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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 8H1T EM 3.00 2023-02-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Ge, W., Yu, C., Li, J., Yu, Z., Li, X., Zhang, Y., Liu, C.P., Li, Y., Tian, C., Zhang, X., Li, G., Zhu, B., Xu, R.M. 10.1038/s41586-023-05841-y 36991118 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Ubiquitin carboxyl-terminal hydrolase BAP1, Ubiquitin, Polycomb group protein ASXL1 Histone PTM erasers, Ubiquitin, Polycomb, Histone_deubiquitination_H2AK119, Transcription-associated Q92560, P0CG47, Q8IXJ9 Q16778, P20671, P68431, P10412, P62805 0.435
1 8H0V EM 3.80 2022-12-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.2 601 201 RNA polymerase II transcribing a chromatosome (type I) Hirano, R., Ehara, H., Kujirai, T., Uejima, T., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1038/s41467-022-35003-z 36435862 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P04908, P68431, P16403, P62805 0.228
2 8H0W EM 4.60 2022-12-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.2 601 196 RNA polymerase II transcribing a chromatosome (type II) Hirano, R., Ehara, H., Kujirai, T., Uejima, T., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1038/s41467-022-35003-z 36435862 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P04908, P68431, P16403, P62805 0.16
3 6A5L EM 5.60 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.182
4 6A5O EM 9.90 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 178 RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.083
5 6A5P EM 7.00 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 168 RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.138
6 6A5R EM 8.70 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 136 RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.11
7 6A5T EM 6.70 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.151
8 6A5U EM 7.60 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.14
9 6INQ EM 6.90 2019-04-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 125 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.149
10 6IR9 EM 3.80 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.264
11 6J4W EM 7.90 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 171 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, F2QTN1, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.123
12 6J4X EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.233
13 6J4Y EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.235
14 6J4Z EM 4.10 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Spt5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.244
15 6J50 EM 4.70 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.195
16 6J51 EM 4.20 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.23
17 6LTJ EM 3.70 2020-02-12 octamer 1 H3.3 canonical_H4 H2A.X canonical_H2B 601 119 Structure of nucleosome-bound human BAF complex He, S., Wu, Z., Tian, Y., Yu, Z., Yu, J., Wang, X., Li, J., Liu, B., Xu, Y. 10.1126/science.aaz9761 32001526 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4 Transcription-associated, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785 P02281, Q6PI79, P06897, P62799 0.007
18 7WBV EM 4.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.267
19 7WBW EM 7.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.137
20 7WBX EM 4.00 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 150 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.298
21 7XSE EM 3.60 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 134 RNA polymerase II elongation complex transcribing a nucleosome (EC42) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.238
22 7XSX EM 3.80 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 108 RNA polymerase II elongation complex transcribing a nucleosome (EC49) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.227
23 7XSZ EM 3.40 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 155 RNA polymerase II elongation complex transcribing a nucleosome (EC115) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.248
24 7XT7 EM 4.20 2022-10-12 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, F2QPX0, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.207
25 7XTD EM 3.90 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.221
26 7XTI EM 3.90 2022-10-12 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 85 RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.223
27 8JH2 EM 5.70 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.145
28 8JH3 EM 3.70 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.255
29 8JH4 EM 3.20 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 178 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.313
30 4LD9 X-ray 3.31 2013-08-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Arnaudo, N., Fernandez, I.S., McLaughlin, S.H., Peak-Chew, S.Y., Rhodes, D., Martino, F. 10.1038/nsmb.2641 23934150 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 Regulatory protein SIR3 Transcription-associated P06701 P02281, P84233, P06897, P62799 -
31 4ZUX X-ray 3.82 2016-02-24 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Morgan, M.T., Haj-Yahya, M., Ringel, A.E., Bandi, P., Brik, A., Wolberger, C. 10.1126/science.aac5681 26912860 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 Ubiquitin carboxyl-terminal hydrolase 8, Transcription and mRNA export factor SUS1, SAGA-associated factor 11, Polyubiquitin-B, SAGA-associated factor 73 Histone PTM erasers, Ubiquitin, SAGA, Transcription-associated, Histone_deubiquitination P50102, Q6WNK7, Q03067, P0CG47, P53165 P02281, P84233, P06897, P62799 -
32 5O9G EM 4.80 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 162 Structure of nucleosome-Chd1 complex Farnung, L., Vos, S.M., Wigge, C., Cramer, P. 10.1038/nature24046 29019976 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Chromo domain-containing protein 1 Transcription-associated, CHD, Chromatin remodelers P32657 P02281, P84233, P06897, P62799 0.018
33 5X0X EM 3.97 2017-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome Liu, X., Li, M., Xia, X., Li, X., Chen, Z. 10.1038/nature22036 28424519 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.372
34 6HTS EM 4.80 2018-11-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Cryo-EM structure of the human INO80 complex bound to nucleosome Ayala, R., Willhoft, O., Aramayo, R.J., Wilkinson, M., McCormack, E.A., Ocloo, L., Wigley, D.B., Zhang, X. 10.1038/s41586-018-0021-6 29643506 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit B INO80, DNA repair, DNA replication, Transcription-associated, Chromatin remodelers Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q9C086 P62805, P06899, P04908, P68431 0.181
35 6I84 EM 4.40 2019-01-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 169 Structure of transcribing RNA polymerase II-nucleosome complex Farnung, L., Vos, S.M., Cramer, P. 10.1038/s41467-018-07870-y 30575770 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4 Transcription-associated, RNA polymerases P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422 P02281, P84233, P06897, P62799 0.241
36 6KW3 EM 7.13 2019-11-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The ClassA RSC-Nucleosome Complex Ye, Y., Wu, H., Chen, K., Clapier, C.R., Verma, N., Zhang, W., Deng, H., Cairns, B.R., Gao, N., Chen, Z. 10.1126/science.aay0033 31672915 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Chromatin structure-remodeling complex protein RSC58, Chromatin structure-remodeling complex protein RSC30, Chromatin structure-remodeling complex protein RSC8, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC6, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex subunit RSC4, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.086
