 8SN5 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.41
60 8JNE EM 4.68 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.13
61 8JHF EM 3.68 2023-11-15 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 160 Native SUV420H1 bound to 167-bp nucleosome Lin, F., Zhang, R., Shao, W., Lei, C., Ma, M., Zhang, Y., Wen, Z., Li, W. 10.1038/s41421-023-00620-5 38052811 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 O60814, P68431, P62805, P0C0S5 0.433
62 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 Histone chaperones, DNA replication, CAF-1, DNA repair Q13111, Q13112 P68431, P62805 0.166
63 8IHT EM 3.72 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Rpd3S bound to the nucleosome Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. 10.1038/s41422-023-00884-2 37845487 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, RCO1 isoform 1, Chromatin modification-related protein EAF3 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q04779, Q12432 P06897, P84233, P62799, P02281 0.345
64 8HY0 EM 3.10 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.463
65 8HE5 EM 6.95 2023-07-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, DNA repair protein Transcription factors, Transcription-associated, RNA polymerases, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R198 P04908, P68431, P62805, P06899 0.105
66 8HAH EM 3.90 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 164 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.159
67 7ENN EM 2.80 2021-07-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The structure of ALC1 bound to the nucleosome Wang, L., Chen, K., Chen, Z. 10.1038/s41467-021-24320-4 34210977 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P62799, P84233, P02281 0.567
68 7A08 EM 3.11 2020-09-23 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 132 CryoEM Structure of cGAS Nucleosome complex Michalski, S., de Oliveira Mann, C.C., Stafford, C.A., Witte, G., Bartho, J., Lammens, K., Hornung, V., Hopfner, K.P. 10.1038/s41586-020-2748-0 32911480 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 P84243, P62807, P62805, Q93077 0.533
69 6UPK EM 4.90 2019-12-11 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 72 Structure of FACT_subnucleosome complex 1 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription-associated, Histone chaperones, FACT, DNA replication, DNA repair Q9Y5B9, Q08945 P62807, P68431, P62805, Q93077 0.203
70 6UPL EM 7.40 2019-12-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 79 Structure of FACT_subnucleosome complex 2 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription-associated, Histone chaperones, FACT, DNA replication, DNA repair Q9Y5B9, Q08945 P62807, P68431, P62805, Q93077 0.173
71 7ZI4 EM 3.20 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Vance, N.R., Ayala, R., Willhoft, O., Tvardovskiy, A., McCormack, E.A., Bartke, T., Zhang, X., Wigley, D.B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit C, INO80 complex subunit B Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q6PI98, Q9C086 P04908, P68431, P62805, P06899 0.462
72 8SN3 EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.429
73 6HTS EM 4.80 2018-11-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Cryo-EM structure of the human INO80 complex bound to nucleosome Ayala, R., Willhoft, O., Aramayo, R.J., Wilkinson, M., McCormack, E.A., Ocloo, L., Wigley, D.B., Zhang, X. 10.1038/s41586-018-0021-6 29643506 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit B Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q9C086 P04908, P68431, P62805, P06899 0.181
74 7XZZ EM 4.07 2022-10-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Cryo-EM structure of the nucleosome in complex with p53 Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.192
75 9OB1 EM 3.20 2026-03-04 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 145 S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2026 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62798, P02293, P04911, P61830 0.374
76 9C9G EM 2.91 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 144 S.c INO80 in complex with S.c 0/80 nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62799, P02293, P04911, P61830 0.445
77 8VWT EM 3.30 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA modification, DNA repair O15527 Q71DI3, P62807, P62805, P0C0S8 0.41
78 8UPF EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.464
79 8T9F EM 2.60 2023-09-06 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 122 Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. 10.1016/j.molcel.2023.07.020 37595555 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 P84233, P02281, P62799, P0C0S5 0.516
