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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 7K6Q EM 3.10 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1 bound to the H4K16ac nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Truong, D.M., Lee, R., Armache, J.P., Boeke, J.D., Armache, K.J. 10.1126/science.abc6663 33479126 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Telomere-associated, Histone PTM writers, Histone_methylation_H3K79_writer Q04089, P0CG48 P02281, P84233, P06897, P62799 0.489
1 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 PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated O96028 Q92133, P02281, P06897, P62799 0.448
2 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 PTM writers, Histone_methylation_H3K4_writer, Euchromatin-associated, Transcription-associated, Histone_methylation_H3K27_writer Q9BZ95 Q92133, P02281, P06897, P62799 0.542
3 7LYB EM 3.28 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Isoform 7 of Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2 D3 Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair, Histone_ubiquitination_H2AK129_writer P38398, Q99728, P61077 P68431, P04908, P06899, P62805 0.458
4 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_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P0CG47 P68431, P04908, P62807, P62805 0.438
5 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.167
6 8SN3 EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.429
7 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 Telomere-associated, Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Ubiquitin P0CG48, P38123, P39706, P38827, P43132, Q03323, Q03012 P02281, P84233, P06897, P62799 0.449
8 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 Histone_methylation_H4K20_writer, Histone PTM writers, Cell cycle, Transcription-associated, Heterochromatin-associated, Nuclear division Q9NQR1 P68431, P04908, P06899, P62805 0.514
9 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 Histone_methylation_H4K20_writer, Histone PTM writers, Cell cycle, Transcription-associated, Heterochromatin-associated, Nuclear division Q9NQR1 P49450, P06899, P04908, P62805 0.446
10 7VVZ EM 8.80 2022-08-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 180 NuA4 bound to the nucleosome Qu, K., Chen, K., Wang, H., Li, X., Chen, Z. 10.1038/s41586-022-05303-x 36198799 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Chromatin modification-related protein EAF1, Actin-related protein 4, Actin, Enhancer of polycomb-like protein 1, SWR1-complex protein 4, Transcription-associated protein 1, Histone acetyltransferase ESA1, Chromatin modification-related protein YNG2, Epl1 arginine anchor, Chromatin modification-related protein EAF6 Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Euchromatin-associated, Histone_acetylation_writer Q06337, P80428, P60010, P43572, P53201, P38811, Q08649, P38806, P47128 P02281, P84233, P06897, P62799 0.108
11 7YI1 EM 2.80 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 Histone PTM writers, NuA4, Transcription-associated, Histone_acetylation_writer, DNA repair Q12432 P02281, P84233, P06897, P62799 0.572
12 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, Histone PTM writers, Euchromatin-associated, Transcription-associated O00255 P02281, P84233, P06897, P62799 0.459
13 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, Histone PTM writers, Histone_ubiquitination_H2BK120_writer, Transcription-associated Q5VTR2, O75150 P68431, P06899, P0C0S8, P62805 0.532
14 8SMW EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.526
15 8SN4 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.439
16 8SN5 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.41
17 8SN6 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.434
18 8SNA EM 4.00 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.405
19 8T3T EM 3.21 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state3 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Telomere-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Transcription-associated Q07457 P02281, P84233, P06897, P62799 0.535
20 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 Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P02281, P84233, P0C0S5, P62799 0.516
21 9DDE EM 3.20 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 162 ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Homo sapiens 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, RING1 and YY1-binding protein, Ubiquitin Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer, Histone PTM readers, Histone_ubiquitination_reader, Ubiquitin P35226, Q99496, Q8N488, P0CG48 P84233, P06897, P10412, P62799, P02281 0.456
22 9EH0 EM 3.60 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 181 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-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 P02281, P06897, A0A310TTQ1, P62799 0.24
23 9IPU EM 4.30 2024-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601L 170 cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Shi, Q., Deng, Z., Zhang, L., Tong, Z., Li, J.B., Chu, G.C., Ai, H., Liu, L. 10.1002/anie.202413651 39363740 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair P61077, Q8IYW5, P62979 Q71DI3, P04908, P07305, P62805, O60814 0.237
24 8HAH EM 3.90 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 164 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.159
25 7UNC EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 155 Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT5 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, O00267 P02281, P84233, Q6AZJ8, P62799 0.344