37 6KW5 EM 10.13 2020-09-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The ClassC RSC-Nucleosome Complex Ye, Y.P., Wu, H., Chen, K.J., Verma, N., Cairns, B., Gao, N., Chen, Z.C. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromatin structure-remodeling complex protein RSC58, Chromatin structure-remodeling complex protein RSC30, Chromatin structure-remodeling complex protein RSC8, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC6, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex subunit RSC4, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P84233, P06897, P62799, A0A1L8G0X3 0.062
38 6NE3 EM 3.90 2019-07-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2 Armache, J.P., Gamarra, N., Johnson, S.L., Leonard, J.D., Wu, S., Narlikar, G.J., Cheng, Y. 10.7554/eLife.46057 31210637 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Transcription-associated, Heterochromatin-associated, Chromatin remodelers, ISWI O60264 P02281, P84233, P06897, P62799 0.42
39 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 2019 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164 P02281, P84233, P06897, P62799 0.26
40 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 2019 Retinoblastoma-binding protein 5 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291 P02281, P84233, P06897, P62799 0.332
41 6T90 EM 3.05 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 141 OCT4-SOX2-bound nucleosome - SHL-6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription-associated, Transcription factors P42212, P48431 P62805, P06899, P04908, P68431 0.451
42 6UPK EM 4.90 2019-12-11 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 72 Structure of FACT_subnucleosome complex 1 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Histone chaperones, FACT, DNA repair, DNA replication, Transcription-associated Q9Y5B9, Q08945 P62805, P62807, P68431, Q93077 0.203
43 6UPL EM 7.40 2019-12-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 79 Structure of FACT_subnucleosome complex 2 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Histone chaperones, FACT, DNA repair, DNA replication, Transcription-associated Q9Y5B9, Q08945 P62805, P62807, P68431, Q93077 0.173
44 6V92 EM 20.00 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 RSC-NCP Patel, A.B., Moore, C.M., Greber, B.J., Luo, J., Zukin, S.A., Ranish, J., Nogales, E. 10.7554/eLife.54449 31886770 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Actin-related protein 7, Actin-like protein ARP9, High temperature lethal protein 1, Chromatin structure-remodeling complex protein RSC14, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC4, Chromatin structure-remodeling complex protein RSC8, Chromatin structure-remodeling complex protein RSC6, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex protein RSC58, Regulator of Ty1 transposition protein 102, Chromatin structure-remodeling complex subunit SFH1, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC30 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers Q12406, Q05123, Q9URQ5, P38210, P32832, Q06488, Q06639, Q02206, P43609, P25632, Q03124, Q07979, P53330, Q06168, P32597, P38781 P62805, O60814, P04908, P68431 0.053
45 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 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.135
46 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 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.177
47 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 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.167
48 6YOV EM 3.42 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 OCT4-SOX2-bound nucleosome - SHL+6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription-associated, Transcription factors P42212, P48431 P62805, P06899, P04908, P68431 0.35
49 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 2021 Isoform 2 of N-lysine methyltransferase KMT5A Histone_methylation_H4K20_writer, Heterochromatin-associated, Transcription-associated, Nuclear division, Histone PTM writers Q9NQR1 P62805, P06899, P04908, P68431 0.514
50 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 2021 Isoform 7 of Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2 D3 E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK125_writer, DNA repair, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Transcription-associated, Histone PTM writers P38398, Q99728, P61077 P62805, P06899, P04908, P68431 0.458
51 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 2021 Ubiquitin, BRCA1-associated RING domain protein 1 E3 ubiquitin-protein ligation, Ubiquitin, DNA repair, Histone_ubiquitination_H2AK125_writer, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Transcription-associated, Histone PTM writers P0CG47, Q99728 P62805, P06899, P04908, P68431 0.566
52 7NKX EM 2.90 2021-08-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 139 RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Chromo domain-containing protein 1, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Heterochromatin-associated, CHD, RNA polymerases, Transcription factors, Transcription-associated, Centromere-associated, Chromatin remodelers, SPT4-SPT5 complex P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P32657, P32914, P27692 P02281, P84233, P06897, P62799 0.444
53 7NKY EM 3.20 2021-07-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 148 RNA Polymerase II-Spt4/5-nucleosome-FACT structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, FACT complex subunit POB3, FACT complex subunit SPT16, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Heterochromatin-associated, Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, Centromere-associated, SPT4-SPT5 complex P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, Q04636, P32558, P32914, P27692 P02281, P84233, P06897, P62799 0.358
54 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 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT5 Histone chaperones, RNA polymerases, Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, Transcription-associated, Histone PTM writers, PAF1C A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, O00267 P02281, P84233, P62799, Q6AZJ8 0.344
55 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 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Histone chaperones, RNA polymerases, Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, Transcription-associated, Histone PTM writers, PAF1C A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P02281, P84233, P62799, Q6AZJ8 0.216
56 7VDT EM 2.80 2022-05-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Yuan, J.J., Chen, K.J., Zhang, W.B., Chen, Z.C. 10.1038/s41586-022-04658-5 35477757 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Isoform 2 of Transcription activator BRG1 Transcription-associated, Chromatin remodelers, SWI/SNF P51532 P02281, P84233, P06897, P62799 0.549
57 7VDV EM 3.40 2022-05-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 The overall structure of human chromatin remodeling PBAF-nucleosome complex Yuan, J.J., Chen, K.J., Zhang, W.B., Chen, Z.C. 10.1038/s41586-022-04658-5 35477757 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Isoform 2 of Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2, PHD finger protein 10, Isoform 2 of Bromodomain-containing protein 7, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Protein polybromo-1 Transcription-associated, PBAF (SWI/SNF), Chromatin remodelers, SWI/SNF P51532, O96019, P60709, Q68CP9, Q8WUB8, Q9NPI1, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q86U86 P02281, P84233, P06897, P62799 0.315
58 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 2022 Histone acetyltransferase ESA1, Enhancer of polycomb-like protein 1, Chromatin modification-related protein YNG2, Chromatin modification-related protein EAF6 Heterochromatin-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 Q08649, P43572, P38806, P47128 P02281, P84233, P06897, P62799 0.314
