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PDBID Method Resolution Release Date NLP types # NLPs H3 H4 H2A H2B H1 Dna variant Dna length Title Authors DOI Publication H3 taxa H4 taxa H2A taxa H2B taxa H1 taxa Release Year Interactors Interactor categories Interactor UIDS Histone UIDS Q-score
0 8U14 EM 3.9 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.352
1 8TXX EM 3.7 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P0CG47 P04908, P68431, P62805, P62807 0.438
2 8SMX EM 3.2 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.549
3 8TXV EM 3.8 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P0CG47 P04908, P68431, P62805, P62807 0.432
4 8TXW EM 3.6 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P0CG47 P04908, P68431, P62805, P62807 0.455
5 8SN5 EM 3.9 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.41
6 8SMY EM 3.2 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.544
7 8SMZ EM 3.2 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.535
8 8SN6 EM 3.7 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.434
9 8SNA EM 4.0 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.405
10 8U13 EM 3.8 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168 Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5 P04908, P68431, P62805, P62807 0.381
11 8UPF EM 3.2 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.464
12 8SN1 EM 3.3 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.526
13 8SN0 EM 3.2 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.547
14 8SN3 EM 3.8 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.429
15 8SN2 EM 3.6 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.452
16 8SN7 EM 3.7 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.445
17 8SN4 EM 3.7 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.439
18 8SMW EM 3.3 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077 P04908, P68431, P62805, P06899 0.526
19 8SN8 EM 3.7 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.443
20 8SN9 EM 3.9 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Transcription-associated, Histone PTM writers, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK13_reader, Histone_ubiquitination_H2AK15_writer, DNA repair Q8IYW5, P61077, P0CG47 P04908, P68431, P62805, P06899 0.424