26 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 PTM writers, Histone_methylation_H3K4_writer, Euchromatin-associated, Transcription-associated, Histone_methylation_H3K27_writer Q9BZ95 Q92133, P02281, P06897, P62799 0.507
27 8TB9 EM 4.00 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601 193 PRC2-J119-450 monomer bound to H1-nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Homo sapiens 2024 Protein Jumonji, Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Histone PTM writers, Histone chaperones, Polycomb, Transcription-associated, Heterochromatin-associated, Histone_methylation_H3K27_writer, Histone PTM erasers Q92833, Q15022, Q15910, O75530, Q09028, Q6ZN18 P84233, P06897, P62799, P07305, P02281 0.261
28 8A3Y EM 3.30 2024-07-31 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 138 Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Farnung, L., Ochmann, M., Garg, G., Vos, S.M., Cramer, P. 10.1016/j.molcel.2022.06.027 35858621 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, SPT6, RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein LEO1, RNA polymerase-associated protein RTF1 homolog, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q6PD62, Q92541, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A8J1LZU9, P84233, Q6AZJ8, P62799 0.231
29 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 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Euchromatin-associated, Ubiquitin P61964, Q15291, P0CG47 P02281, P06897, P02302, P62799 0.237
30 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164 P02281, P84233, P06897, P62799 0.26
31 6PX3 EM 4.10 2019-08-28 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Set2 bound to nucleosome Bilokapic, S., Halic, M. 10.1038/s41467-019-11726-4 31439846 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis Xenopus laevis 2019 Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone-lysine N-methyltransferase Histone PTM writers, Histone_methylation_H3K36_writer, Euchromatin-associated, Transcription-associated, Ubiquitin P0CH09, G0S676 P02281, P0CH09, P02302, P62799 0.261
32 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 Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P02281, P84233, P0C0S5, P62799 0.227
33 8HXZ EM 3.40 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Cryo-EM structure of Eaf3 CHD in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 Histone PTM writers, NuA4, Transcription-associated, Histone_acetylation_writer, DNA repair Q12432 P02281, P84233, P06897, P62799 0.326
34 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.35
35 8SN7 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.445
36 8T3W EM 3.25 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state2 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Telomere-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Transcription-associated Q07457 P02281, P84233, P06897, P62799 0.52
37 8T3Y EM 3.47 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state1 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Telomere-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Transcription-associated Q07457 P02281, P84233, P06897, P62799 0.503
38 8TAS EM 4.10 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 193 PRC2 monomer bound to nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Histone PTM writers, Histone chaperones, Polycomb, Transcription-associated, Heterochromatin-associated, Histone_methylation_H3K27_writer Q15022, Q15910, O75530, Q09028, Q6ZN18 P02281, P84233, P06897, P62799 0.259
39 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P06897, P02302, P62799 0.464
40 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_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5 P68431, P04908, P62807, P62805 0.381
41 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 Histone_methylation_H4K20_writer, Histone PTM writers, Cell cycle, Transcription-associated, Heterochromatin-associated, Nuclear division P21827, Q9NQR1 P02281, P84233, P06897, P62799 -
42 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q03164, Q15291, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.31
43 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, Q6CRQ4 Q92133, P02281, Q6AZJ8, P62799 0.385
44 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated, Ubiquitin Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, P0CG47, Q6CRQ4 P84233, P62799, Q92133, P02281, Q6AZJ8 0.372
45 7E8I EM 3.10 2021-06-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Dai, L., Dai, Y., Han, J., Huang, Y., Wang, L., Huang, J., Zhou, Z. 10.1016/j.molcel.2021.05.010 34102105 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 BRCA1-associated RING domain protein 1, Polyubiquitin-B Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, Ubiquitin, DNA repair, Histone_ubiquitination_H2AK129_writer Q99728, P0CG47 P02281, P84233, P06897, P62799 0.456
46 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 O60814, P04908, Q71DI3, P62805 0.514
47 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.254
48 8GRM EM 3.05 2023-04-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.chempr.2023.01.012 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 COMMD3 protein, Ring1B, Ubiquitin, UbcH5b Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer, Ubiquitin P35226, Q99496, P0CG47, P62837 O60814, P68431, P04908, P62805 0.516
49 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 Telomere-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair Q07457, P06104 P62805, O60814, P04908, P68431 0.393