59 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 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 Heterochromatin-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 Q06337, P80428, P60010, P43572, P53201, P38811, Q08649, P38806, P47128 P02281, P84233, P06897, P62799 0.108
60 7X3T EM 5.40 2023-09-20 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 339 Cryo-EM structure of ISW1a-dinucleosome Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI one complex protein 3, ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P43596, P38144 P02281, P84233, P06897, P62799 0.192
61 7X3W EM 3.10 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of ISW1-N1 nucleosome Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, P84233, P06897, P62799 0.489
62 7X3X EM 3.20 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of N1 nucleosome-RA Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, P84233, P06897, P62799 0.44
63 7ZI4 EM 3.20 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Vance, N.R., Ayala, R., Willhoft, O., Tvardovskiy, A., McCormack, E.A., Bartke, T., Zhang, X., Wigley, D.B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit C, INO80 complex subunit B INO80, DNA repair, DNA replication, Transcription-associated, Chromatin remodelers Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q6PI98, Q9C086 P62805, P06899, P04908, P68431 0.462
64 8BVW EM 4.00 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 206 RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P02281, P84233, P06897, P62799 0.234
65 8BYQ EM 4.10 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P02281, P84233, P06897, P62799 0.187
66 8BZ1 EM 3.80 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2 Transcription-associated, Transcription factors, RNA polymerases A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, I3LJZ9, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657 P02281, P84233, P06897, P62799 0.244
67 8EVH EM 2.85 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 141 CX3CR1 nucleosome and wild type PU.1 complex Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Single-chain variable fragment, Transcription factor PU.1 Transcription-associated, Transcription factors P17433 P62805, Q16778, Q16777, P68431 0.509
68 8EVI EM 2.64 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 143 CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Single-chain variable fragment, Transcription factor PU.1 Transcription-associated, Transcription factors P17433 P62805, Q16778, Q16777, P68431 0.559
69 8EVJ EM 4.10 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 138 CX3CR1 nucleosome bound PU.1 and C/EBPa Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 ScFv, Transcription factor PU.1 Transcription-associated, Transcription factors P17433 P62805, Q16778, Q16777, P68431 0.31
70 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 2023 Isoform 2 of Menin Transcription-associated, Histone_methylation_H3K4_writer, Histone PTM writers O00255 P02281, P84233, P06897, P62799 0.459
71 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 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM writers, Histone_ubiquitination_H2BK120_writer Q5VTR2, O75150 P62805, P0C0S8, P06899, P68431 0.532
72 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 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM writers, Histone_ubiquitination_H2BK120_writer Q5VTR2, O75150 P62805, P0C0S8, P06899, P68431 0.532
73 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 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone_methylation_H4K20_writer, Heterochromatin-associated, Histone PTM writers Q4FZB7 O60814, P62805, P0C0S5, P68431 0.433
74 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 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone_methylation_H4K20_writer, Heterochromatin-associated, Histone PTM writers Q4FZB7 P62805, O60814, P04908, P68431 0.456
75 8OF4 EM 2.94 2023-08-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome Bound human SIRT6 (Composite) Smirnova, E., Bignon, E., Schultz, P., Papai, G., Ben Shem, A. 10.7554/eLife.87989 38415718 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Histone PTM erasers, Histone_deacetylation, Histone_deacetylation_H3K9, DNA repair, Transcription-associated Q8N6T7 P02281, P84233, P06897, P62799 0.446
76 8OSJ EM 6.20 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 128 Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription-associated, Transcription factors O08785, Q9WTL8 P62805, P06899, P04908, P68431 0.219
77 8OSK EM 3.60 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 124 Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription-associated, Transcription factors O08785, Q9WTL8 P62805, P06899, P04908, P68431 0.267
78 8OSL EM 4.90 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription-associated, Transcription factors O08785, Q9WTL8 P62805, P06899, P04908, P68431 0.177
79 8OTS EM 3.30 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 OCT4 and MYC-MAX co-bound to a nucleosome Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Green fluorescent protein,POU domain, class 5, transcription factor 1, Myc proto-oncogene protein, Protein max Transcription-associated, Transcription factors P42212, P01106, P61244 P62805, P06899, P04908, P68431 0.404
80 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.526
81 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.549
82 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.544
83 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.535
84 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.547
85 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.526
86 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.452
87 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.429
88 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.439
89 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.41
90 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.434
91 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.445
92 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.443
93 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.424
94 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.405
95 8SPS EM 3.00 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P62805, Q16778, Q16777, P68431 0.434
96 8SPU EM 2.80 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of ESRRB nucleosome bound OCT4 at site c Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P62805, Q16778, Q16777, P68431 0.496
97 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 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Rco1, histone N-terminal tail Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P22579, P32561, Q12432, Q04779 P02281, P02302, P06897, P62799 0.464
98 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.352
99 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 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.464
100 8X15 EM 3.20 2024-03-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 137 Structure of nucleosome-bound SRCAP-C in the apo state Yu, J., Wang, Q., Yu, Z., Li, W., Wang, L., Xu, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2, Actin, cytoplasmic 1, N-terminally processed, Actin-like protein 6A, DNA methyltransferase 1-associated protein 1, YEATS domain-containing protein 4 Transcription-associated, SWI/SNF, Chromatin remodelers, INO80 Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, P62807, P68431, Q93077 0.218
101 8X19 EM 3.20 2024-03-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state Yu, J., Wang, Q., Yu, Z., Li, W., Wang, L., Xu, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2, Actin, cytoplasmic 1, Actin-like protein 6A, DNA methyltransferase 1-associated protein 1, YEATS domain-containing protein 4 Transcription-associated, SWI/SNF, Chromatin remodelers, INO80 Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, P62807, P68431, Q93077 0.292
