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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 7MBN EM 4.02 2021-12-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Ayoub, A., Park, S.H., Lee, Y.T., Cho, U.S., Dou, Y. 10.1021/acs.biochem.1c00603 34928138 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.217
1 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
2 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
3 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
4 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
5 9B2T EM 2.99 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Haspin bound to nucleosome in position 2 Hicks, C.W., Gliech, C.R., Rahman, S., Zhang, X., Eneim, A.S., Vasquez, S.J., Holland, A.J., Wolberger, C. 10.1038/s41594-025-01502-y 39979508 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Serine/threonine-protein kinase haspin Nuclear division, Histone_phosphorylation_H3T3_writer, Histone PTM writers Q8TF76 P06897, P84233, P62799, P02281 0.502
6 8X2Z EM 3.90 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.237
7 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
8 8TB9 EM 4.00 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601 193 PRC2-J119-450 monomer bound to H1-nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Homo sapiens 2024 Protein Jumonji, Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Histone chaperones, Polycomb, Histone PTM erasers Q92833, Q15022, Q15910, O75530, Q09028, Q6ZN18 P06897, P07305, P62799, P02281, P84233 0.261
9 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
10 8GUI EM 2.81 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1-nucleosome complex (Model I) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK120_writer Q5VTR2, O75150 P68431, P62805, P06899, P0C0S8 0.532
11 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
12 7UND EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 131 Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 Q6AZJ8, P84233, P62799, P02281 0.216
13 7TAN EM 3.00 2022-05-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of VRK1 C-terminal tail bound to nucleosome core particle Budziszewski, G.R., Zhao, Y., Spangler, C.J., Kedziora, K.M., Williams, M.R., Azzam, D.N., Skrajna, A., Koyama, Y., Cesmat, A.P., Simmons, H.C., Arteaga, E.C., Strauss, J.D., Kireev, D., McGinty, R.K. 10.1093/nar/gkac198 35390161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Serine/threonine-protein kinase VRK1 Nuclear division, Histone_phosphorylation_H3T3_writer, Cell cycle, Histone PTM writers Q99986 Q71DI3, P62807, P62805, P0C0S8 0.56
14 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
15 7AT8 EM 4.40 2020-12-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Finogenova, K., Bonnet, J., Poepsel, S., Schafer, I.B., Finkl, K., Schmid, K., Litz, C., Strauss, M., Benda, C., Muller, J. 10.7554/eLife.61964 33211010 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2, Polycomb protein SUZ12 Transcription-associated, Histone_methylation_H3K27_writer, Histone PTM writers, Heterochromatin-associated, Polycomb Q15910, Q15022 P06897, P84233, P62799, P02281 0.29
16 6KIW EM 4.00 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2C, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Ubiquitin, Euchromatin-associated Q8NEZ4, Q15291, P62979, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.33
17 6KIV EM 4.00 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Ubiquitin, Euchromatin-associated Q03164, Q15291, P62979, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.343
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 6NN6 EM 3.90 2019-02-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of Dot1L-H2BK120ub nucleosome complex Anderson, C.J., Baird, M.R., Hsu, A., Barbour, E.H., Koyama, Y., Borgnia, M.J., McGinty, R.K. 10.1016/j.celrep.2019.01.058 30759380 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, F5H388 P06897, P84233, P62799, P02281 0.371
21 9WMV EM 4.66 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 168 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.168
22 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
23 9FGQ EM 2.50 2024-07-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 132 Structure of human APC3loop 375-381 bound to the NCP Cirillo, L., Young, R., Veerapathiran, S., Roberti, A., Martin, M., Abubacar, A., Perosa, C., Coates, C., Muhammad, R., Roumeliotis, T.I., Choudhary, J.S., Alfieri, C., Pines, J. 10.1038/s44318-024-00194-2 39143240 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Cell division cycle protein 27 homolog APC/C, Cell cycle, Histone PTM writers P30260 P68431, P62805, Q6FI13, P33778 0.651
24 9EGX EM 2.90 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A310TTQ1, P06897, P62799, P02281 0.25
25 8X32 EM 4.40 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ Complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.114
26 8X30 EM 4.30 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 Structure of piccolo NuA4 and H2A.Z nucleosome 2:1 complex Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, Q540A3, P38806, P47128 Q12692, P02309, P02293, P61830 0.165
27 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
28 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
29 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
30 7XPX EM 3.20 2022-06-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Cryo-EM structure of the histone methyltransferase SET8 bound to H4K20Ecx-nucleosome Shi, L., Huang, L., Long, H., Song, A., Zhou, Z. 10.1096/fj.202101821R 35532550 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 N-lysine methyltransferase KMT5A Transcription-associated, Histone PTM writers, Cell cycle, Heterochromatin-associated, Nuclear division, Histone_methylation_H4K20_writer Q9NQR1 P06897, P84233, P62799, P02281 0.475