50 8IEJ EM 3.12 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 RNF20-RNF40/hRad6A-Ub/nucleosome complex Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.molcel.2023.08.001 37633270 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1B, E3 ubiquitin-protein ligase BRE1A, Ubiquitin-conjugating enzyme E2 A Histone PTM writers, Histone_ubiquitination_H2BK120_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair O75150, Q5VTR2, P49459 P62805, O60814, P04908, P68431 0.461
51 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.311
52 8UPF EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.464
53 9DGG EM 2.98 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 ncPRC1RYBP bound to unmodified nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer P35226, Q99496 P02281, P84233, P06897, P62799 0.47
54 9EH1 EM 3.10 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerase I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, Superkiller complex protein 8, N-terminally processed, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Histone PTM writers, Histone_methylation_H3K36_writer, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Euchromatin-associated, Transcription-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q96ST2, Q6PD62, Q92541, B7Z4W0, Q9GZS3, A0A2R8YHB3, P63272, Q9BYW2 P02281, P06897, A0A310TTQ1, P62799 0.237
55 8X7K EM 3.27 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair P61077, Q8IYW5 O60814, P04908, Q71DI3, P62805 0.423
56 8X7J EM 3.39 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair P61077, Q8IYW5, P62979 O60814, P04908, Q71DI3, P62805 0.391
57 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.177
58 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 PTM writers, Cell cycle, Histone_phosphorylation_H3T3_writer Q99986 P0C0S8, P62807, Q71DI3, P62805 0.56
59 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 O60814, P04908, Q71DI3, P62805 0.571
60 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 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Euchromatin-associated, Ubiquitin B4DIJ7, P61964, Q9UBL3, Q15291, P0CG47, Q9C005 P02281, P84233, P06897, P62799 0.263
61 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P02281, P84233, P06897, P62799 0.551
62 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, F5H388 P02281, P84233, P06897, P62799 0.371
63 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 PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated P46995 P02281, P84233, Q6AZJ8, P62799 0.473
64 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 PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated Q9BYW2 P20671, P06899, Q6PI79, P62799 0.509
65 7SCY EM 4.10 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to single BRCT Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 DNA repair, Histone PTM writers, Histone_PARylation_writer P09874 P68431, P04908, P06899, P62805 0.273
66 7SCZ EM 3.50 2022-01-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to multiple BRCTs Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 DNA repair, Histone PTM writers, Histone_PARylation_writer P09874 P68431, P04908, P06899, P62805 0.425
67 8HAK EM 4.50 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.214
68 8PP7 EM 2.91 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 human RYBP-PRC1 bound to mononucleosome Ciapponi, M., Karlukova, E., Schkolziger, S., Benda, C., Muller, J. 10.1038/s41594-024-01258-x 38528151 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer P35226, Q99496 P84040, P84051, P02299, P02283 0.511
69 8SN8 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.443
70 8SN9 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.424
71 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_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P0CG47 P68431, P04908, P62807, P62805 0.455
72 9DBY EM 2.80 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, RING1 and YY1-binding protein, Ubiquitin Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer, Histone PTM readers, Histone_ubiquitination_reader, Ubiquitin P35226, Q99496, Q8N488, P0CG48 P02281, P84233, P06897, P62799 0.39
73 9EH2 EM 3.10 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 65 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16, FACT complex subunit SSRP1 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, DNA replication, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated, DNA repair, FACT 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 P02281, P06897, A0A310TTQ1, P62799 0.252
74 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 Histone PTM writers, APC/C, Cell cycle P30260 Q6FI13, P33778, P68431, P62805 0.651
75 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 PTM writers, Histone_methylation_H3K4_writer, Euchromatin-associated, Transcription-associated, Histone_methylation_H3K27_writer Q9BZ95 Q92133, P02281, P06897, P62799 0.464
76 9EGZ EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-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 P02281, P06897, A0A310TTQ1, P62799 0.261
77 8X2Y EM 4.10 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class1 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P0AEX9, P08515, P38806 Q12692, P02309, P02293, P61830 0.229
78 9EGX EM 2.90 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P02281, P06897, A0A310TTQ1, P62799 0.25
79 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, J3QS39 P02281, P84233, P06897, P62799 0.356