102 8X1C EM 3.20 2024-03-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of nucleosome-bound SRCAP-C in the ADP-bound state Yu, J., Wang, Q., Yu, Z., Li, W., Wang, L., Xu, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2, Actin, cytoplasmic 1, Actin-like protein 6A, DNA methyltransferase 1-associated protein 1, YEATS domain-containing protein 4 Transcription-associated, SWI/SNF, Chromatin remodelers, INO80 Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, P62807, P68431, Q93077 0.297
103 4KUD X-ray 3.20 2013-08-07 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B alphasat_146 146 Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle Yang, D., Fang, Q., Wang, M., Ren, R., Wang, H., He, M., Sun, Y., Yang, N., Xu, R.M. 10.1038/nsmb.2637 23934152 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae 2013 Regulatory protein SIR3 Transcription-associated P06701 P02309, P61830, P04912, P02293 -
104 8HE5 EM 6.95 2023-07-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, DNA repair protein Transcription-associated, Transcription factors, RNA polymerases, DNA repair C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R198 P62805, P06899, P04908, P68431 0.105
105 3TU4 X-ray 3.00 2011-11-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Armache, K.J., Garlick, J.D., Canzio, D., Narlikar, G.J., Kingston, R.E. 10.1126/science.1210915 22096199 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2011 Regulatory protein SIR3 Transcription-associated P06701 P02281, P84233, P06897, P62799 -
106 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 2014 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 E3 ubiquitin-protein ligation, Polycomb, Histone_ubiquitination_H2AK119_writer, Transcription-associated, Histone PTM writers P35226, Q99496 P02281, P84233, P06897, P62799 -
107 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 2016 Guanine nucleotide exchange factor SRM1, N-lysine methyltransferase SETD8 Histone_methylation_H4K20_writer, Heterochromatin-associated, Transcription-associated, Nuclear division, Histone PTM writers P21827, Q9NQR1 P02281, P84233, P06897, P62799 -
108 5X0Y EM 4.69 2017-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome Liu, X., Li, M., Xia, X., Li, X., Chen, Z. 10.1038/nature22036 28424519 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.315
109 5Z3L EM 4.31 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex in apo state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.261
110 5Z3O EM 3.62 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex in ADP state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.349
111 5Z3U EM 4.31 2019-05-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P62799, Q6AZJ8 0.372
112 5Z3V EM 4.22 2019-05-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P62799, Q6AZJ8 0.356
113 6G0L EM 10.00 2018-08-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 176 Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome Sundaramoorthy, R., Hughes, A.L., El-Mkami, H., Norman, D.G., Ferreira, H., Owen-Hughes, T. 10.7554/eLife.35720 30079888 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2018 Chromo domain-containing protein 1 Transcription-associated, CHD, Chromatin remodelers P32657 Q92133, P06897, P62799, A0A1L8G0X3 0.095
114 6GEJ EM 3.60 2018-10-17 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 154 Chromatin remodeller-nucleosome complex at 3.6 A resolution. Willhoft, O., Ghoneim, M., Lin, C.L., Chua, E.Y.D., Wilkinson, M., Chaban, Y., Ayala, R., McCormack, E.A., Ocloo, L., Rueda, D.S., Wigley, D.B. 10.1126/science.aat7716 30309918 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 2018 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2 INO80, Euchromatin-associated, Transcription-associated, SWR1 (INO80), Chromatin remodelers Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P61830, P04911, P02293 0.372
115 6GEN EM 3.60 2018-10-17 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 173 Chromatin remodeller-nucleosome complex at 4.5 A resolution. Willhoft, O., Ghoneim, M., Lin, C.L., Chua, E.Y.D., Wilkinson, M., Chaban, Y., Ayala, R., McCormack, E.A., Ocloo, L., Rueda, D.S., Wigley, D.B. 10.1126/science.aat7716 30309918 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 2018 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2 INO80, Euchromatin-associated, Transcription-associated, SWR1 (INO80), Chromatin remodelers Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P61830, P04911, P02293 0.195
116 6IRO EM 3.40 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 the crosslinked complex of ISWI-nucleosome in the ADP-bound state Yan, L., Wu, H., Li, X., Gao, N., Chen, Z. 10.1038/s41594-019-0199-9 30872815 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, P84233, P06897, P62799 0.435
117 6JYL EM 3.37 2019-05-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state Yan, L., Wu, H., Li, X., Gao, N., Chen, Z. 10.1038/s41594-019-0199-9 30872815 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.452
118 6K1P EM 3.87 2019-05-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The complex of ISWI-nucleosome in the ADP.BeF-bound state Yan, L., Wu, H., Li, X., Gao, N., Chen, Z. 10.1038/s41594-019-0199-9 30872815 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.42
119 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 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q03164, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.461
120 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 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q03164, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.343
121 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 2019 Histone-lysine N-methyltransferase 2C, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q8NEZ4, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.33
122 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 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers Q03164, Q15291, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.338
123 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 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers Q03164, Q15291, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.31
124 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 (strain ATCC 204508 / S288c) Xenopus laevis 2019 Histone-lysine N-methyltransferase Transcription-associated, Histone_methylation_H3K36_writer, Histone PTM writers G0S676 P02281, P02302, P62799, P0CH09 0.364
125 6OM3 X-ray 3.30 2019-07-10 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle De Ioannes, P., Leon, V.A., Kuang, Z., Wang, M., Boeke, J.D., Hochwagen, A., Armache, K.J. 10.1038/s41467-019-10609-y 31263106 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Origin recognition complex subunit 1 Transcription-associated, ORC, DNA replication P54784 P02281, P84233, P06897, P62799 -
126 6PA7 EM 2.94 2020-06-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 166 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Xu, T.H., Liu, M., Zhou, X.E., Liang, G., Zhao, G., Xu, H.E., Melcher, K., Jones, P.A. 10.1038/s41586-020-2747-1 32968275 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 DNA (cytosine-5)-methyltransferase 3A, DNA (cytosine-5)-methyltransferase 3B Transcription-associated, DNA modification Q9Y6K1, Q9UBC3 P02281, P84233, P06897, P62799 0.403
127 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 (strain ATCC 204508 / S288c) Xenopus laevis 2019 Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone-lysine N-methyltransferase Transcription-associated, Ubiquitin, Histone_methylation_H3K36_writer, Histone PTM writers P0CH09, G0S676 P02281, P02302, P62799, P0CH09 0.261