80 8SN9 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.424
81 8SN7 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.445
82 8SN4 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.439
83 8SMW EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.526
84 8OX1 EM 2.70 2023-08-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 Structure of TRF1core in complex with telomeric nucleosome Hu, H., van Roon, A.M., Ghanim, G.E., Ahsan, B., Oluwole, A.O., Peak-Chew, S.Y., Robinson, C.V., Nguyen, T.H.D. 10.1126/sciadv.adi4148 37624885 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Telomeric repeat-binding factor 1 Cell cycle, DNA repair, Telomere-associated, Shelterin P54274 P62807, P68431, P62805, Q93077 0.579
85 8IEG EM 3.44 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.molcel.2023.08.001 37633270 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1, Ubiquitin-conjugating enzyme E2 2 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, DNA repair, Telomere-associated Q07457, P06104 O60814, P04908, P68431, P62805 0.393
86 8HAJ EM 4.80 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 164 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.2
87 8HAI EM 4.70 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.212
88 8BVW EM 4.00 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 206 RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Cell cycle, Transcription factors, RNA polymerases, DNA repair, Euchromatin-associated P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P06897, P84233, P62799, P02281 0.234
89 7ZS9 EM 3.10 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription factors, RNA polymerases, Transcription-associated, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P06897, P84233, P62799, P02281 0.34
90 7YRD EM 3.20 2023-08-16 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 histone methyltransferase Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. 10.1016/j.molcel.2023.07.001 37536340 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 Q71DI3, P62805, P06899, P0C0S5 0.484
91 7W9V EM 3.95 2022-07-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L., Kutateladze, T.G., Kurumizaka, H. 10.1016/j.isci.2022.104563 35754730 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.307
92 7OTQ EM 4.80 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome Bacic, L., Gaullier, G., Sabantsev, A., Lehmann, L.C., Brackmann, K., Dimakou, D., Halic, M., Hewitt, G., Boulton, S., Deindl, S., Workman, J.L. 10.7554/eLife.71420 34486521 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.282
93 7LYB EM 3.28 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Isoform 7 of Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair P38398, Q99728, P61077 P04908, P68431, P62805, P06899 0.458
94 7CCR EM 4.90 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of the 2:2 cGAS-nucleosome complex Cao, D., Han, X., Fan, X., Xu, R.M., Zhang, X. 10.1038/s41422-020-00422-4 33051594 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 P04908, P68431, P62805, P06899 0.152
95 6USJ EM 10.50 2020-10-14 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Structure of two nucleosomes bridged by human PARP2 Gaullier, G., Roberts, G., Muthurajan, U.M., Bowerman, S., Rudolph, J., Mahadevan, J., Jha, A., Rae, P.S., Luger, K. 10.1371/journal.pone.0240932 33141820 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Poly [ADP-ribose] polymerase 2 Histone_PARylation_writer, DNA repair, Histone PTM writers Q9UGN5 P04908, P68431, P62805, P06899 0.092
96 7CCQ EM 3.80 2020-10-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of the 1:1 cGAS-nucleosome complex Cao, D., Han, X., Fan, X., Xu, R.M., Zhang, X. 10.1038/s41422-020-00422-4 33051594 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 P04908, P68431, P62805, P06899 0.371
97 7ZSA EM 4.00 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription factors, RNA polymerases, Transcription-associated, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P06897, P84233, P62799, P02281 0.342
98 10YF EM 3.00 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite) Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q96KK5, Q71DI3, P62805, Q5QNW6 0.494
99 7XTD EM 3.90 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.221
100 9R2M EM 3.50 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Chakraborty, D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.39
101 9CB7 EM 4.04 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers P53115, P40154 P62799, P02293, P04911, P61830 0.288
102 8U13 EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168 Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5 P04908, P68431, P62805, P62807 0.381
103 8SN0 EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.547