31 7VVZ EM 8.80 2022-08-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 180 NuA4 bound to the nucleosome Qu, K., Chen, K., Wang, H., Li, X., Chen, Z. 10.1038/s41586-022-05303-x 36198799 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Chromatin modification-related protein EAF1, Actin-related protein 4, Actin, Enhancer of polycomb-like protein 1, SWR1-complex protein 4, Transcription-associated protein 1, Histone acetyltransferase ESA1, Chromatin modification-related protein YNG2, Epl1 arginine anchor, Chromatin modification-related protein EAF6 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Euchromatin-associated Q06337, P80428, P60010, P43572, P53201, P38811, Q08649, P38806, P47128 P06897, P84233, P62799, P02281 0.108
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 6KIU EM 3.20 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Ubiquitin, Euchromatin-associated Q03164, Q15291, P62979, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.461
34 4R8P X-ray 3.28 2014-11-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle McGinty, R.K., Henrici, R.C., Tan, S. 10.1038/nature13890 25355358 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2014 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Polycomb, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496 P06897, P84233, P62799, P02281 -
35 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
36 6W5N EM 6.00 2021-03-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Lee, Y.T., Ayoub, A., Park, S.H., Sha, L., Xu, J., Mao, F., Zheng, W., Zhang, Y., Cho, U.S., Dou, Y. 10.1038/s41467-021-23268-9 34012049 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.167
37 7CRO EM 3.75 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD2 Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated O96028 P06897, Q92133, P62799, P02281 0.448
38 9EH1 EM 3.10 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerase I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, Superkiller complex protein 8, N-terminally processed, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Transcription factors, Histone PTM writers, Transcription-associated, RNA polymerases, Histone_methylation_H3K4_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q96ST2, Q6PD62, Q92541, B7Z4W0, Q9GZS3, A0A2R8YHB3, P63272, Q9BYW2 A0A310TTQ1, P06897, P62799, P02281 0.237
39 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
40 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
41 8T9G EM 6.20 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 215 Automethylated PRC2 dimer bound to nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Transcription-associated, Histone_methylation_H3K27_writer, Histone PTM writers, Heterochromatin-associated, Histone chaperones, Polycomb Q15022, Q15910, O75530, Q09028, Q6ZN18 P06897, P84233, P62799, P02281 0.163
42 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
43 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
44 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
45 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
46 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
47 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
48 8DU4 EM 3.55 2022-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Rahman, S., Hoffmann, N.A., Worden, E.J., Smith, M.L., Namitz, K.E.W., Knutson, B.A., Cosgrove, M.S., Wolberger, C. 10.1073/pnas.2205691119 36095189 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 WD repeat-containing protein 5, Retinoblastoma-binding protein 5, Polyubiquitin-B Transcription-associated, COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Ubiquitin, Euchromatin-associated P61964, Q15291, P0CG47 P02302, P06897, P62799, P02281 0.237
49 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
50 7EA8 EM 3.10 2021-07-14 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 122 Human SETD2 bound to a nucleosome containing oncohistone mutations Liu, Y., Zhang, Y., Xue, H., Cao, M., Bai, G., Mu, Z., Yao, Y., Sun, S., Fang, D., Huang, J. 10.1038/s41421-021-00261-6 33972509 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Histone-lysine N-methyltransferase SETD2 Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated Q9BYW2 P06899, P20671, Q6PI79, P62799 0.509
51 7BWD EM 4.32 2021-04-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Dot1L-H2BK34ub Nucleosome Complex Liu, L., Lou, Z.Y., Ai, H.S., Cao, L. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P62979 O60814, P04908, P68431, P62805 0.332
52 6NJ9 EM 2.96 2019-02-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C. 10.1016/j.cell.2019.02.002 30765112 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P06897, P84233, P62799, P02281 0.551
53 8HAL EM 4.40 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 151 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Transcription-associated, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P04908, P68431, P62805, P06899 0.195
54 8PP7 EM 2.91 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 human RYBP-PRC1 bound to mononucleosome Ciapponi, M., Karlukova, E., Schkolziger, S., Benda, C., Muller, J. 10.1038/s41594-024-01258-x 38528151 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Polycomb, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496 P84040, P84051, P02283, P02299 0.511
