0 |
7C0M |
EM |
3.90 |
2020-09-16 |
octamer, octamer |
2 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
Human cGAS-nucleosome complex |
Kujirai, T., Zierhut, C., Takizawa, Y., Kim, R., Negishi, L., Uruma, N., Hirai, S., Funabiki, H., Kurumizaka, H. |
10.1126/science.abd0237 |
32912999 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8N884 |
P68431, P04908, P06899, P62805 |
0.225 |
1 |
7LYB |
EM |
3.28 |
2021-07-28 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c |
Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. |
10.1038/s41586-021-03716-8 |
34321665 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2021 |
Isoform 7 of Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2 D3 |
Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair, Histone_ubiquitination_H2AK129_writer |
P38398, Q99728, P61077 |
P68431, P04908, P06899, P62805 |
0.458 |
2 |
8TXX |
EM |
3.70 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P0CG47 |
P68431, P04908, P62807, P62805 |
0.438 |
3 |
8SN3 |
EM |
3.80 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P61077, P0CG47 |
P68431, P04908, P06899, P62805 |
0.429 |
4 |
6HTS |
EM |
4.80 |
2018-11-07 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
150 |
Cryo-EM structure of the human INO80 complex bound to nucleosome |
Ayala, R., Willhoft, O., Aramayo, R.J., Wilkinson, M., McCormack, E.A., Ocloo, L., Wigley, D.B., Zhang, X. |
10.1038/s41586-018-0021-6 |
29643506 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2018 |
RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit B |
INO80, Chromatin remodelers, DNA replication, Cell cycle, Transcription-associated, DNA repair |
Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q9C086 |
P68431, P04908, P06899, P62805 |
0.181 |
5 |
6UPL |
EM |
7.40 |
2019-12-11 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
79 |
Structure of FACT_subnucleosome complex 2 |
Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. |
10.1038/s41586-019-1820-0 |
31775157 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2019 |
FACT complex subunit SPT16, FACT complex subunit SSRP1 |
Histone chaperones, DNA replication, Transcription-associated, DNA repair, FACT |
Q9Y5B9, Q08945 |
P62807, P68431, Q93077, P62805 |
0.173 |
6 |
7CCR |
EM |
4.90 |
2020-10-07 |
octamer, octamer |
2 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Structure of the 2:2 cGAS-nucleosome complex |
Cao, D., Han, X., Fan, X., Xu, R.M., Zhang, X. |
10.1038/s41422-020-00422-4 |
33051594 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8N884 |
P68431, P04908, P06899, P62805 |
0.152 |
7 |
7XFH |
EM |
2.90 |
2023-04-19 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
132 |
Structure of nucleosome-AAG complex (A-30I, post-catalytic state) |
Zheng, L., Tsai, B., Gao, N. |
10.1038/s41421-023-00560-0 |
37339965 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
DNA-3-methyladenine glycosylase |
DNA repair, DNA modification |
P29372 |
P02281, P84233, P06897, P62799 |
0.515 |
8 |
7YI1 |
EM |
2.80 |
2023-06-14 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
151 |
Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome |
Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. |
10.1038/s41586-023-06349-1 |
37468628 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Chromatin modification-related protein EAF3 |
Histone PTM writers, NuA4, Transcription-associated, Histone_acetylation_writer, DNA repair |
Q12432 |
P02281, P84233, P06897, P62799 |
0.572 |
9 |
8G57 |
EM |
3.07 |
2023-04-26 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
150 |
Structure of nucleosome-bound Sirtuin 6 deacetylase |
Chio, U.S., Rechiche, O., Bryll, A.R., Zhu, J., Leith, E.M., Feldman, J.L., Peterson, C.L., Tan, S., Armache, J.P. |
10.1126/sciadv.adf7586 |
37058572 |
Xenopus laevis |
Xenopus laevis |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
NAD-dependent protein deacylase sirtuin-6 |
Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair |
Q8N6T7 |
P84233, P04908, P06899, P62799 |
0.493 |
10 |
8OF4 |
EM |
2.94 |
2023-08-09 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
Nucleosome Bound human SIRT6 (Composite) |
Smirnova, E., Bignon, E., Schultz, P., Papai, G., Ben Shem, A. |
10.7554/eLife.87989 |
38415718 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
NAD-dependent protein deacylase sirtuin-6 |
Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair |
Q8N6T7 |
P02281, P84233, P06897, P62799 |
0.446 |
11 |
8SMW |
EM |
3.30 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5, P61077 |
P68431, P04908, P06899, P62805 |
0.526 |
12 |
8SN4 |
EM |
3.70 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P61077, P0CG47 |
P68431, P04908, P06899, P62805 |
0.439 |
13 |
8SN5 |
EM |
3.90 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P61077, P0CG47 |
P68431, P04908, P06899, P62805 |
0.41 |
14 |
8SN6 |
EM |
3.70 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P61077, P0CG47 |
P68431, P04908, P06899, P62805 |
0.434 |
15 |
8SNA |
EM |
4.00 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P61077, P0CG47 |
P68431, P04908, P06899, P62805 |
0.405 |
16 |
8T9F |
EM |
2.60 |
2023-09-06 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
H2A.Z |
canonical_H2B |
|
601 |
122 |
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 |
Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. |
10.1016/j.molcel.2023.07.020 |
37595555 |
Xenopus laevis |
Xenopus laevis |
Homo sapiens |
Xenopus laevis |
Xenopus laevis |
2023 |
Histone-lysine N-methyltransferase KMT5B |
Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair |
Q4FZB7 |
P02281, P84233, P0C0S5, P62799 |
0.516 |
17 |
8XBT |
EM |
4.12 |
2024-03-27 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
156 |
The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding |
Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. |
10.1038/s41586-024-07196-4 |
38509361 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
DNA repair protein RAD51 homolog 1 |
DNA repair |
Q06609 |
P68431, P04908, P06899, P62805 |
0.199 |
18 |
8XBU |
EM |
4.24 |
2024-03-27 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
156 |
The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding |
Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. |
10.1038/s41586-024-07196-4 |
38509361 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
DNA repair protein RAD51 homolog 1 |
DNA repair |
Q06609 |
P68431, P04908, P06899, P62805 |
0.171 |
19 |
9IPU |
EM |
4.30 |
2024-10-02 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
H1.0 |
601L |
170 |
cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome |
Shi, Q., Deng, Z., Zhang, L., Tong, Z., Li, J.B., Chu, G.C., Ai, H., Liu, L. |
10.1002/anie.202413651 |
39363740 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
2024 |
Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
P61077, Q8IYW5, P62979 |