128 6R1U EM 4.36 2019-04-24 octamer 1 H3.3,canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Marabelli, C., Marrocco, B., Pilotto, S., Chittori, S., Picaud, S., Marchese, S., Ciossani, G., Forneris, F., Filippakopoulos, P., Schoehn, G., Rhodes, D., Subramaniam, S., Mattevi, A. 10.1016/j.celrep.2019.03.061 30970244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Lysine-specific histone demethylase 1B, Putative oxidoreductase GLYR1 Histone PTM erasers, Histone_demethylation_H3K4, Histone PTM readers, Transcription-associated, Histone_methylation_H3K36_reader Q8NB78, Q49A26 P02281, P84233, P06897, P62799 0.198
129 6R25 EM 4.61 2019-04-24 octamer 1 H3.3,canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3 Marabelli, C., Marrocco, B., Pilotto, S., Chittori, S., Picaud, S., Marchese, S., Ciossani, G., Forneris, F., Filippakopoulos, P., Schoehn, G., Rhodes, D., Subramaniam, S., Mattevi, A. 10.1016/j.celrep.2019.03.061 30970244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Lysine-specific histone demethylase 1B, NPAC Histone PTM erasers, Histone_demethylation_H3K4, Histone PTM readers, Transcription-associated, Histone_methylation_H3K36_reader Q8NB78, Q49A26 P02281, P84233, P06897, P62799 0.186
130 6T9L EM 3.60 2020-01-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 SAGA DUB module bound to a ubiqitinated nucleosome Wang, H., Dienemann, C., Stutzer, A., Urlaub, H., Cheung, A.C.M., Cramer, P. 10.1038/s41586-020-1933-5 31969703 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Ubiquitin carboxyl-terminal hydrolase 8, Transcription and mRNA export factor SUS1, SAGA-associated factor 11, SAGA-associated factor 73, Polyubiquitin-C Histone PTM erasers, Ubiquitin, SAGA, Transcription-associated, Histone_deubiquitination P50102, Q6WNK7, Q03067, P53165, P0CG48 P02281, P84233, P06897, P62799 0.394
131 6TDA EM 15.00 2020-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Wagner, F.R., Dienemann, C., Wang, H., Stutzer, A., Tegunov, D., Urlaub, H., Cramer, P. 10.1038/s41586-020-2088-0 32188943 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC8, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex protein RSC6, Chromatin structure-remodeling complex protein RSC58, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC4, Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers Q06168, P43609, P32832, Q03124, P25632, Q07979, Q9URQ5, Q02206, P32597, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.081
132 6UXW EM 8.96 2020-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 SWI/SNF nucleosome complex with ADP-BeFx Han, Y., Reyes, A.A., Malik, S., He, Y. 10.1038/s41586-020-2087-1 32188938 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Transcription regulatory protein SNF2, SWI/SNF chromatin-remodeling complex subunit SWI1, SWI/SNF chromatin-remodeling complex subunit SNF5, SWI/SNF complex subunit SWI3, Transcription regulatory protein SNF12, Transcription regulatory protein SNF6, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers, SWI/SNF P22082, P09547, P18480, P32591, P53628, P18888, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.122
133 6VZ4 EM 3.90 2020-12-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state Baker, R.W., Reimer, J.M., Carman, P.J., Turegun, B., Arakawa, T., Dominguez, R., Leschziner, A.E. 10.1038/s41594-020-00528-8 33288924 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers P32597, Q12406, Q05123, P53330 P02281, Q92133, P06897, P62799 -
134 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 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_methylation_H3K27_writer, Histone_methylation_H3K9_writer, Polycomb, Transcription-associated, Histone PTM writers Q15910, Q15022 P02281, P84233, P06897, P62799 0.29
135 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 2021 BRCA1-associated RING domain protein 1, Polyubiquitin-B E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK125_writer, DNA repair, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Ubiquitin, Transcription-associated, Histone PTM writers Q99728, P0CG47 P02281, P84233, P06897, P62799 0.456
136 7EG6 EM 3.10 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Snf5 Finger Helix bound to the nucleosome He, Z.Y., Chen, K.J., Ye, Y.P., Chen, Z.C. 10.1038/s41421-021-00262-5 33907182 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 SWI/SNF chromatin-remodeling complex subunit SNF5 Transcription-associated, Chromatin remodelers, SWI/SNF P18480 P02281, P84233, P06897, P62799 0.513
137 7EGP EM 6.90 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 166 The structure of SWI/SNF-nucleosome complex He, Z.Y., Chen, K.J., Ye, Y.P., Chen, Z.C. 10.1038/s41421-021-00262-5 33907182 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Transcription regulatory protein SNF2, SWI/SNF chromatin-remodeling complex subunit SWI1, SWI/SNF chromatin-remodeling complex subunit SNF5, SWI/SNF complex subunit SWI3, Transcription regulatory protein SNF12, Transcription regulatory protein SNF6, SWI/SNF global transcription activator complex subunit SWP82, Regulator of Ty1 transposition protein 102, Actin-related protein 7, Actin-like protein ARP9 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers, SWI/SNF P22082, P09547, P18480, P32591, P53628, P18888, P43554, P53330, Q12406, Q05123 P02281, P84233, P62799, Q6AZJ8 0.105
138 7MBM EM NaN 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 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.198
139 7MBN EM NaN 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 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.217
140 7OH9 EM 3.00 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome with TBP and TFIIA bound at SHL -6 Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription-associated, Transcription factors P13393, P32773, P32774 P02281, P84233, P06897, P62799 0.49
141 7OHA EM 2.90 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 122 nucleosome with TBP and TFIIA bound at SHL +2 Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription-associated, Transcription factors P13393, P32773, P32774 P02281, P84233, P06897, P62799 0.516
142 7OHB EM 3.40 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 TBP-nucleosome complex Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein Transcription-associated, Transcription factors P13393 P02281, P84233, P06897, P62799 0.435
143 7SSA EM 3.20 2023-04-05 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 137 Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome Donovan, B.T., Chen, H., Eek, P., Meng, Z., Jipa, C., Tan, S., Bai, L., Poirier, M.G. 10.1016/j.molcel.2023.03.006 36996811 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 2023 Centromere-binding protein 1 Transcription-associated P17106 P04911, P84233, P62799, P02293 0.449
144 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 2022 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.307
145 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 2022 N-lysine methyltransferase KMT5A Histone_methylation_H4K20_writer, Heterochromatin-associated, Transcription-associated, Nuclear division, Histone PTM writers Q9NQR1 P02281, P84233, P06897, P62799 0.475
146 7Y8R EM 4.40 2022-12-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 165 The nucleosome-bound human PBAF complex Wang, L., Yu, J., Yu, Z., Wang, Q., Li, W., Ren, Y., Chen, Z., He, S., Xu, Y. 10.1038/s41467-022-34859-5 36496390 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Transcription activator BRG1, ACTB protein (Fragment), Actin-like protein 6A, AT-rich interactive domain-containing protein 2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, PHD finger protein 10, Bromodomain-containing protein 7, Protein polybromo-1 Transcription-associated, PBAF (SWI/SNF), Chromatin remodelers, SWI/SNF P51532, P60709, O96019, Q68CP9, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q8WUB8, Q9NPI1, Q86U86 P62805, P62807, P68431, Q93077 0.172