55 7E8D EM 2.80 2021-11-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 172 NSD2 E1099K mutant bound to nucleosome Sato, K., Kumar, A., Hamada, K., Okada, C., Oguni, A., Machiyama, A., Sakuraba, S., Nishizawa, T., Nureki, O., Kono, H., Ogata, K., Sengoku, T. 10.1038/s41467-021-26913-5 34782608 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Histone-lysine N-methyltransferase NSD2 Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated O96028 P68431, P62805, P06899, P0C0S8 0.556
56 6UH5 EM 3.50 2019-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structural basis of COMPASS eCM recognition of the H2Bub nucleosome Hsu, P.L., Shi, H., Leonen, C., Kang, J., Chatterjee, C., Zheng, N. 10.1016/j.molcel.2019.10.013 31733991 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, Ubiquitin, Spp1 Telomere-associated, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Ubiquitin, Euchromatin-associated Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, P0CG47, Q6CRQ4 P62799, P02281, Q6AZJ8, Q92133, P84233 0.372
57 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
58 9M76 EM 4.10 2026-03-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 UHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain. Naschberger, A., Baradaran, R., Sayed, A., Fischle, W. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 E3 ubiquitin-protein ligase UHRF1 Histone PTM readers, Histone PTM writers, E3 ubiquitin-protein ligation Q96T88 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.239
59 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
60 8T3W EM 3.25 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state2 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Telomere-associated Q07457 P06897, P84233, P62799, P02281 0.52
61 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
62 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
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 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
66 8GUJ EM 2.80 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1-nucleosome complex (Model II) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK120_writer Q5VTR2, O75150 P68431, P62805, P06899, P0C0S8 0.532
67 7EA5 EM 3.30 2021-07-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Yeast Set2 bound to a nucleosome containing oncohistone mutations Liu, Y., Zhang, Y., Xue, H., Cao, M., Bai, G., Mu, Z., Yao, Y., Sun, S., Fang, D., Huang, J. 10.1038/s41421-021-00261-6 33972509 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-36 specific Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated P46995 Q6AZJ8, P84233, P62799, P02281 0.473
68 7CRP EM 3.20 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode) Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD3 Histone_methylation_H3K4_writer, Histone_methylation_H3K27_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated Q9BZ95 P06897, Q92133, P62799, P02281 0.542
69 6UGM EM 3.70 2019-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structural basis of COMPASS eCM recognition of an unmodified nucleosome Hsu, P.L., Shi, H., Leonen, C., Kang, J., Chatterjee, C., Zheng, N. 10.1016/j.molcel.2019.10.013 31733991 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, H3 N-terminus, Spp1 Telomere-associated, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, Q6CRQ4 Q6AZJ8, Q92133, P62799, P02281 0.385
70 6NQA EM 3.54 2019-02-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C. 10.1016/j.cell.2019.02.002 30765112 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG48 P06897, P84233, P62799, P02281 0.436
71 6J99 EM 4.10 2019-02-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Yao, T., Jing, W., Hu, Z., Tan, M., Cao, M., Wang, Q., Li, Y., Yuan, G., Lei, M., Huang, J. 10.1038/s41422-019-0146-7 30770869 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P62979 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.132
72 8TAS EM 4.10 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 193 PRC2 monomer bound to nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Transcription-associated, Histone_methylation_H3K27_writer, Histone PTM writers, Heterochromatin-associated, Histone chaperones, Polycomb Q15022, Q15910, O75530, Q09028, Q6ZN18 P06897, P84233, P62799, P02281 0.259
73 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
74 9EGZ EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_methylation_H3K36_writer, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 A0A310TTQ1, P06897, P62799, P02281 0.261
75 9DGG EM 2.98 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 ncPRC1RYBP bound to unmodified nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Polycomb, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496 P06897, P84233, P62799, P02281 0.47
76 9DBY EM 2.80 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, RING1 and YY1-binding protein, Ubiquitin Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Histone PTM readers, Histone_ubiquitination_reader, Polycomb, Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496, Q8N488, P0CG48 P06897, P84233, P62799, P02281 0.39
77 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
78 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
79 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
80 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
81 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
82 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
83 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
84 8HAN EM 4.20 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Transcription-associated, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P04908, P68431, P62805, P06899 0.209