Q71DI3, P04908, P07305, P62805, O60814 |
0.237 |
20 |
8HAH |
EM |
3.90 |
2023-05-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
164 |
Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) |
Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. |
10.1038/s41467-023-39735-4 |
37460559 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
Histone acetyltransferase p300 |
Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair |
Q09472 |
P68431, P04908, P06899, P62805 |
0.159 |
21 |
8BYQ |
EM |
4.10 |
2023-05-03 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
198 |
RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) |
Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. |
10.1016/j.molcel.2023.04.011 |
37148879 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta |
RNA polymerases, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated, DNA repair |
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 |
22 |
7XZX |
EM |
4.53 |
2022-10-12 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
171 |
Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain |
Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. |
10.1093/pnasnexus/pgac177 |
36714865 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
Cellular tumor antigen p53 |
DNA repair, Transcription factors, Cell cycle, Transcription-associated |
P04637 |
P68431, P04908, P06899, P62805 |
0.146 |
23 |
6R90 |
EM |
4.50 |
2019-06-12 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
145 |
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A |
Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. |
10.1038/s41586-019-1259-3 |
31142837 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2019 |
DNA damage-binding protein 1, DNA damage-binding protein 2 |
DNA repair, UV-DDB complex, DCX complex |
Q16531, Q92466 |
P68431, P04908, P06899, P62805 |
0.278 |
24 |
7CCQ |
EM |
3.80 |
2020-10-07 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Structure of the 1:1 cGAS-nucleosome complex |
Cao, D., Han, X., Fan, X., Xu, R.M., Zhang, X. |
10.1038/s41422-020-00422-4 |
33051594 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8N884 |
P68431, P04908, P06899, P62805 |
0.371 |
25 |
7YRG |
EM |
4.20 |
2023-12-13 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
H2A.Z |
canonical_H2B |
|
alphasat_146 |
146 |
histone methyltransferase |
Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. |
10.1016/j.molcel.2023.07.001 |
37536340 |
Xenopus laevis |
Xenopus laevis |
Homo sapiens |
Xenopus laevis |
Xenopus laevis |
2023 |
[histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B |
Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair |
Q4FZB7 |
P02281, P84233, P0C0S5, P62799 |
0.227 |
26 |
8HXZ |
EM |
3.40 |
2023-09-27 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
164 |
Cryo-EM structure of Eaf3 CHD in complex with nucleosome |
Li, W., Cui, H., Lu, Z., Wang, H. |
10.1038/s41594-023-01121-5 |
37798513 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Chromatin modification-related protein EAF3 |
Histone PTM writers, NuA4, Transcription-associated, Histone_acetylation_writer, DNA repair |
Q12432 |
P02281, P84233, P06897, P62799 |
0.326 |
27 |
8KD2 |
EM |
3.02 |
2023-09-13 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
174 |
Rpd3S in complex with 187bp nucleosome |
Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. |
10.1038/s41422-023-00869-1 |
37666978 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P32561, P22579, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.35 |
28 |
8OX1 |
EM |
2.70 |
2023-08-30 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
telomeric_human |
145 |
Structure of TRF1core in complex with telomeric nucleosome |
Hu, H., van Roon, A.M., Ghanim, G.E., Ahsan, B., Oluwole, A.O., Peak-Chew, S.Y., Robinson, C.V., Nguyen, T.H.D. |
10.1126/sciadv.adi4148 |
37624885 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
Telomeric repeat-binding factor 1 |
DNA repair, Shelterin, Cell cycle, Telomere-associated |
P54274 |
P62807, P68431, Q93077, P62805 |
0.579 |
29 |
8SN7 |
EM |
3.70 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P61077, P0CG47 |
P68431, P04908, P06899, P62805 |
0.445 |
30 |
8TOF |
EM |
2.80 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
176 |
Rpd3S bound to an H3K36Cme3 modified nucleosome |
Markert, J.W., Vos, S.M., Farnung, L. |
10.1038/s41467-023-43968-8 |
38065958 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2024 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Rco1, histone N-terminal tail |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q12432, Q04779 |
P02281, P06897, P02302, P62799 |
0.464 |
31 |
8U13 |
EM |
3.80 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5 |
P68431, P04908, P62807, P62805 |
0.381 |
32 |
8VWV |
EM |
3.60 |
2024-10-30 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
146 |
OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) |
Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. |
10.1038/s41467-024-55497-z |
39715760 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
N-glycosylase/DNA lyase |
DNA repair, DNA modification |
O15527 |
P0C0S8, P62807, Q71DI3, P62805 |
0.359 |
33 |
9EOZ |
EM |
3.10 |
2024-11-06 |
octamer |
1 |
H3.3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
144 |
Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 |
Ren, M., Gut, F., Fan, Y., Ma, J., Shan, X., Yikilmazsoy, A., Likhodeeva, M., Hopfner, K.P., Zhou, C. |
10.1038/s41467-024-53811-3 |
39477986 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
N-glycosylase/DNA lyase |
DNA repair, DNA modification |
O15527 |
P62807, P84243, Q93077, P62805 |
0.465 |
34 |
8B0A |
EM |
3.00 |
2023-09-20 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
149 |
Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome |
Bacic, L., Gaullier, G., Mohapatra, J., Mao, G., Brackmann, K., Panfilov, M., Liszczak, G., Sabantsev, A., Deindl, S. |
10.1038/s41467-024-45237-8 |
38307862 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Chromodomain-helicase-DNA-binding protein 1-like |
CHD, DNA repair, Chromatin remodelers |
Q86WJ1 |
P02281, P84233, P06897, P62799 |
0.483 |
35 |
7YWX |
EM |
12.00 |
2022-05-18 |
octamer |
1 |
cenH3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
|
162 |
Structure of the human CCAN CENP-A alpha-satellite complex |
Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. |
10.1126/science.abn3810 |
35420891 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein S, Centromere protein T, Centromere protein U, Centromere protein W, Centromere protein X, Centromere protein C |
Fanconi anemia core complex, CENP-A NAC/CAD, DNA repair, Cell cycle, Transcription-associated, Centromere-associated, Nuclear division, Kinetochore |
Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q8N2Z9, Q96BT3, Q71F23, Q5EE01, A8MT69, Q03188 |
P62807, P49450, Q93077, P62805 |
0.054 |
36 |
6UPK |
EM |