104 8KD4 EM 2.93 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.373
105 8IEJ EM 3.12 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 RNF20-RNF40/hRad6A-Ub/nucleosome complex Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.molcel.2023.08.001 37633270 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1B, E3 ubiquitin-protein ligase BRE1A, Ubiquitin-conjugating enzyme E2 A Transcription-associated, Histone PTM writers, E3 ubiquitin-protein ligation, DNA repair, Histone_ubiquitination_H2BK120_writer O75150, Q5VTR2, P49459 O60814, P04908, P68431, P62805 0.461
106 8HXY EM 3.10 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.44
107 8BYQ EM 4.10 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Cell cycle, Transcription factors, RNA polymerases, DNA repair, Euchromatin-associated P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P06897, P84233, P62799, P02281 0.187
108 8B0A EM 3.00 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome Bacic, L., Gaullier, G., Mohapatra, J., Mao, G., Brackmann, K., Panfilov, M., Liszczak, G., Sabantsev, A., Deindl, S. 10.1038/s41467-024-45237-8 38307862 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.483
109 7YWX EM 12.00 2022-05-18 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 162 Structure of the human CCAN CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein S, Centromere protein T, Centromere protein U, Centromere protein W, Centromere protein X, Centromere protein C CENP-A NAC/CAD, Transcription-associated, Cell cycle, Centromere-associated, Fanconi anemia core complex, Nuclear division, Kinetochore, DNA repair Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q8N2Z9, Q96BT3, Q71F23, Q5EE01, A8MT69, Q03188 P49450, P62807, P62805, Q93077 0.054
110 7XZX EM 4.53 2022-10-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 171 Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.146
111 6R92 EM 4.80 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.22
112 6R91 EM 4.10 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.212
113 9RZE EM 8.53 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 181 State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Histone-lysine N-methyltransferase SETD2, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit SPT16 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A8D1KNW4, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q9BYW2, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.068
114 9QCS EM 4.38 2026-01-14 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 129 Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.185
115 9QCR EM 4.37 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 129 DNA-PK bound to 153 bp H2AX nucleosome model 2 Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.234
116 9J8W EM 3.38 2025-11-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-UV-DDB complex containing CPD Matsumoto, S., Takizawa, Y., Ogasawara, M., Hashimoto, K., Negishi, L., Xu, W., Tachibana, H., Yamamoto, J., Iwai, S., Sugasawa, K., Kurumizaka, H. 10.1038/s41467-025-65486-5 41219227 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q92466 P04908, P68431, P62805, P06899 0.397
117 8X7J EM 3.39 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair P61077, Q8IYW5, P62979 O60814, Q71DI3, P04908, P62805 0.391
118 8W9F EM 4.40 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Wang, C., Chu, C., Guo, Z., Zhan, X. 10.1126/sciadv.adk7678 38598631 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 O60814, P04908, P68431, P62805 0.156
119 8U14 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.352
120 8SN8 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.443
121 8SN2 EM 3.60 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.452
122 8KD3 EM 2.90 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.376
123 8KD2 EM 3.02 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 174 Rpd3S in complex with 187bp nucleosome Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.35
124 8JHO EM 7.60 2023-09-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 340 Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 P06897, P84233, P62799, P02281 0.067
125 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 Histone chaperones, DNA replication, CAF-1, DNA repair Q13111, Q13112 P68431, P62805 0.304
126 7SCY EM 4.10 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to single BRCT Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 Histone_PARylation_writer, DNA repair, Histone PTM writers P09874 P04908, P68431, P62805, P06899 0.273