80 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 PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated O96028 P68431, P06899, P0C0S8, P62805 0.556
81 4R8P X-ray 3.28 2014-11-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle McGinty, R.K., Henrici, R.C., Tan, S. 10.1038/nature13890 25355358 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2014 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer P35226, Q99496 P02281, P84233, P06897, P62799 -
82 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P02281, P84233, Q6AZJ8, P62799 0.144
83 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated, Ubiquitin Q8NEZ4, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.33
84 6USJ EM 10.50 2020-10-14 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Structure of two nucleosomes bridged by human PARP2 Gaullier, G., Roberts, G., Muthurajan, U.M., Bowerman, S., Rudolph, J., Mahadevan, J., Jha, A., Rae, P.S., Luger, K. 10.1371/journal.pone.0240932 33141820 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Poly [ADP-ribose] polymerase 2 DNA repair, Histone PTM writers, Histone_PARylation_writer Q9UGN5 P68431, P04908, P06899, P62805 0.092
85 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.135
86 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P62979 O60814, P68431, P04908, P62805 0.332
87 7JZV EM 3.90 2021-02-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Witus, S.R., Burrell, A.L., Farrell, D.P., Kang, J., Wang, M., Hansen, J.M., Pravat, A., Tuttle, L.M., Stewart, M.D., Brzovic, P.S., Chatterjee, C., Zhao, W., DiMaio, F., Kollman, J.M., Klevit, R.E. 10.1038/s41594-020-00556-4 33589814 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 BRCA1,Ubiquitin-conjugating enzyme E2 D3, BRCA1-associated RING domain protein 1 Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair, Histone_ubiquitination_H2AK129_writer P38398, Q99728 Q6FI13, O60814, Q71DI3, P62805 0.313
88 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.217
89 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.373
90 8T9G EM 6.20 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 215 Automethylated PRC2 dimer bound to nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Histone PTM writers, Histone chaperones, Polycomb, Transcription-associated, Heterochromatin-associated, Histone_methylation_H3K27_writer Q15022, Q15910, O75530, Q09028, Q6ZN18 P02281, P84233, P06897, P62799 0.163
91 8HAI EM 4.70 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.212
92 7LYC EM 2.94 2021-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Ubiquitin, BRCA1-associated RING domain protein 1 Histone PTM writers, Histone_ubiquitination_H2AK127_writer, E3 ubiquitin-protein ligation, Transcription-associated, Histone_ubiquitination_H2AK125_writer, Ubiquitin, DNA repair, Histone_ubiquitination_H2AK129_writer P0CG47, Q99728 P68431, P04908, P06899, P62805 0.566
93 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 Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P06899, P0C0S5, Q71DI3, P62805 0.484
94 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P62979 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.132
95 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 PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3 P02281, P84233, Q6AZJ8, P62799 0.132
96 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 PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated G0S676 P02281, P0CH09, P02302, P62799 0.364
97 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 Histone_methylation_H4K20_writer, Histone PTM writers, Cell cycle, Transcription-associated, Heterochromatin-associated, Nuclear division Q9NQR1 P02281, P84233, P06897, P62799 0.475
98 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.23
99 8HAG EM 3.20 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.29
100 8HAL EM 4.40 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 151 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer, Transcription-associated Q92793 P68431, P04908, P06899, P62805 0.195
101 8HAM EM 4.50 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 165 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer, Transcription-associated Q92793 P68431, P04908, P06899, P62805 0.242
102 8HAN EM 4.20 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer, Transcription-associated Q92793 P68431, P04908, P06899, P62805 0.209
103 8IHM EM 3.58 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Eaf3 CHD domain bound to the nucleosome Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. 10.1038/s41422-023-00884-2 37845487 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Rco1-ABR, Chromatin modification-related protein EAF3 Histone PTM writers, NuA4, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair Q04779, Q12432 P02281, P84233, P06897, P62799 0.434
104 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q04779, Q12432 P02281, P84233, P06897, P62799 0.345
105 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 Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 O60814, P68431, P04908, P62805 0.456
106 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.067
107 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.376
108 8SMY EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.544
109 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_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P0CG47 P68431, P04908, P62807, P62805 0.432
110 8U14 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.352
111 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 O60814, P68431, P04908, P62805 0.156