4.90 |
2019-12-11 |
hexamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
72 |
Structure of FACT_subnucleosome complex 1 |
Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. |
10.1038/s41586-019-1820-0 |
31775157 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2019 |
FACT complex subunit SPT16, FACT complex subunit SSRP1 |
Histone chaperones, DNA replication, Transcription-associated, DNA repair, FACT |
Q9Y5B9, Q08945 |
P62807, P68431, Q93077, P62805 |
0.203 |
37 |
5KGF |
EM |
4.54 |
2016-07-27 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution |
Wilson, M.D., Benlekbir, S., Fradet-Turcotte, A., Sherker, A., Julien, J.P., McEwan, A., Noordermeer, S.M., Sicheri, F., Rubinstein, J.L., Durocher, D. |
10.1038/nature18951 |
27462807 |
Xenopus laevis |
Xenopus laevis |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2016 |
Tumor suppressor p53-binding protein 1, Ubiquitin |
Histone_ubiquitination_H2AK15_reader, Telomere-associated, Histone PTM readers, Ubiquitin, DNA repair, Histone_methylation_H4K20_reader |
Q12888, P0CG47 |
P0C0S8, P84233, P62807, P62799 |
0.301 |
38 |
6X5A |
EM |
4.36 |
2020-09-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells |
Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. |
10.1038/s41586-020-2749-z |
32911481 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8C6L5 |
P0C0S8, P62807, Q71DI3, P62805 |
0.265 |
39 |
7E8I |
EM |
3.10 |
2021-06-30 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin |
Dai, L., Dai, Y., Han, J., Huang, Y., Wang, L., Huang, J., Zhou, Z. |
10.1016/j.molcel.2021.05.010 |
34102105 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2021 |
BRCA1-associated RING domain protein 1, Polyubiquitin-B |
Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, Ubiquitin, DNA repair, Histone_ubiquitination_H2AK129_writer |
Q99728, P0CG47 |
P02281, P84233, P06897, P62799 |
0.456 |
40 |
7XT7 |
EM |
4.20 |
2022-10-12 |
octamer |
1 |
H3.3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
126 |
RNA polymerase II elongation complex transcribing a nucleosome (EC49B) |
Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. |
10.1126/science.abp9466 |
35981082 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p |
Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated, DNA repair, FACT |
C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, F2QPX0, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 |
P84243, P06899, P04908, P62805 |
0.207 |
41 |
7XTD |
EM |
3.90 |
2022-09-07 |
octamer |
1 |
H3.3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
123 |
RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) |
Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. |
10.1126/science.abp9466 |
35981082 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p |
Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated, DNA repair, FACT |
C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 |
P84243, P06899, P04908, P62805 |
0.221 |
42 |
7YI5 |
EM |
3.96 |
2023-06-14 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
151 |
Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state |
Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. |
10.1038/s41586-023-06349-1 |
37468628 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.254 |
43 |
7ZS9 |
EM |
3.10 |
2022-11-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
209 |
Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) |
Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. |
10.1038/s41594-022-00865-w |
36411341 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2022 |
General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta |
RNA polymerases, Transcription factors, Euchromatin-associated, Transcription-associated, DNA repair |
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 |
44 |
7ZSB |
EM |
6.60 |
2022-11-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
219 |
Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C |
Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. |
10.1038/s41594-022-00865-w |
36411341 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2022 |
General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta |
RNA polymerases, Transcription factors, Euchromatin-associated, Transcription-associated, DNA repair |
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 |
45 |
8BVW |
EM |
4.00 |
2023-05-03 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
206 |
RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) |
Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. |
10.1016/j.molcel.2023.04.011 |
37148879 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta |
RNA polymerases, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated, DNA repair |
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 |
46 |
8IEG |
EM |
3.44 |
2023-09-06 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex |
Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. |
10.1016/j.molcel.2023.08.001 |
37633270 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
E3 ubiquitin-protein ligase BRE1, Ubiquitin-conjugating enzyme E2 2 |
Telomere-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair |
Q07457, P06104 |
P62805, O60814, P04908, P68431 |
0.393 |
47 |
8IEJ |
EM |
3.12 |
2023-09-06 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
RNF20-RNF40/hRad6A-Ub/nucleosome complex |
Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. |
10.1016/j.molcel.2023.08.001 |
37633270 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
E3 ubiquitin-protein ligase BRE1B, E3 ubiquitin-protein ligase BRE1A, Ubiquitin-conjugating enzyme E2 A |
Histone PTM writers, Histone_ubiquitination_H2BK120_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair |
O75150, Q5VTR2, P49459 |
P62805, O60814, P04908, P68431 |
0.461 |
48 |
8KD6 |
EM |
3.07 |
2023-09-13 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
164 |
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 |
Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. |
10.1038/s41422-023-00869-1 |
37666978 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P32561, P22579, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.311 |
49 |
8UPF |
EM |
3.20 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5, P61077 |
P68431, P04908, P06899, P62805 |
0.464 |
50 |
8X7K |
EM |
3.27 |
2024-08-07 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
143 |
Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) |
Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. |
10.1101/2024.01.02.573964 |
0 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
P61077, Q8IYW5 |
O60814, P04908, Q71DI3, P62805 |
0.423 |
51 |
7U50 |
EM |
3.40 |
2022-09-07 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
143 |
APE1 bound to a nucleosome core particle with AP-site at SHL-6 |
Weaver, T.M., Hoitsma, N.M., Spencer, J.J., Gakhar, L., Schnicker, N.J., Freudenthal, B.D. |