127 7C0M EM 3.90 2020-09-16 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Human cGAS-nucleosome complex Kujirai, T., Zierhut, C., Takizawa, Y., Kim, R., Negishi, L., Uruma, N., Hirai, S., Funabiki, H., Kurumizaka, H. 10.1126/science.abd0237 32912999 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 P04908, P68431, P62805, P06899 0.225
128 6X59 EM 2.98 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 The mouse cGAS catalytic domain binding to human assembled nucleosome Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. 10.1038/s41586-020-2749-z 32911481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.54
129 6R90 EM 4.50 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DCX complex, DNA repair, UV-DDB complex Q16531, Q92466 P04908, P68431, P62805, P06899 0.278
130 10YE EM 2.50 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q71DI3, Q99879, P62805, P0C0S8 0.57
131 9WMW EM 3.62 2025-12-24 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 75 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.229
132 7LYC EM 2.94 2021-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Ubiquitin, BRCA1-associated RING domain protein 1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Ubiquitin, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair P0CG47, Q99728 P04908, P68431, P62805, P06899 0.566
133 7XSX EM 3.80 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 108 RNA polymerase II elongation complex transcribing a nucleosome (EC49) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.227
134 7XFH EM 2.90 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 132 Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-3-methyladenine glycosylase DNA modification, DNA repair P29372 P06897, P84233, P62799, P02281 0.515
135 7NKY EM 3.20 2021-07-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 148 RNA Polymerase II-Spt4/5-nucleosome-FACT structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, FACT complex subunit POB3, FACT complex subunit SPT16, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, RNA polymerases, Transcription factors, Centromere-associated, Histone chaperones, Heterochromatin-associated, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, Q04636, P32558, P32914, P27692 P06897, P84233, P62799, P02281 0.358
136 9EIL EM 3.20 2025-07-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 141 SIRT6 bound to an H3K27Ac nucleosome Wang, Z.A., Markert, J., Whedon, S.D., Abeywardana, M.Y., Sheng, X., Nam, E., Lee, K., Chen, M., Waterbury, A., Zhao, Y., Farnung, L., Cole, P.A. 10.1016/j.jbc.2025.108446 40147774 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P06897, P84233, P62799, P02281 0.395
137 9T4V EM 6.60 2025-11-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 ALC1/CHD1L in an intermediate conformation, bound to a PARylated nucleosome Bridges, H.R., Bacic, L., Deindl, S., Gaullier, G. 10.1101/2025.11.10.687450 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P06897, P84233, P62799, P02281 0.188
138 9KQ2 EM 3.90 2025-11-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of RNF168'-RNF168-UbcH5c complex bound to nucleosome Yang, X., Zhu, H., Shi, L., Song, T., Gong, W., He, S., Shan, S., Xu, C., Zhou, Z. 10.1093/nar/gkaf735 40794873 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 E3 ubiquitin-protein ligase RNF168 Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5 A0A310TTQ1, Q6AZJ8, A0A8J0U496, A0A8J1LTD2 0.45
139 9IGX EM 3.56 2026-01-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Ku70/80 bound to 153 bp nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P04908, P68431, P62805, P06899 0.293
140 9IGW EM 3.32 2026-01-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 132 Ku70/80 bound to 147 bp nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P04908, P68431, P62805, P06899 0.321
141 9DWK EM 4.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 105 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5 Weaver, T.M., Ryan, B.J., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.297
142 9DWI EM 3.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite) Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.405
143 9C9T EM 3.16 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 147 S.c INO80 in complex with S.c 0/40 nucleosome, Class 2 Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62799, P02293, P04911, P61830 0.399
144 8W9E EM 3.60 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Wang, C., Chu, C., Guo, Z., Zhan, X. 10.1126/sciadv.adk7678 38598631 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P22579, P32561, Q12432, Q04779 O60814, P04908, P68431, P62805 0.188
145 8SN1 EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.526
146 8KD7 EM 3.09 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Transcription-associated, Cell cycle, Histone PTM writers, Histone_acetylation_writer, NuA4, Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated P32561, P22579, Q12432, Q04779 P06897, P84233, P62799, P02281 0.324
