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 |