147 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 2023 Chromatin modification-related protein EAF3 DNA repair, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 Q12432 P02281, P84233, P06897, P62799 0.572
148 8G88 EM 2.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 168 Human Oct4 bound to nucleosome with human nMatn1 sequence Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P02281, P84233, P62799, Q6AZJ8 0.199
149 8G8B EM 4.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 168 Nucleosome with human nMatn1 sequence in complex with Human Oct4 Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P02281, P84233, P62799, Q6AZJ8 0.233
150 8G8G EM 3.20 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 174 Interaction of H3 tail in LIN28B nucleosome with Oct4 Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P02281, P84233, P62799, Q6AZJ8 0.218
151 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 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.29
152 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 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.159
153 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 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.212
154 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 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.2
155 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 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.214
156 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 2023 CREB-binding protein Transcription-associated, Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P62805, P06899, P04908, P68431 0.195
157 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 2023 CREB-binding protein Transcription-associated, Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P62805, P06899, P04908, P68431 0.242
158 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 2023 CREB-binding protein Transcription-associated, Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P62805, P06899, P04908, P68431 0.209
159 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 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.35
160 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 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 E3 ubiquitin-protein ligation, Polycomb, Histone_ubiquitination_H2AK119_writer, Transcription-associated, Histone PTM writers P35226, Q99496 P02283, A0A0B4KFZ9, P84051, A0A7L0PXJ3 0.511
161 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 2023 E3 ubiquitin-protein ligase BRE1 E3 ubiquitin-protein ligation, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457 P02281, P84233, P06897, P62799 0.535
162 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 2023 E3 ubiquitin-protein ligase BRE1 E3 ubiquitin-protein ligation, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457 P02281, P84233, P06897, P62799 0.52
163 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 2023 E3 ubiquitin-protein ligase BRE1 E3 ubiquitin-protein ligation, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457 P02281, P84233, P06897, P62799 0.503
164 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 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone_methylation_H4K20_writer, Heterochromatin-associated, Histone PTM writers Q4FZB7 P02281, P84233, P62799, P0C0S5 0.516
165 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., Armache, K.-J. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone_methylation_H4K20_writer, Heterochromatin-associated, Histone PTM writers Q4FZB7 P02281, P84233, P06897, P62799 0.393
166 4JJN X-ray 3.09 2013-05-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome Wang, F., Li, G., Altaf, M., Lu, C., Currie, M.A., Johnson, A., Moazed, D. 10.1073/pnas.1300126110 23650358 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae 2013 Regulatory protein SIR3 Transcription-associated P06701 P02309, P61830, P04912, P02294 -
167 6T7A EM 3.70 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Transcription factor SOX-11 Transcription-associated, Transcription factors P35716 P62805, O60814, P04908, Q71DI3 0.37
168 6T7B EM 5.10 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of human Sox2 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Transcription factor SOX-2 Transcription-associated, Transcription factors P48431 P62805, O60814, P04908, Q71DI3 0.217
169 6T7C EM 4.00 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Transcription factor SOX-11 Transcription-associated, Transcription factors P35716 P62805, O60814, P04908, Q71DI3 0.355
170 6T7D EM 4.40 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 117 Structure of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Transcription factor SOX-11 Transcription-associated, Transcription factors P35716 P62805, O60814, P04908, Q71DI3 0.323
171 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 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, H3 N-terminus, Spp1 COMPASS, Histone_methylation_H3K4_writer, Telomere-associated, Transcription-associated, Histone PTM writers Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, Q6CRQ4 P02281, Q92133, P62799, Q6AZJ8 0.385
172 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 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, Ubiquitin, Spp1 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Telomere-associated, Transcription-associated, Histone PTM writers Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, P0CG47, Q6CRQ4 P02281, Q6AZJ8, Q92133, P62799, P84233 0.372
173 6VYP X-ray 4.99 2020-05-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 191 Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Kim, S.A., Zhu, J., Yennawar, N., Eek, P., Tan, S. 10.1016/j.molcel.2020.04.019 32396821 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Lysine-specific histone demethylase 1A, REST corepressor 1 Transcription-associated, Histone PTM erasers, Histone_demethylation_H3K9, Histone_demethylation_H3K4 O60341, Q9UKL0 P02281, P84233, P06897, P62799 -
174 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 2021 Histone-lysine N-methyltransferase NSD2 Transcription-associated, Euchromatin-associated, Histone_methylation_H3K36_writer, Histone PTM writers O96028 P62805, P0C0S8, P06899, P68431 0.556
175 7E9C EM 3.50 2022-09-07 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 130 Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M. 0 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 2022 Origin recognition complex subunit 1 Transcription-associated, ORC, DNA replication P54784 P02309, P61830, P04912, P02294 0.311
176 7E9F EM 4.00 2022-09-07 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 123 Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M. 0 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 2022 Origin recognition complex subunit 1 Transcription-associated, ORC, DNA replication P54784 P02309, P61830, P04912, P02294 0.319
177 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 2022 cDNA FLJ56846, highly similar to Zinc finger protein HRX, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2, Retinoblastoma-binding protein 5, Polyubiquitin-B, Protein dpy-30 homolog COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers B4DIJ7, P61964, Q9UBL3, Q15291, P0CG47, Q9C005 P02281, P84233, P06897, P62799 0.263
178 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 2022 WD repeat-containing protein 5, Retinoblastoma-binding protein 5, Polyubiquitin-B COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers P61964, Q15291, P0CG47 P02281, P02302, P06897, P62799 0.237
179 6S01 EM 3.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Wang, H., Farnung, L., Dienemann, C., Cramer, P. 10.1038/s41594-019-0345-4 31819277 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.529