147 8JHG EM 3.58 2023-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Native SUV420H1 bound to 167-bp nucleosome Lin, F., Zhang, R., Shao, W., Lei, C., Ma, M., Zhang, Y., Wen, Z., Li, W. 10.1038/s41421-023-00620-5 38052811 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, DNA repair Q4FZB7 O60814, P04908, P68431, P62805 0.456
148 7YQK EM 3.38 2022-08-17 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 145 cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 Ai, H., Chu, G.C., Gong, Q., Tong, Z.B., Deng, Z., Liu, X., Yang, F., Xu, Z., Li, J.B., Tian, C., Liu, L. 10.1021/jacs.2c06156 36166692 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 UDR motif of 53BP1, TP53-binding protein 1, Polyubiquitin-B Histone PTM readers, Histone_methylation_H4K20_reader, Ubiquitin, Histone_ubiquitination_H2AK15_reader, DNA repair, Telomere-associated Q12888, P0CG47 O60814, P16104, P68431, P62805 0.424
149 7YI1 EM 2.80 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, DNA repair Q12432 P06897, P84233, P62799, P02281 0.572
150 9R04 EM 4.20 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Chakraborty, D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.232
151 9GEV EM 3.47 2025-08-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Sharma, M., Aggarwal, P., Hopfner, K.P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, INO80 complex subunit B, INO80 complex subunit C, Actin-related protein 5 Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9C086, Q6PI98, Q9H9F9 P04908, P68431, P62805, Q16778 0.4
152 9EOZ EM 3.10 2024-11-06 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 144 Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Ren, M., Gut, F., Fan, Y., Ma, J., Shan, X., Yikilmazsoy, A., Likhodeeva, M., Hopfner, K.P., Zhou, C. 10.1038/s41467-024-53811-3 39477986 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA modification, DNA repair O15527 P62807, P62805, Q93077, P84243 0.465
153 9Q80 EM 3.39 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 151 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P16104, P68431, P62805, P06899 0.3
154 9GW2 EM 4.84 2025-11-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 125 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16 Transcription-associated, Histone PTM writers, Histone_methylation_H3K36_writer, Histone chaperones, FACT, DNA replication, DNA repair, Euchromatin-associated Q9BYW2, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.359
155 9DWH EM 3.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite) Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta DNA repair P06746 Q71DI3, P62807, P62805, P0C0S8 0.384
156 8X7I EM 3.27 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair P61077, Q8IYW5, P62979 O60814, Q71DI3, P04908, P62805 0.443
157 8VWV EM 3.60 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA modification, DNA repair O15527 Q71DI3, P62807, P62805, P0C0S8 0.359
158 8TXX EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P0CG47 P04908, P68431, P62805, P62807 0.438
159 8HAK EM 4.50 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 p300, Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, DNA repair Q09472 P04908, P68431, P62805, P06899 0.214
160 7XTI EM 3.90 2022-10-12 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 85 RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.223
161 6Y5D EM 4.10 2020-09-23 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Structure of human cGAS (K394E) bound to the nucleosome Pathare, G.R., Decout, A., Gluck, S., Cavadini, S., Makasheva, K., Hovius, R., Kempf, G., Weiss, J., Kozicka, Z., Guey, B., Melenec, P., Fierz, B., Thoma, N.H., Ablasser, A. 10.1038/s41586-020-2750-6 32911482 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 O60814, Q71DI3, P62805, Q6FI13 0.195
162 9S3G EM 6.40 2025-11-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 67 State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Histone-lysine N-methyltransferase SETD2, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A8D1KNW4, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q9BYW2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267, Q9Y5B9, Q08945 O60814, Q71DI3, P04908, P62805 0.187
163 9GE5 EM 3.35 2025-08-20 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 113 CryoEM structure of the human INO80-Hexasome complex Aggarwal, P., Sharma, M., Hopfner, K.P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, INO80 complex subunit B, INO80 complex subunit C, Actin-related protein 5 Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9C086, Q6PI98, Q9H9F9 P04908, P68431, P62805, P33778 -