85 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
86 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
87 8GRM EM 3.05 2023-04-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.chempr.2023.01.012 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 COMMD3 protein, Ring1B, Ubiquitin, UbcH5b Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Polycomb, Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496, P0CG47, P62837 O60814, P04908, P68431, P62805 0.516
88 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
89 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
90 7MBM EM 4.76 2021-12-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Ayoub, A., Park, S.H., Lee, Y.T., Cho, U.S., Dou, Y. 10.1021/acs.biochem.1c00603 34928138 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.198
91 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
92 7K6Q EM 3.10 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1 bound to the H4K16ac nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Truong, D.M., Lee, R., Armache, J.P., Boeke, J.D., Armache, K.J. 10.1126/science.abc6663 33479126 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Telomere-associated, Histone PTM writers Q04089, P0CG48 P06897, P84233, P62799, P02281 0.489
93 7D1Z EM 3.15 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of SET8-nucleosome complex Ho, C.H., Takizawa, Y., Kobayashi, W., Arimura, Y., Kimura, H., Kurumizaka, H. 10.26508/lsa.202000919 33574035 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Isoform 2 of N-lysine methyltransferase KMT5A Transcription-associated, Histone PTM writers, Cell cycle, Heterochromatin-associated, Nuclear division, Histone_methylation_H4K20_writer Q9NQR1 P04908, P68431, P62805, P06899 0.514
94 6VEN EM 3.37 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Yeast COMPASS in complex with a ubiquitinated nucleosome Worden, E.J., Zhang, X., Wolberger, C. 10.7554/eLife.53199 31922488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Ubiquitin, COMPASS component SWD3, COMPASS component SWD1, Histone-lysine N-methyltransferase, H3 lysine-4 specific, COMPASS component BRE2, COMPASS component SDC1, COMPASS component SPP1 Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers, COMPASS, Ubiquitin, Telomere-associated P0CG48, P38123, P39706, P38827, P43132, Q03323, Q03012 P06897, P84233, P62799, P02281 0.449
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 7UNC EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 155 Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, O00267 Q6AZJ8, P84233, P62799, P02281 0.344
97 9DDE EM 3.20 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 162 ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Homo sapiens 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, RING1 and YY1-binding protein, Ubiquitin Transcription-associated, Histone PTM writers, Histone_methylation_H3K27_writer, Heterochromatin-associated, Histone PTM readers, Histone_ubiquitination_reader, Polycomb, Ubiquitin, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK119_writer P35226, Q99496, Q8N488, P0CG48 P06897, P62799, P02281, P10412, P84233 0.456
98 9WMU EM 4.28 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 171 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.189
99 9WMS EM 3.40 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 118 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.227
100 9B2S EM 3.01 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Haspin bound to nucleosome in position 1 Hicks, C.W., Gliech, C.R., Rahman, S., Zhang, X., Eneim, A.S., Vasquez, S.J., Holland, A.J., Wolberger, C. 10.1038/s41594-025-01502-y 39979508 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Serine/threonine-protein kinase haspin Nuclear division, Histone_phosphorylation_H3T3_writer, Histone PTM writers Q8TF76 Q6AZJ8, P84233, P62799, P02281 0.536
101 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
102 8T3Y EM 3.47 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state1 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Telomere-associated Q07457 P06897, P84233, P62799, P02281 0.503
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 7CRR EM 3.48 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 Native NSD3 bound to 187-bp nucleosome Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD3 Histone_methylation_H3K4_writer, Histone_methylation_H3K27_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated Q9BZ95 P06897, Q92133, P62799, P02281 0.464
108 7CRQ EM 3.15 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD3 Histone_methylation_H3K4_writer, Histone_methylation_H3K27_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated Q9BZ95 P06897, Q92133, P62799, P02281 0.507
109 6PWV EM 6.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 core complex bound to the nucleosome Park, S.H., Ayoub, A., Lee, Y.T., Xu, J., Kim, H., Zheng, W., Zhang, B., Sha, L., An, S., Zhang, Y., Cianfrocco, M.A., Su, M., Dou, Y., Cho, U.S. 10.1038/s41467-019-13550-2 31804488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2, Protein dpy-30 homolog Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3, Q9C005 P06897, P84233, P62799, P02281 0.188
110 6NZO EM 3.80 2019-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Set2 bound to nucleosome Bilokapic, S., Halic, M. 10.1038/s41467-019-11726-4 31439846 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase Histone_methylation_H3K36_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated G0S676 P02302, P0CH09, P62799, P02281 0.364