10.1038/s41467-022-33057-7 |
36104361 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
DNA-(apurinic or apyrimidinic site) endonuclease |
DNA repair |
P27695 |
P0C0S8, P62807, Q71DI3, P62805 |
0.415 |
52 |
8X7J |
EM |
3.39 |
2024-08-07 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
144 |
Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy |
Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. |
10.1101/2024.01.02.573964 |
0 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
P61077, Q8IYW5, P62979 |
O60814, P04908, Q71DI3, P62805 |
0.391 |
53 |
7JO9 |
EM |
3.30 |
2020-09-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
1:1 cGAS-nucleosome complex |
Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q. |
10.1126/science.abd0609 |
32913000 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8C6L5 |
P0C0S8, P62807, Q71DI3, P62805 |
0.483 |
54 |
6XJD |
EM |
6.80 |
2020-09-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
Two mouse cGAS catalytic domain binding to human assembled nucleosome |
Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. |
10.1038/s41586-020-2749-z |
32911481 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8C6L5 |
P0C0S8, P62807, Q71DI3, P62805 |
0.196 |
55 |
7JOA |
EM |
3.30 |
2020-09-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
2:1 cGAS-nucleosome complex |
Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q. |
10.1126/science.abd0609 |
32913000 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8C6L5 |
P0C0S8, P62807, Q71DI3, P62805 |
0.474 |
56 |
7SCY |
EM |
4.10 |
2022-01-12 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Nuc147 bound to single BRCT |
Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. |
10.1016/j.molcel.2021.11.014 |
34919819 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
Poly [ADP-ribose] polymerase 1 |
DNA repair, Histone PTM writers, Histone_PARylation_writer |
P09874 |
P68431, P04908, P06899, P62805 |
0.273 |
57 |
7SCZ |
EM |
3.50 |
2022-01-19 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Nuc147 bound to multiple BRCTs |
Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. |
10.1016/j.molcel.2021.11.014 |
34919819 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
Poly [ADP-ribose] polymerase 1 |
DNA repair, Histone PTM writers, Histone_PARylation_writer |
P09874 |
P68431, P04908, P06899, P62805 |
0.425 |
58 |
7XFJ |
EM |
3.00 |
2023-11-08 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
131 |
Structure of nucleosome-AAG complex (T-50I, post-catalytic state) |
Zheng, L., Tsai, B., Gao, N. |
10.1038/s41421-023-00560-0 |
37339965 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
DNA-3-methyladenine glycosylase |
DNA repair, DNA modification |
P29372 |
P02281, P84233, P06897, P62799 |
0.466 |
59 |
7ZSA |
EM |
4.00 |
2022-11-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
209 |
Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) |
Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. |
10.1038/s41594-022-00865-w |
36411341 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2022 |
General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta |
RNA polymerases, Transcription factors, Euchromatin-associated, Transcription-associated, DNA repair |
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 |
60 |
8HAK |
EM |
4.50 |
2023-05-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
145 |
Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) |
Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. |
10.1038/s41467-023-39735-4 |
37460559 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
Histone acetyltransferase p300 |
Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair |
Q09472 |
P68431, P04908, P06899, P62805 |
0.214 |
61 |
8SN8 |
EM |
3.70 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P61077, P0CG47 |
P68431, P04908, P06899, P62805 |
0.443 |
62 |
8SN9 |
EM |
3.90 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P61077, P0CG47 |
P68431, P04908, P06899, P62805 |
0.424 |
63 |
8TXW |
EM |
3.60 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P0CG47 |
P68431, P04908, P62807, P62805 |
0.455 |
64 |
9EH2 |
EM |
3.10 |
2024-12-18 |
hexamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
|
65 |
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream |
Markert, J.W., Soffers, J.H., Farnung, L. |
10.1126/science.adn6319 |
39666822 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2024 |
DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16, FACT complex subunit SSRP1 |
Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, DNA replication, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated, DNA repair, FACT |
A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2, Q9Y5B9, Q08945 |
P02281, P06897, A0A310TTQ1, P62799 |
0.252 |
65 |
7YQK |
EM |
3.38 |
2022-08-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
H2A.X |
canonical_H2B |
|
601 |
145 |
cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 |
Ai, H., Chu, G.C., Gong, Q., Tong, Z.B., Deng, Z., Liu, X., Yang, F., Xu, Z., Li, J.B., Tian, C., Liu, L. |
10.1021/jacs.2c06156 |
36166692 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
UDR motif of 53BP1, TP53-binding protein 1, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_reader, Telomere-associated, Histone PTM readers, Ubiquitin, DNA repair, Histone_methylation_H4K20_reader |
Q12888, P0CG47 |
P16104, O60814, P68431, P62805 |
0.424 |
66 |
7NKY |
EM |
3.20 |
2021-07-07 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
148 |
RNA Polymerase II-Spt4/5-nucleosome-FACT structure |
Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. |
10.1038/s41594-021-00578-6 |
33846633 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2021 |
DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, FACT complex subunit POB3, FACT complex subunit SPT16, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 |
Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, Transcription-associated, Heterochromatin-associated, SPT4-SPT5 complex, Centromere-associated, DNA repair, FACT |
P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, Q04636, P32558, P32914, P27692 |
P02281, P84233, P06897, P62799 |
0.358 |
67 |
8CEO |
EM |
3.60 |
2023-03-08 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
209 |
Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome |
Schilbach, S., Wang, H., Dienemann, C., Cramer, P. |
10.1073/pnas.2220542120 |
37014863 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Saccharomyces cerevisiae |
Xenopus laevis |
2023 |