180 7TN2 EM 2.30 2022-03-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A Cryo-EM maps Nodelman, I.M., Das, S., Faustino, A.M., Fried, S.D., Bowman, G.D., Armache, J.P. 10.1038/s41594-021-00719-x 35173352 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Chromo domain-containing protein 1 Transcription-associated, CHD, Chromatin remodelers P32657 P02281, P84233, P06897, P62799 -
181 7ZS9 EM 3.10 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P02281, P84233, P06897, P62799 0.34
182 7ZSA EM 4.00 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P02281, P84233, P06897, P62799 0.342
183 7ZSB EM 6.60 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 219 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P02281, P84233, P06897, P62799 0.277
184 8CBN EM 3.34 2023-12-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.392
185 8CBQ EM 4.00 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.304
186 8CEO EM 3.60 2023-03-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Schilbach, S., Wang, H., Dienemann, C., Cramer, P. 10.1073/pnas.2220542120 37014863 Xenopus laevis Xenopus laevis Xenopus laevis Saccharomyces cerevisiae 2023 General transcription and DNA repair factor IIH helicase subunit XPD, TFB1 isoform 1, RNA polymerase II transcription factor B subunit 2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, TOA1 isoform 1, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta, Mediator of RNA polymerase II transcription subunit 6, Mediator of RNA polymerase II transcription subunit 8, Mediator of RNA polymerase II transcription subunit 11, Mediator of RNA polymerase II transcription subunit 17, Mediator of RNA polymerase II transcription subunit 18, Mediator of RNA polymerase II transcription subunit 20, Mediator of RNA polymerase II transcription subunit 22, Mediator of RNA polymerase II transcription subunit 4, Mediator of RNA polymerase II transcription subunit 7, Mediator of RNA polymerase II transcription subunit 9, Mediator of RNA polymerase II transcription subunit 10, Mediator of RNA polymerase II transcription subunit 14, Mediator of RNA polymerase II transcription subunit 19, Mediator of RNA polymerase II transcription subunit 21, Mediator of RNA polymerase II transcription subunit 31, Mediator of RNA polymerase II transcription subunit 1 RNA polymerases, DNA repair, Mediator, Transcription factors, Transcription-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145, P38782, P38304, Q99278, P32569, P32585, P34162, P32570, Q12343, Q08278, P33308, Q06213, P19263, P25046, P47822, P38633, Q12321 P02281, P84233, P06897, P62799 0.222
187 8F86 EM 3.10 2023-04-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 SIRT6 bound to an H3K9Ac nucleosome Wang, Z.A., Markert, J.W., Whedon, S.D., Yapa Abeywardana, M., Lee, K., Jiang, H., Suarez, C., Lin, H., Farnung, L., Cole, P.A. 10.1021/jacs.2c13512 36930461 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Histone PTM erasers, Histone_deacetylation, Histone_deacetylation_H3K9, DNA repair, Transcription-associated Q8N6T7 P02281, P84233, P06897, P62799 0.434
188 8G57 EM 3.07 2023-04-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Structure of nucleosome-bound Sirtuin 6 deacetylase Chio, U.S., Rechiche, O., Bryll, A.R., Zhu, J., Leith, E.M., Feldman, J.L., Peterson, C.L., Tan, S., Armache, J.P. 10.1126/sciadv.adf7586 37058572 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens 2023 NAD-dependent protein deacylase sirtuin-6 Histone PTM erasers, Histone_deacetylation, Histone_deacetylation_H3K9, DNA repair, Transcription-associated Q8N6T7 P06899, P84233, P04908, P62799 0.493
189 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 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.44
190 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 2023 Chromatin modification-related protein EAF3 DNA repair, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 Q12432 P02281, P84233, P06897, P62799 0.326
191 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 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.463
192 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 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, RCO1 isoform 1, Chromatin modification-related protein EAF3 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Transcription-associated P22579, P32561, A0A8H4BXB0, A0A8H4F719 A0A310TTQ1, A0A8J0U496, Q6AZJ8, A0A8J1LTD2 0.345
193 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 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.067
194 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 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.373
195 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 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.378
196 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 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.311
197 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 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.324
198 8PC5 EM 3.02 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.521
199 8PC6 EM 3.04 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.484
200 8PEO EM 2.69 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.548
201 8PEP EM 3.33 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.399
202 8V4Y EM 2.80 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1) Chio, U.S., Palovcak, E., Smith, A.A.A., Autzen, H., Munoz, E.N., Yu, Z., Wang, F., Agard, D.A., Armache, J.P., Narlikar, G.J., Cheng, Y. 10.1038/s41467-024-46178-y 38472177 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Transcription-associated, Heterochromatin-associated, Chromatin remodelers, ISWI O60264 P02281, P84233, P06897, P62799 0.53
203 8V6V EM 2.80 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of doubly-bound SNF2h-nucleosome complex Chio, U.S., Palovcak, E., Smith, A.A.A., Autzen, H., Munoz, E.N., Yu, Z., Wang, F., Agard, D.A., Armache, J.P., Narlikar, G.J., Cheng, Y. 10.1038/s41467-024-46178-y 38472177 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Transcription-associated, Heterochromatin-associated, Chromatin remodelers, ISWI O60264 P02281, P84233, P06897, P62799 0.477
204 8V7L EM 2.90 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 140 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 2) Chio, U.S., Palovcak, E., Smith, A.A.A., Autzen, H., Munoz, E.N., Yu, Z., Wang, F., Agard, D.A., Armache, J.P., Narlikar, G.J., Cheng, Y. 10.1038/s41467-024-46178-y 38472177 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Transcription-associated, Heterochromatin-associated, Chromatin remodelers, ISWI O60264 P02281, P84233, P06897, P62799 0.456
205 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 2020 Ubiquitin, COMPASS component SWD3, COMPASS component SWD1, Histone-lysine N-methyltransferase, H3 lysine-4 specific, COMPASS component BRE2, COMPASS component SDC1, COMPASS component SPP1 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Telomere-associated, Transcription-associated, Histone PTM writers P0CG48, P38123, P39706, P38827, P43132, Q03323, Q03012 P02281, P84233, P06897, P62799 0.449
206 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 2021 BRCA1,Ubiquitin-conjugating enzyme E2 D3, BRCA1-associated RING domain protein 1 E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK125_writer, DNA repair, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Transcription-associated, Histone PTM writers P38398, Q99728 P62805, Q6FI13, O60814, Q71DI3 0.313
207 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 2020 Histone-lysine N-methyltransferase NSD2 Transcription-associated, Euchromatin-associated, Histone_methylation_H3K36_writer, Histone PTM writers O96028 P02281, Q92133, P06897, P62799 0.448
208 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 2020 Histone-lysine N-methyltransferase NSD3 Transcription-associated, Histone_methylation_H3K27_writer, Histone_methylation_H3K4_writer, Histone PTM writers Q9BZ95 P02281, Q92133, P06897, P62799 0.542