112 8X2Z EM 3.90 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.237
113 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.198
114 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated, Ubiquitin Q03164, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.343
115 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3, Q9C005 P02281, P84233, P06897, P62799 0.188
116 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291 P02281, P84233, P06897, P62799 0.332
117 6X0N EM 10.00 2020-09-16 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Bilokapic, S., Suskiewicz, M.J., Ahel, I., Halic, M. 10.1038/s41586-020-2725-7 32939087 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2 DNA repair, Histone PTM writers, Histone_PARylation_writer Q9NWY4, Q9UGN5 P02281, P84233, P06897, P62799 0.113
118 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 Histone PTM writers, Polycomb, Transcription-associated, Heterochromatin-associated, Histone_methylation_H3K27_writer Q15910, Q15022 P02281, P84233, P06897, P62799 0.29
119 7K6P EM 3.20 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1 bound to the unacetylated H4 nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Truong, D.M., Lee, R., Armache, J.P., Boeke, J.D., Armache, K.J. 10.1126/science.abc6663 33479126 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Telomere-associated, Histone PTM writers, Histone_methylation_H3K79_writer Q04089, P0CG48 P02281, P84233, P06897, P62799 0.473
120 7UND EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 131 Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P02281, P84233, Q6AZJ8, P62799 0.216
121 8GRQ EM 3.87 2023-04-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.chempr.2023.01.012 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair, Histone_ubiquitination_H2AK129_writer P38398, Q99728, P61077 O60814, P04908, Q71DI3, P62805 0.352
122 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 Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 O60814, P68431, P0C0S5, P62805 0.433
123 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.324
124 8SMX EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.549
125 8SMZ EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.535
126 8SN1 EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.526
127 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 O60814, P68431, P04908, P62805 0.188
128 8X32 EM 4.40 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ Complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.114
129 8X7I EM 3.27 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair P61077, Q8IYW5, P62979 O60814, P04908, Q71DI3, P62805 0.443
130 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, Histone PTM writers, Histone_ubiquitination_H2BK120_writer, Transcription-associated Q5VTR2, O75150 P68431, P06899, P0C0S8, P62805 0.532
131 7W9V EM 3.95 2022-07-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L., Kutateladze, T.G., Kurumizaka, H. 10.1016/j.isci.2022.104563 35754730 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.307
132 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated, Ubiquitin Q03164, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.461
133 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P02281, P84233, P06897, P62799 0.38
134 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 PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q03164, Q15291, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.338
135 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 Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG48 P02281, P84233, P06897, P62799 0.436
136 8HAJ EM 4.80 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 164 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.2
137 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.378
138 8SN2 EM 3.60 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.452
139 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 O60814, P68431, P04908, P62805 0.263
140 8X2X EM 3.80 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P0AEX9, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.261
141 8X30 EM 4.30 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 Structure of piccolo NuA4 and H2A.Z nucleosome 2:1 complex Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, Q540A3, P38806, P47128 Q12692, P02309, P02293, P61830 0.165
142 8X31 EM 6.20 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.123
143 9EGY EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 160 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P02281, P06897, A0A310TTQ1, P62799 0.256
144 7VVU EM 3.40 2022-08-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 180 NuA4 HAT module bound to the nucleosome Qu, K., Chen, K., Wang, H., Li, X., Chen, Z. 10.1038/s41586-022-05303-x 36198799 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Histone acetyltransferase ESA1, Enhancer of polycomb-like protein 1, Chromatin modification-related protein YNG2, Chromatin modification-related protein EAF6 Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Euchromatin-associated, Histone_acetylation_writer Q08649, P43572, P38806, P47128 P02281, P84233, P06897, P62799 0.314
145 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.463
146 8SN0 EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.547
147 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 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.44
148 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 Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P02281, P84233, P06897, P62799 0.393