General transcription and DNA repair factor IIH helicase subunit XPD, TFB1 isoform 1, RNA polymerase II transcription factor B subunit 2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, TOA1 isoform 1, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta, Mediator of RNA polymerase II transcription subunit 6, Mediator of RNA polymerase II transcription subunit 8, Mediator of RNA polymerase II transcription subunit 11, Mediator of RNA polymerase II transcription subunit 17, Mediator of RNA polymerase II transcription subunit 18, Mediator of RNA polymerase II transcription subunit 20, Mediator of RNA polymerase II transcription subunit 22, Mediator of RNA polymerase II transcription subunit 4, Mediator of RNA polymerase II transcription subunit 7, Mediator of RNA polymerase II transcription subunit 9, Mediator of RNA polymerase II transcription subunit 10, Mediator of RNA polymerase II transcription subunit 14, Mediator of RNA polymerase II transcription subunit 19, Mediator of RNA polymerase II transcription subunit 21, Mediator of RNA polymerase II transcription subunit 31, Mediator of RNA polymerase II transcription subunit 1 |
RNA polymerases, Transcription factors, Mediator, Euchromatin-associated, Transcription-associated, DNA repair |
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 |
68 |
6USJ |
EM |
10.50 |
2020-10-14 |
octamer, octamer |
2 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
160 |
Structure of two nucleosomes bridged by human PARP2 |
Gaullier, G., Roberts, G., Muthurajan, U.M., Bowerman, S., Rudolph, J., Mahadevan, J., Jha, A., Rae, P.S., Luger, K. |
10.1371/journal.pone.0240932 |
33141820 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Poly [ADP-ribose] polymerase 2 |
DNA repair, Histone PTM writers, Histone_PARylation_writer |
Q9UGN5 |
P68431, P04908, P06899, P62805 |
0.092 |
69 |
6ZHY |
EM |
3.00 |
2020-12-23 |
hexamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
110 |
Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class. |
Lehmann, L.C., Bacic, L., Hewitt, G., Brackmann, K., Sabantsev, A., Gaullier, G., Pytharopoulou, S., Degliesposti, G., Okkenhaug, H., Tan, S., Costa, A., Skehel, J.M., Boulton, S.J., Deindl, S. |
10.1016/j.celrep.2020.108529 |
33357431 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2020 |
Chromodomain-helicase-DNA-binding protein 1-like |
CHD, DNA repair, Chromatin remodelers |
Q86WJ1 |
P02281, P84233, P06897, P62799 |
0.516 |
70 |
7JZV |
EM |
3.90 |
2021-02-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
139 |
Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome |
Witus, S.R., Burrell, A.L., Farrell, D.P., Kang, J., Wang, M., Hansen, J.M., Pravat, A., Tuttle, L.M., Stewart, M.D., Brzovic, P.S., Chatterjee, C., Zhao, W., DiMaio, F., Kollman, J.M., Klevit, R.E. |
10.1038/s41594-020-00556-4 |
33589814 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2021 |
BRCA1,Ubiquitin-conjugating enzyme E2 D3, BRCA1-associated RING domain protein 1 |
Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair, Histone_ubiquitination_H2AK129_writer |
P38398, Q99728 |
Q6FI13, O60814, Q71DI3, P62805 |
0.313 |
71 |
7OTQ |
EM |
4.80 |
2021-09-15 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
149 |
Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome |
Bacic, L., Gaullier, G., Sabantsev, A., Lehmann, L.C., Brackmann, K., Dimakou, D., Halic, M., Hewitt, G., Boulton, S., Deindl, S., Workman, J.L. |
10.7554/eLife.71420 |
34486521 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2021 |
Chromodomain-helicase-DNA-binding protein 1-like |
CHD, DNA repair, Chromatin remodelers |
Q86WJ1 |
P02281, P84233, P06897, P62799 |
0.282 |
72 |
7Y60 |
EM |
3.80 |
2023-08-16 |
H3_H4_tetramer, H3_H4_tetramer |
2 |
canonical_H3 |
canonical_H4 |
|
|
|
601 |
108 |
Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome |
Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. |
10.1126/science.add8673 |
37616371 |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B |
CAF-1, DNA repair, DNA replication, Histone chaperones |
Q13111, Q13112 |
P68431, P62805 |
0.304 |
73 |
7Y61 |
EM |
5.60 |
2023-08-16 |
H3_H4_tetramer, H3_H4_tetramer |
2 |
canonical_H3 |
canonical_H4 |
|
|
|
601 |
92 |
Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome |
Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. |
10.1126/science.add8673 |
37616371 |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B |
CAF-1, DNA repair, DNA replication, Histone chaperones |
Q13111, Q13112 |
P68431, P62805 |
0.189 |
74 |
8J6S |
EM |
3.80 |
2023-08-16 |
H3_H4_tetramer, H3_H4_tetramer |
2 |
canonical_H3 |
canonical_H4 |
|
|
|
601 |
99 |
Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome |
Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. |
10.1126/science.add8673 |
37616371 |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B |
CAF-1, DNA repair, DNA replication, Histone chaperones |
Q13111, Q13112 |
P68431, P62805 |
0.301 |
75 |
8KD4 |
EM |
2.93 |
2023-09-13 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
164 |
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 |
Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. |
10.1038/s41422-023-00869-1 |
37666978 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P32561, P22579, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.373 |
76 |
8OL1 |
EM |
3.50 |
2024-02-14 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) |
Xu, P., Liu, Y., Liu, C., Guey, B., Li, L., Melenec, P., Ricci, J., Ablasser, A. |
10.1038/s41586-024-07112-w |
38418882 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
Cyclic GMP-AMP synthase, SPRY domain-containing SOCS box protein 3, Elongin-C, Elongin-B |
Synthesis of second messengers, Transcription factors, E3 ubiquitin-protein ligation, Transcription-associated, 2'3'-cGAMP, DNA repair, Antiviral defense |
Q8N884, Q6PJ21, Q15369, Q15370 |
Q96KK5, Q71DI3, Q99878, Q93079, P62805, Q99877 |
0.4 |
77 |
8HAI |
EM |
4.70 |
2023-05-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
147 |
Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) |
Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. |
10.1038/s41467-023-39735-4 |
37460559 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
Histone acetyltransferase p300 |
Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair |
Q09472 |
P68431, P04908, P06899, P62805 |
0.212 |
78 |
7ENN |
EM |
2.80 |
2021-07-14 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
146 |
The structure of ALC1 bound to the nucleosome |
Wang, L., Chen, K., Chen, Z. |
10.1038/s41467-021-24320-4 |
34210977 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2021 |
Chromodomain-helicase-DNA-binding protein 1-like |
CHD, DNA repair, Chromatin remodelers |
Q86WJ1 |
P02281, P84233, P06897, P62799 |
0.567 |
79 |
7XTI |
EM |
3.90 |
2022-10-12 |
hexamer |
1 |
H3.3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
85 |
RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) |
Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. |
10.1126/science.abp9466 |
35981082 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p |
Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated, DNA repair, FACT |
C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 |
P84243, P06899, P04908, P62805 |