111 6JM9 EM 7.30 2019-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 123 cryo-EM structure of DOT1L bound to unmodified nucleosome Jang, S., Kang, C., Yang, H.S., Jung, T., Hebert, H., Chung, K.Y., Kim, S.J., Hohng, S., Song, J.J. 10.1101/gad.323790.118 30923167 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific Histone_methylation_H3K79_writer, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3 Q6AZJ8, P84233, P62799, P02281 0.132
112 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
113 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
114 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
115 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
116 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
117 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
118 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
119 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
120 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
121 7UD5 EM 4.25 2022-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Rahman, S., Hoffmann, N.A., Worden, E.J., Smith, M.L., Namitz, K.E.W., Knutson, B.A., Cosgrove, M.S., Wolberger, C. 10.1073/pnas.2205691119 36095189 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 cDNA FLJ56846, highly similar to Zinc finger protein HRX, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2, Retinoblastoma-binding protein 5, Polyubiquitin-B, Protein dpy-30 homolog Transcription-associated, COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers, Ubiquitin, Euchromatin-associated B4DIJ7, P61964, Q9UBL3, Q15291, P0CG47, Q9C005 P06897, P84233, P62799, P02281 0.263
122 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
123 6W5M EM 4.60 2021-03-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Lee, Y.T., Ayoub, A., Park, S.H., Sha, L., Xu, J., Mao, F., Zheng, W., Zhang, Y., Cho, U.S., Dou, Y. 10.1038/s41467-021-23268-9 34012049 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.177
124 6O96 EM 3.50 2019-04-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Vasilyev, N., Chen, R., Nudler, E., Armache, J.-P., Armache, K.J. 10.1016/j.molcel.2019.03.029 30981630 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Polyubiquitin-B Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P06897, P84233, P62799, P02281 0.38
125 6KIX EM 4.10 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-NCP complex, binding mode1 Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q03164, Q15291, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.338
126 6JMA EM 6.80 2019-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 114 cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Jang, S., Kang, C., Yang, H.S., Jung, T., Hebert, H., Chung, K.Y., Kim, S.J., Hohng, S., Song, J.J. 10.1101/gad.323790.118 30923167 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 Q6AZJ8, P84233, P62799, P02281 0.144
127 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
128 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
129 9M77 EM 3.70 2026-03-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 The activated state of human UHRF1 bound to a mononucleosome, with the finger loop ordered and linker 4 disordered. Naschberger, A., Baradaran, R., Sayed, A., Fischle, W. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 E3 ubiquitin-protein ligase UHRF1 Histone PTM readers, Histone PTM writers, E3 ubiquitin-protein ligation Q96T88 A0A310TTQ1, Q6AZJ8, P62799, P02281 0.282
130 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
131 8X2X EM 3.80 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P0AEX9, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.261
132 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
133 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
134 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
135 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
136 8GPN EM 3.20 2023-02-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 Human menin in complex with H3K79Me2 nucleosome Lin, J., Wu, Y., Tian, G., Yu, D., Yang, E., Lam, W.H., Liu, Z., Jing, Y., Dang, S., Bao, X., Wong, J.W.H., Zhai, Y., Li, X.D. 10.1126/science.adc9318 36795828 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Isoform 2 of Menin Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers, Euchromatin-associated O00255 P06897, P84233, P62799, P02281 0.459
137 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
138 7VVU EM 3.40 2022-08-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 180 NuA4 HAT module bound to the nucleosome Qu, K., Chen, K., Wang, H., Li, X., Chen, Z. 10.1038/s41586-022-05303-x 36198799 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Histone acetyltransferase ESA1, Enhancer of polycomb-like protein 1, Chromatin modification-related protein YNG2, Chromatin modification-related protein EAF6 Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4, Euchromatin-associated Q08649, P43572, P38806, P47128 P06897, P84233, P62799, P02281 0.314
139 7D20 EM 3.00 2021-02-10 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 136 Cryo-EM structure of SET8-CENP-A-nucleosome complex Ho, C.H., Takizawa, Y., Kobayashi, W., Arimura, Y., Kimura, H., Kurumizaka, H. 10.26508/lsa.202000919 33574035 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Isoform 2 of N-lysine methyltransferase KMT5A Transcription-associated, Histone PTM writers, Cell cycle, Heterochromatin-associated, Nuclear division, Histone_methylation_H4K20_writer Q9NQR1 P49450, P04908, P62805, P06899 0.446