164 9GFB EM 3.55 2025-08-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 CryoEM structure of the human INO80 core-nucleosome complex state N-7 Sharma, M., Aggarwal, P., Hopfner, K.P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, INO80 complex subunit B, INO80 complex subunit C, Actin-related protein 5 Cell cycle, Chromatin remodelers, Transcription-associated, INO80, DNA replication, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9C086, Q6PI98, Q9H9F9 P04908, P68431, P62805, Q16778 -
165 8JND EM 3.66 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P04908, P68431, P62805, P06899 0.19
166 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 Histone chaperones, DNA replication, CAF-1, DNA repair Q13111, Q13112 P68431, P62805 0.301
167 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 Histone chaperones, DNA replication, CAF-1, DNA repair Q13111, Q13112 P68431, P62805 0.189
168 7XT7 EM 4.20 2022-10-12 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, F2QPX0, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.207
169 5KGF EM 4.54 2016-07-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Wilson, M.D., Benlekbir, S., Fradet-Turcotte, A., Sherker, A., Julien, J.P., McEwan, A., Noordermeer, S.M., Sicheri, F., Rubinstein, J.L., Durocher, D. 10.1038/nature18951 27462807 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2016 Tumor suppressor p53-binding protein 1, Ubiquitin Histone PTM readers, Histone_methylation_H4K20_reader, Ubiquitin, Histone_ubiquitination_H2AK15_reader, DNA repair, Telomere-associated Q12888, P0CG47 P62807, P84233, P0C0S8, P62799 0.301
170 6XJD EM 6.80 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Two mouse cGAS catalytic domain binding to human assembled nucleosome Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. 10.1038/s41586-020-2749-z 32911481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8C6L5 Q71DI3, P62807, P62805, P0C0S8 0.196
171 10YG EM 3.40 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite) Boesch, D.J., Weaver, T.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA ligase 3 DNA repair P49916 Q71DI3, Q99879, P62805, P0C0S8 0.488
172 9EH2 EM 3.10 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 65 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_methylation_H3K36_writer, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2, Q9Y5B9, Q08945 A0A310TTQ1, P06897, P62799, P02281 0.252
173 8GRQ EM 3.87 2023-04-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.chempr.2023.01.012 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK129_writer, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, DNA repair P38398, Q99728, P61077 O60814, Q71DI3, P04908, P62805 0.352
174 8CEO EM 3.60 2023-03-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Schilbach, S., Wang, H., Dienemann, C., Cramer, P. 10.1073/pnas.2220542120 37014863 Xenopus laevis Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPD, TFB1 isoform 1, RNA polymerase II transcription factor B subunit 2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, TOA1 isoform 1, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta, Mediator of RNA polymerase II transcription subunit 6, Mediator of RNA polymerase II transcription subunit 8, Mediator of RNA polymerase II transcription subunit 11, Mediator of RNA polymerase II transcription subunit 17, Mediator of RNA polymerase II transcription subunit 18, Mediator of RNA polymerase II transcription subunit 20, Mediator of RNA polymerase II transcription subunit 22, Mediator of RNA polymerase II transcription subunit 4, Mediator of RNA polymerase II transcription subunit 7, Mediator of RNA polymerase II transcription subunit 9, Mediator of RNA polymerase II transcription subunit 10, Mediator of RNA polymerase II transcription subunit 14, Mediator of RNA polymerase II transcription subunit 19, Mediator of RNA polymerase II transcription subunit 21, Mediator of RNA polymerase II transcription subunit 31, Mediator of RNA polymerase II transcription subunit 1 Transcription factors, RNA polymerases, Transcription-associated, Mediator, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145, P38782, P38304, Q99278, P32569, P32585, P34162, P32570, Q12343, Q08278, P33308, Q06213, P19263, P25046, P47822, P38633, Q12321 P06897, P84233, P62799, P02281 0.222
175 6Y5E EM 3.15 2020-09-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Pathare, G.R., Decout, A., Gluck, S., Cavadini, S., Makasheva, K., Hovius, R., Kempf, G., Weiss, J., Kozicka, Z., Guey, B., Melenec, P., Fierz, B., Thoma, N.H., Ablasser, A. 10.1038/s41586-020-2750-6 32911482 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884 O60814, Q71DI3, P62805, Q16777 0.43