0.223 |
80 |
7LYC |
EM |
2.94 |
2021-06-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) |
Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. |
10.1038/s41586-021-03716-8 |
34321665 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2021 |
Ubiquitin, BRCA1-associated RING domain protein 1 |
Histone PTM writers, Histone_ubiquitination_H2AK127_writer, E3 ubiquitin-protein ligation, Transcription-associated, Histone_ubiquitination_H2AK125_writer, Ubiquitin, DNA repair, Histone_ubiquitination_H2AK129_writer |
P0CG47, Q99728 |
P68431, P04908, P06899, P62805 |
0.566 |
81 |
7YRD |
EM |
3.20 |
2023-08-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
H2A.Z |
canonical_H2B |
|
alphasat_146 |
146 |
histone methyltransferase |
Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. |
10.1016/j.molcel.2023.07.001 |
37536340 |
Xenopus laevis |
Xenopus laevis |
Homo sapiens |
Xenopus laevis |
Xenopus laevis |
2023 |
[histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B |
Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair |
Q4FZB7 |
P06899, P0C0S5, Q71DI3, P62805 |
0.484 |
82 |
6ZHX |
EM |
2.50 |
2020-12-23 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class. |
Lehmann, L.C., Bacic, L., Hewitt, G., Brackmann, K., Sabantsev, A., Gaullier, G., Pytharopoulou, S., Degliesposti, G., Okkenhaug, H., Tan, S., Costa, A., Skehel, J.M., Boulton, S.J., Deindl, S. |
10.1016/j.celrep.2020.108529 |
33357431 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2020 |
Chromodomain-helicase-DNA-binding protein 1-like |
CHD, DNA repair, Chromatin remodelers |
Q86WJ1 |
P02281, P84233, P06897, P62799 |
0.625 |
83 |
7XFM |
EM |
3.10 |
2023-04-19 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
133 |
Structure of nucleosome-AAG complex (A-53I, post-catalytic state) |
Zheng, L., Tsai, B., Gao, N. |
10.1038/s41421-023-00560-0 |
37339965 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
DNA-3-methyladenine glycosylase |
DNA repair, DNA modification |
P29372 |
P02281, P84233, P06897, P62799 |
0.466 |
84 |
7YI4 |
EM |
3.96 |
2023-06-14 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
151 |
Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state |
Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. |
10.1038/s41586-023-06349-1 |
37468628 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.23 |
85 |
8HAG |
EM |
3.20 |
2023-05-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
147 |
Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) |
Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. |
10.1038/s41467-023-39735-4 |
37460559 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
Histone acetyltransferase p300 |
Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair |
Q09472 |
P68431, P04908, P06899, P62805 |
0.29 |
86 |
8IHM |
EM |
3.58 |
2024-03-20 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
158 |
Eaf3 CHD domain bound to the nucleosome |
Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. |
10.1038/s41422-023-00884-2 |
37845487 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2024 |
Rco1-ABR, Chromatin modification-related protein EAF3 |
Histone PTM writers, NuA4, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
Q04779, Q12432 |
P02281, P84233, P06897, P62799 |
0.434 |
87 |
8IHT |
EM |
3.72 |
2024-03-20 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
158 |
Rpd3S bound to the nucleosome |
Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. |
10.1038/s41422-023-00884-2 |
37845487 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2024 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, RCO1 isoform 1, Chromatin modification-related protein EAF3 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q04779, Q12432 |
P02281, P84233, P06897, P62799 |
0.345 |
88 |
8JHG |
EM |
3.58 |
2023-11-22 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
160 |
Native SUV420H1 bound to 167-bp nucleosome |
Lin, F., Zhang, R., Shao, W., Lei, C., Ma, M., Zhang, Y., Wen, Z., Li, W. |
10.1038/s41421-023-00620-5 |
38052811 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
Histone-lysine N-methyltransferase KMT5B |
Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair |
Q4FZB7 |
O60814, P68431, P04908, P62805 |
0.456 |
89 |
8JHO |
EM |
7.60 |
2023-09-27 |
octamer, octamer |
2 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
340 |
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome |
Li, W., Cui, H., Lu, Z., Wang, H. |
10.1038/s41594-023-01121-5 |
37798513 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.067 |
90 |
8KD3 |
EM |
2.90 |
2023-09-13 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
164 |
Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA |
Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. |
10.1038/s41422-023-00869-1 |
37666978 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P32561, P22579, Q12432, Q04779 |
P02281, A0A310TTQ1, P62799, Q6AZJ8 |
0.376 |
91 |
8SMY |
EM |
3.20 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5, P61077 |
P68431, P04908, P06899, P62805 |
0.544 |
92 |
8TXV |
EM |
3.80 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
Q8IYW5, P0CG47 |
P68431, P04908, P62807, P62805 |
0.432 |
93 |
8U14 |
EM |
3.90 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5, P61077 |
P68431, P04908, P06899, P62805 |
0.352 |
94 |
8W9F |
EM |
4.40 |
2024-05-15 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_147 |
147 |
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 |
Wang, C., Chu, C., Guo, Z., Zhan, X. |
10.1126/sciadv.adk7678 |
38598631 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q12432, Q04779 |
O60814, P68431, P04908, P62805 |
0.156 |
95 |
8F86 |
EM |
3.10 |
2023-04-05 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
148 |
SIRT6 bound to an H3K9Ac nucleosome |
Wang, Z.A., Markert, J.W., Whedon, S.D., Yapa Abeywardana, M., Lee, K., Jiang, H., Suarez, C., Lin, H., Farnung, L., Cole, P.A. |
10.1021/jacs.2c13512 |
36930461 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
NAD-dependent protein deacylase sirtuin-6 |
Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair |
Q8N6T7 |
P02281, P84233, P06897, P62799 |
0.434 |
96 |
7XZZ |
EM |
4.07 |
2022-10-12 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
155 |
Cryo-EM structure of the nucleosome in complex with p53 |
Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. |
10.1093/pnasnexus/pgac177 |
36714865 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
Cellular tumor antigen p53 |
DNA repair, Transcription factors, Cell cycle, Transcription-associated |
P04637 |
P68431, P04908, P06899, P62805 |
0.192 |
97 |
6Y5E |
EM |
3.15 |
2020-09-23 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
153 |
Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) |
Pathare, G.R., Decout, A., Gluck, S., Cavadini, S., Makasheva, K., Hovius, R., Kempf, G., Weiss, J., Kozicka, Z., Guey, B., Melenec, P., Fierz, B., Thoma, N.H., Ablasser, A. |