140 6PX3 EM 4.10 2019-08-28 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Set2 bound to nucleosome Bilokapic, S., Halic, M. 10.1038/s41467-019-11726-4 31439846 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis Xenopus laevis 2019 Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone-lysine N-methyltransferase Transcription-associated, Histone PTM writers, Histone_methylation_H3K36_writer, Ubiquitin, Euchromatin-associated P0CH09, G0S676 P02302, P0CH09, P62799, P02281 0.261
141 9EGY EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 160 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A310TTQ1, P06897, P62799, P02281 0.256
142 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
143 9EH0 EM 3.60 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 181 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_methylation_H3K36_writer, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 A0A310TTQ1, P06897, P62799, P02281 0.24
144 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
145 8X31 EM 6.20 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.123
146 8X2Y EM 4.10 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class1 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Cell cycle, Transcription-associated, Histone PTM writers, Histone_acetylation_writer, NuA4 Q08649, P0AEX9, P08515, P38806 Q12692, P02309, P02293, P61830 0.229
147 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
148 8T3T EM 3.21 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state3 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Telomere-associated Q07457 P06897, P84233, P62799, P02281 0.535
149 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
150 6W5I EM 6.90 2021-03-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Lee, Y.T., Ayoub, A., Park, S.H., Sha, L., Xu, J., Mao, F., Zheng, W., Zhang, Y., Cho, U.S., Dou, Y. 10.1038/s41467-021-23268-9 34012049 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164, Q9UBL3 P06897, P84233, P62799, P02281 0.135
151 6PWX EM 4.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of RbBP5 bound to the nucleosome Park, S.H., Ayoub, A., Lee, Y.T., Xu, J., Kim, H., Zheng, W., Zhang, B., Sha, L., An, S., Zhang, Y., Cianfrocco, M.A., Su, M., Dou, Y., Cho, U.S. 10.1038/s41467-019-13550-2 31804488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Retinoblastoma-binding protein 5 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291 P06897, P84233, P62799, P02281 0.332
152 6NOG EM 3.90 2019-02-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C. 10.1016/j.cell.2019.02.002 30765112 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, J3QS39 P06897, P84233, P62799, P02281 0.356
153 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
154 8HAM EM 4.50 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 165 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Transcription-associated, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P04908, P68431, P62805, P06899 0.242
155 8A3Y EM 3.30 2024-07-31 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 138 Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Farnung, L., Ochmann, M., Garg, G., Vos, S.M., Cramer, P. 10.1016/j.molcel.2022.06.027 35858621 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, SPT6, RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein LEO1, RNA polymerase-associated protein RTF1 homolog, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q6PD62, Q92541, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267 Q6AZJ8, P84233, A0A8J1LZU9, P62799 0.231
156 7XCT EM 2.72 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 O60814, Q71DI3, P04908, P62805 0.514
157 7XCR EM 2.57 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Histone PTM writers, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 O60814, Q71DI3, P04908, P62805 0.571
158 7K6P EM 3.20 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1 bound to the unacetylated H4 nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Truong, D.M., Lee, R., Armache, J.P., Boeke, J.D., Armache, K.J. 10.1126/science.abc6663 33479126 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Ubiquitin, Telomere-associated, Histone PTM writers Q04089, P0CG48 P06897, P84233, P62799, P02281 0.473
159 6KIZ EM 4.50 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-NCP complex, binding mode2 Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q03164, Q15291, P61964, Q9UBL3 P06897, P84233, P62799, P02281 0.31
160 5HQ2 X-ray 4.50 2016-03-23 split_octasome 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 73 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Girish, T.S., McGinty, R.K., Tan, S. 10.1016/j.jmb.2016.02.025 26953260 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 Guanine nucleotide exchange factor SRM1, N-lysine methyltransferase SETD8 Cell cycle, Histone PTM writers, Transcription-associated, Heterochromatin-associated, Nuclear division, Histone_methylation_H4K20_writer P21827, Q9NQR1 P06897, P84233, P62799, P02281 -
161 6PWW EM 4.40 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Park, S.H., Ayoub, A., Lee, Y.T., Xu, J., Kim, H., Zheng, W., Zhang, B., Sha, L., An, S., Zhang, Y., Cianfrocco, M.A., Su, M., Dou, Y., Cho, U.S. 10.1038/s41467-019-13550-2 31804488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Histone PTM writers, Euchromatin-associated Q15291, P61964, Q03164 P06897, P84233, P62799, P02281 0.26
162 9WMT EM 3.59 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 121 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.225
163 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
164 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