209 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 2020 Histone-lysine N-methyltransferase NSD3 Transcription-associated, Histone_methylation_H3K27_writer, Histone_methylation_H3K4_writer, Histone PTM writers Q9BZ95 P02281, Q92133, P06897, P62799 0.507
210 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 2020 Histone-lysine N-methyltransferase NSD3 Transcription-associated, Histone_methylation_H3K27_writer, Histone_methylation_H3K4_writer, Histone PTM writers Q9BZ95 P02281, Q92133, P06897, P62799 0.464
211 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 2021 Histone-lysine N-methyltransferase SETD2 Transcription-associated, Heterochromatin-associated, Histone PTM writers, Histone_methylation_H3K36_writer Q9BYW2 Q6PI79, P06899, P62799, P20671 0.509
212 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 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Transcription-associated, Histone_methylation_H4K20_writer, Heterochromatin-associated, Histone PTM writers Q4FZB7 P62805, P06899, P0C0S5, Q71DI3 0.484
213 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 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Transcription-associated, Histone_methylation_H4K20_writer, Heterochromatin-associated, Histone PTM writers Q4FZB7 P02281, P84233, P62799, P0C0S5 0.227
214 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 2021 Histone-lysine N-methyltransferase, H3 lysine-36 specific Transcription-associated, Histone_methylation_H3K36_writer, Histone PTM writers P46995 P02281, P84233, P62799, Q6AZJ8 0.473
215 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 2023 COMMD3 protein, Ring1B, Ubiquitin, UbcH5b E3 ubiquitin-protein ligation, Ubiquitin, Polycomb, Histone_ubiquitination_H2AK119_writer, Transcription-associated, Histone PTM writers P35226, Q99496, P0CG47, P62837 P62805, O60814, P04908, P68431 0.516
216 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 2023 E3 ubiquitin-protein ligase BRE1, Ubiquitin-conjugating enzyme E2 2 E3 ubiquitin-protein ligation, DNA repair, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457, P06104 P62805, O60814, P04908, P68431 0.393
217 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 2023 E3 ubiquitin-protein ligase BRE1B, E3 ubiquitin-protein ligase BRE1A, Ubiquitin-conjugating enzyme E2 A E3 ubiquitin-protein ligation, DNA repair, Histone_ubiquitination_H2BK120_writer, Transcription-associated, Histone PTM writers O75150, Q5VTR2, P49459 P62805, O60814, P04908, P68431 0.461
218 8WG5 EM 3.05 2023-12-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Ai, H.S., He, Z.Z., Deng, Z.H., Liu, L. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Ubiquitin carboxyl-terminal hydrolase 16, Ubiquitin B Transcription-associated, Histone_deubiquitination_H2AK119, Ubiquitin Q9Y5T5, P0CG47 P62805, O60814, P04908, P68431 0.306
219 8OL1 EM 3.50 2024-02-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Xu, P., Liu, Y., Liu, C., Guey, B., Li, L., Melenec, P., Ricci, J., Ablasser, A. 10.1038/s41586-024-07112-w 38418882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Cyclic GMP-AMP synthase, SPRY domain-containing SOCS box protein 3, Elongin-C, Elongin-B Antiviral defense, Synthesis of second messengers, E3 ubiquitin-protein ligation, DNA repair, Transcription factors, Transcription-associated, 2'3'-cGAMP Q8N884, Q6PJ21, Q15369, Q15370 Q71DI3, Q99878, Q99877, Q96KK5, P62805, Q93079 0.4
220 6FTX EM 4.50 2018-08-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 159 Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome Sundaramoorthy, R., Hughes, A.L., El-Mkami, H., Norman, D.G., Ferreira, H., Owen-Hughes, T. 10.7554/eLife.35720 30079888 Petromyzon marinus,Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis 2018 Polyubiquitin-B, Chromatin-remodeling ATPase Transcription-associated, Ubiquitin, CHD, Chromatin remodelers P0CG47, P32657 Q28D68, P06897, S4RAZ3, P62799, P02302 0.23
221 6IY2 EM 3.47 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B MMTV 147 Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.427
222 6IY3 EM 3.67 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B MMTV 147 Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.399
223 6Z6P EM 4.43 2021-02-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 HDAC-PC-Nuc Lee, J.H., Bollschweiler, D., Schafer, T., Huber, R. 10.1126/sciadv.abd4413 33523989 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone deacetylase HDA1, HDA1 complex subunit 3,HDA1 complex subunit 3, HDA1 complex subunit 2 Transcription-associated, Histone PTM erasers, Histone_deacetylation, HDA1 P53973, Q06623, Q06629 P02281, P06897, Q6AZJ8, P62799, P84233 0.189
224 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 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 E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK125_writer, DNA repair, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Transcription-associated, Histone PTM writers P38398, Q99728, P61077 P62805, O60814, P04908, Q71DI3 0.352
225 8HQY EM 3.05 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 136 Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom Tong, Z., Ai, H., Xu, Z., He, K., Chu, G.C., Shi, Q., Deng, Z., Xue, Q., Sun, M., Du, Y., Liang, L., Li, J.B., Pan, M., Liu, L. 10.1038/s41594-023-01141-1 38177667 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Protein SSX2, Polyubiquitin-B (Fragment) Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK119_reader, Histone PTM readers Q16385, P0CG47 P62805, O60814, P04908, Q71DI3 0.47
226 8OTT EM 3.30 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 MYC-MAX bound to a nucleosome at SHL+5.8 Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Myc proto-oncogene protein, Protein max Transcription-associated, Transcription factors P01106, P61244 P62805, P06899, P04908, P68431 0.411
227 8OW0 EM 3.40 2023-08-09 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601_modified 121 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Dendooven, T., Zhang, Z., Yang, J., McLaughlin, S.H., Schwab, J., Scheres, S.H.W., Yatskevich, S., Barford, D. 10.1126/sciadv.adg7480 37506202 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae 2023 Centromere-binding protein 1, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Inner kinetochore subunit CNN1, Inner kinetochore subunit AME1, Inner kinetochore subunit WIP1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2 Kinetochore, CCAN, Transcription-associated, Centromere-associated, Nuclear division P17106, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P43618, P38313, Q2V2P8, Q12493, Q06162 P02309, P04911, P02293, P36012 0.2
228 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 2021 Isoform 2 of N-lysine methyltransferase KMT5A Histone_methylation_H4K20_writer, Heterochromatin-associated, Transcription-associated, Nuclear division, Histone PTM writers Q9NQR1 P62805, P06899, P04908, P49450 0.446
229 7YWX EM 12.00 2022-05-18 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 162 Structure of the human CCAN CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein S, Centromere protein T, Centromere protein U, Centromere protein W, Centromere protein X, Centromere protein C Kinetochore, DNA repair, Fanconi anemia core complex, CENP-A NAC/CAD, Transcription-associated, Centromere-associated, Nuclear division Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q8N2Z9, Q96BT3, Q71F23, Q5EE01, A8MT69, Q03188 P62805, P62807, P49450, Q93077 0.054
230 7YYH EM 8.90 2022-05-18 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 153 Structure of the human CCANdeltaT CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein U, Centromere protein C Kinetochore, CENP-A NAC/CAD, Transcription-associated, Centromere-associated, Nuclear division Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q71F23, Q03188 P62805, P62807, P49450, Q93077 0.075