10.1038/s41586-020-2750-6 |
32911482 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8N884 |
Q16777, O60814, Q71DI3, P62805 |
0.43 |
98 |
6X0N |
EM |
10.00 |
2020-09-16 |
octamer, octamer |
2 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
157 |
Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin |
Bilokapic, S., Suskiewicz, M.J., Ahel, I., Halic, M. |
10.1038/s41586-020-2725-7 |
32939087 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2020 |
Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2 |
DNA repair, Histone PTM writers, Histone_PARylation_writer |
Q9NWY4, Q9UGN5 |
P02281, P84233, P06897, P62799 |
0.113 |
99 |
6Y5D |
EM |
4.10 |
2020-09-23 |
octamer, octamer |
2 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
153 |
Structure of human cGAS (K394E) bound to the nucleosome |
Pathare, G.R., Decout, A., Gluck, S., Cavadini, S., Makasheva, K., Hovius, R., Kempf, G., Weiss, J., Kozicka, Z., Guey, B., Melenec, P., Fierz, B., Thoma, N.H., Ablasser, A. |
10.1038/s41586-020-2750-6 |
32911482 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8N884 |
Q6FI13, O60814, Q71DI3, P62805 |
0.195 |
100 |
7XSX |
EM |
3.80 |
2022-09-07 |
octamer |
1 |
H3.3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
108 |
RNA polymerase II elongation complex transcribing a nucleosome (EC49) |
Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. |
10.1126/science.abp9466 |
35981082 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p |
Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated, DNA repair, FACT |
C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 |
P84243, P06899, P04908, P62805 |
0.227 |
101 |
7ZI4 |
EM |
3.20 |
2023-04-19 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
158 |
Cryo-EM structure of the human INO80 complex bound to a WT nucleosome |
Vance, N.R., Ayala, R., Willhoft, O., Tvardovskiy, A., McCormack, E.A., Bartke, T., Zhang, X., Wigley, D.B. |
|
0 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit C, INO80 complex subunit B |
INO80, Chromatin remodelers, DNA replication, Cell cycle, Transcription-associated, DNA repair |
Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q6PI98, Q9C086 |
P68431, P04908, P06899, P62805 |
0.462 |
102 |
8GRQ |
EM |
3.87 |
2023-04-12 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome |
Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. |
10.1016/j.chempr.2023.01.012 |
0 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a |
Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair, Histone_ubiquitination_H2AK129_writer |
P38398, Q99728, P61077 |
O60814, P04908, Q71DI3, P62805 |
0.352 |
103 |
8HE5 |
EM |
6.95 |
2023-07-05 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
154 |
RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome |
Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. |
10.1016/j.jmb.2023.168130 |
37120012 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, DNA repair protein |
RNA polymerases, Transcription factors, Euchromatin-associated, Transcription-associated, DNA repair |
C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R198 |
P68431, P04908, P06899, P62805 |
0.105 |
104 |
8J6T |
EM |
6.60 |
2023-08-16 |
H3_H4_tetramer, H3_H4_tetramer |
2 |
canonical_H3 |
canonical_H4 |
|
|
|
601 |
92 |
Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome |
Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. |
10.1126/science.add8673 |
37616371 |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B |
CAF-1, DNA repair, DNA replication, Histone chaperones |
Q13111, Q13112 |
P68431, P62805 |
0.166 |
105 |
8JHF |
EM |
3.68 |
2023-11-15 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
H2A.Z |
canonical_H2B |
|
601 |
160 |
Native SUV420H1 bound to 167-bp nucleosome |
Lin, F., Zhang, R., Shao, W., Lei, C., Ma, M., Zhang, Y., Wen, Z., Li, W. |
10.1038/s41421-023-00620-5 |
38052811 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
Histone-lysine N-methyltransferase KMT5B |
Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair |
Q4FZB7 |
O60814, P68431, P0C0S5, P62805 |
0.433 |
106 |
8JNE |
EM |
4.68 |
2024-03-27 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
156 |
The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding |
Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. |
10.1038/s41586-024-07196-4 |
38509361 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
DNA repair protein RAD51 homolog 1 |
DNA repair |
Q06609 |
P68431, P04908, P06899, P62805 |
0.13 |
107 |
8KD7 |
EM |
3.09 |
2023-09-13 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
152 |
Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA |
Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. |
10.1038/s41422-023-00869-1 |
37666978 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P32561, P22579, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.324 |
108 |
8SMX |
EM |
3.20 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5, P61077 |
P68431, P04908, P06899, P62805 |
0.549 |
109 |
8SMZ |
EM |
3.20 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5, P61077 |
P68431, P04908, P06899, P62805 |
0.535 |
110 |
8SN1 |
EM |
3.30 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5, P61077 |
P68431, P04908, P06899, P62805 |
0.526 |
111 |
8VX6 |
EM |
3.20 |
2024-10-09 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
155 |
Human OGG1 bound at the nucleosomal DNA entry site |
You, Q., Feng, X., Cai, Y., Baylin, S.B., Li, H. |
10.1038/s42003-024-06919-7 |
39341999 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2024 |
N-glycosylase/DNA lyase |
DNA repair, DNA modification |
O15527 |
P02281, P84233, P06897, P62799 |
0.424 |
112 |
8W9E |
EM |
3.60 |
2024-05-15 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_147 |
147 |
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 |
Wang, C., Chu, C., Guo, Z., Zhan, X. |
10.1126/sciadv.adk7678 |
38598631 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q12432, Q04779 |
O60814, P68431, P04908, P62805 |
0.188 |
113 |
8X7I |
EM |
3.27 |
2024-08-07 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy |
Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. |
10.1101/2024.01.02.573964 |
0 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair |
P61077, Q8IYW5, P62979 |
O60814, P04908, Q71DI3, P62805 |
0.443 |
114 |
7W9V |
EM |
3.95 |
2022-07-13 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) |
Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L., Kutateladze, T.G., Kurumizaka, H. |
10.1016/j.isci.2022.104563 |
35754730 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2022 |
Histone acetyltransferase p300 |
Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair |
Q09472 |
P68431, P04908, P06899, P62805 |
0.307 |
115 |
6X59 |
EM |
2.98 |
2020-09-16 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
145 |
The mouse cGAS catalytic domain binding to human assembled nucleosome |
Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. |
10.1038/s41586-020-2749-z |
32911481 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8C6L5 |
P0C0S8, P62807, Q71DI3, P62805 |
0.54 |
116 |
6R8Z |
EM |
3.90 |
2019-06-12 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
145 |
Cryo-EM structure of NCP_THF2(-1)-UV-DDB |
Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. |
10.1038/s41586-019-1259-3 |
31142837 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2019 |
DNA damage-binding protein 1, DNA damage-binding protein 2 |
DNA repair, UV-DDB complex, DCX complex |
Q16531, Q92466 |
P68431, P04908, P06899, P62805 |
0.307 |
117 |
6R91 |
EM |
4.10 |
2019-06-12 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
145 |
Cryo-EM structure of NCP_THF2(-3)-UV-DDB |
Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. |
10.1038/s41586-019-1259-3 |
31142837 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2019 |
DNA damage-binding protein 1, DNA damage-binding protein 2 |
DNA repair, UV-DDB complex, DCX complex |
Q16531, Q92466 |
P68431, P04908, P06899, P62805 |
0.212 |
118 |
6R92 |
EM |
4.80 |
2019-06-12 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
145 |
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B |
Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. |
10.1038/s41586-019-1259-3 |
31142837 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2019 |
DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 2 |
DNA repair, UV-DDB complex, DCX complex |
Q16531, Q92466 |
P68431, P04908, P06899, P62805 |
0.22 |
119 |
7A08 |
EM |
3.11 |
2020-09-23 |
octamer |
1 |
H3.3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
132 |
CryoEM Structure of cGAS Nucleosome complex |
Michalski, S., de Oliveira Mann, C.C., Stafford, C.A., Witte, G., Bartho, J., Lammens, K., Hornung, V., Hopfner, K.P. |
10.1038/s41586-020-2748-0 |
32911480 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2020 |
Cyclic GMP-AMP synthase |
DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense |
Q8C6L5 |
P62807, P84243, Q93077, P62805 |
0.533 |
120 |
8HAJ |
EM |
4.80 |
2023-05-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
164 |
Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) |
Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. |
10.1038/s41467-023-39735-4 |
37460559 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2023 |
Histone acetyltransferase p300 |
Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair |
Q09472 |
P68431, P04908, P06899, P62805 |
0.2 |
121 |
8JND |
EM |
3.66 |
2024-03-27 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
156 |
The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding |
Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. |
10.1038/s41586-024-07196-4 |
38509361 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
DNA repair protein RAD51 homolog 1 |
DNA repair |
Q06609 |
P68431, P04908, P06899, P62805 |
0.19 |
122 |
8JNF |
EM |
6.91 |
2024-03-27 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601_modified |
123 |
The cryo-EM structure of the RAD51 filament bound to the nucleosome |
Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. |
10.1038/s41586-024-07196-4 |
38509361 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
DNA repair protein RAD51 homolog 1 |
DNA repair |
Q06609 |
P68431, P04908, P06899, P62805 |
0.143 |
123 |
8KD5 |
EM |
2.90 |
2023-09-13 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
160 |
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 |
Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. |
10.1038/s41422-023-00869-1 |
37666978 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P32561, P22579, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.378 |
124 |
8SN2 |
EM |
3.60 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5, P61077 |
P68431, P04908, P06899, P62805 |
0.452 |
125 |
8VWT |
EM |
3.30 |
2024-10-30 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) |
Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. |
10.1038/s41467-024-55497-z |
39715760 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
N-glycosylase/DNA lyase |
DNA repair, DNA modification |
O15527 |
P0C0S8, P62807, Q71DI3, P62805 |
0.41 |
126 |
8W9D |
EM |
3.90 |
2024-05-15 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_147 |
147 |
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 |
Wang, C., Chu, C., Guo, Z., Zhan, X. |
10.1126/sciadv.adk7678 |
38598631 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Unclear peptide |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q12432, Q04779 |
O60814, P68431, P04908, P62805 |
0.263 |
127 |
8HY0 |
EM |
3.10 |
2023-09-27 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
170 |
Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome |
Li, W., Cui, H., Lu, Z., Wang, H. |
10.1038/s41594-023-01121-5 |
37798513 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.463 |
128 |
8SN0 |
EM |
3.20 |
2024-01-17 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
147 |
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) |
Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. |
10.1016/j.molcel.2023.12.036 |
38242129 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2024 |
E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 |
Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair |
Q8IYW5, P61077 |
P68431, P04908, P06899, P62805 |
0.547 |
129 |
6R8Y |
EM |
4.30 |
2019-06-12 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
alphasat_146 |
145 |
Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB |
Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. |
10.1038/s41586-019-1259-3 |
31142837 |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Homo sapiens |
Xenopus laevis |
2019 |
DNA damage-binding protein 1, DNA damage-binding protein 2 |
DNA repair, UV-DDB complex, DCX complex |
Q16531, Q92466 |
P68431, P04908, P06899, P62805 |
0.313 |
130 |
8HXY |
EM |
3.10 |
2023-09-27 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
170 |
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome |
Li, W., Cui, H., Lu, Z., Wang, H. |
10.1038/s41594-023-01121-5 |
37798513 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 |
Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair |
P22579, P32561, Q12432, Q04779 |
P02281, P84233, P06897, P62799 |
0.44 |
131 |
8T9H |
EM |
3.37 |
2023-09-13 |
octamer |
1 |
canonical_H3 |
canonical_H4 |
canonical_H2A |
canonical_H2B |
|
601 |
99 |
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 |
Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. |
10.1016/j.molcel.2023.07.020 |
37595555 |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
Xenopus laevis |
2023 |
Histone-lysine N-methyltransferase KMT5B |
Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair |
Q4FZB7 |
P02281, P84233, P06897, P62799 |
0.393 |