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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 7YYH EM 8.90 2022-05-18 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 153 Structure of the human CCANdeltaT CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein U, Centromere protein C Kinetochore, CENP-A NAC/CAD, Transcription-associated, Centromere-associated, Nuclear division Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q71F23, Q03188 P62805, P62807, P49450, Q93077 0.075
1 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 2023 DNA-3-methyladenine glycosylase DNA repair P29372 P02281, P84233, P06897, P62799 0.466
2 7ZI4 EM 3.20 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Vance, N.R., Ayala, R., Willhoft, O., Tvardovskiy, A., McCormack, E.A., Bartke, T., Zhang, X., Wigley, D.B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit C, INO80 complex subunit B INO80, DNA repair, DNA replication, Transcription-associated, Chromatin remodelers Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q6PI98, Q9C086 P62805, P06899, P04908, P68431 0.462
3 7Y00 EM 3.96 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, P06899, P04908, P68431 0.32
4 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 2022 Cellular tumor antigen p53 DNA repair P04637 P62805, P06899, P04908, P68431 0.192
5 7XZY EM 3.97 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 165 Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, P06899, P04908, P68431 0.256
6 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 2022 Cellular tumor antigen p53 DNA repair P04637 P62805, P06899, P04908, P68431 0.146
7 7XNP EM 2.90 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 123 Structure of nucleosome-AAG complex (A-55I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.563
8 7XFN EM 2.80 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Structure of nucleosome-DI complex (-55I, Apo state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.55
9 7XFL EM 2.80 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 134 Structure of nucleosome-AAG complex (A-53I, free state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.55
10 7VZ4 EM 1.89 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Takizawa, Y., Ho, C.H., Sato, S., Danev, R., Kurumizaka, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P62805, P06899, P04908, P68431 0.724
11 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 2023 DNA-3-methyladenine glycosylase DNA repair P29372 P02281, P84233, P06897, P62799 0.466
12 7XFI EM 2.90 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 136 Structure of nucleosome-DI complex (-50I, Apo state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.525
13 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 2023 DNA-3-methyladenine glycosylase DNA repair P29372 P02281, P84233, P06897, P62799 0.515
14 7XFC EM 2.90 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Structure of nucleosome-DI complex (-30I, Apo state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.569
15 7X3X EM 3.20 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of N1 nucleosome-RA Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, P84233, P06897, P62799 0.44
16 7X3W EM 3.10 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of ISW1-N1 nucleosome Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, P84233, P06897, P62799 0.489
17 7X3V EM 3.09 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of IOC3-N2 nucleosome Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI one complex protein 3 Chromatin remodelers, ISWI P43596 P02281, P84233, P06897, P62799 0.502
18 8BVW EM 4.00 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 206 RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P02281, P84233, P06897, P62799 0.234
19 8BYQ EM 4.10 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P02281, P84233, P06897, P62799 0.187
20 8BZ1 EM 3.80 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2 Transcription-associated, Transcription factors, RNA polymerases A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, I3LJZ9, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657 P02281, P84233, P06897, P62799 0.244
21 8DK5 EM 2.71 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of 187bp LIN28b nucleosome with site 0 mutation Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Single-chain variable fragment P62805, Q16778, Q16777, P68431 0.535
22 8OF4 EM 2.94 2023-08-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome Bound human SIRT6 (Composite) Smirnova, E., Bignon, E., Schultz, P., Papai, G., Ben Shem, A. 10.7554/eLife.87989 38415718 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Histone PTM erasers, Histone_deacetylation, Histone_deacetylation_H3K9, DNA repair, Transcription-associated Q8N6T7 P02281, P84233, P06897, P62799 0.446
23 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 2024 DNA repair protein RAD51 homolog 1 Q06609 P62805, P06899, P04908, P68431 0.13
24 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 2024 DNA repair protein RAD51 homolog 1 Q06609 P62805, P06899, P04908, P68431 0.19
25 8JL9 EM 2.65 2023-10-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 155 Cryo-EM structure of the human nucleosome with scFv Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Ehara, H., Sekine, S.I., Hayashi, G., Takizawa, Y., Kurumizaka, H. 10.1093/nar/gkad754 37718728 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P62805, P06899, P04908, P68431 0.569
26 8JHG EM 3.58 2023-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Native SUV420H1 bound to 167-bp nucleosome Lin, F., Zhang, R., Shao, W., Lei, C., Ma, M., Zhang, Y., Wen, Z., Li, W. 10.1038/s41421-023-00620-5 38052811 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone_methylation_H4K20_writer, Heterochromatin-associated, Histone PTM writers Q4FZB7 P62805, O60814, P04908, P68431 0.456
27 8IHL EM 7.64 2024-01-17 octamer, hexamer, hexamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 353 Overlapping tri-nucleosome Nishimura, M., Fujii, T., Tanaka, H., Maehara, K., Morishima, K., Shimizu, M., Kobayashi, Y., Nozawa, K., Takizawa, Y., Sugiyama, M., Ohkawa, Y., Kurumizaka, H. 10.1038/s42003-023-05694-1 38191828 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 P62805, P06899, P04908, P68431 0.109
28 8GUK EM 2.51 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Human nucleosome core particle (free form) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P62805, P0C0S8, P06899, P68431 0.588
29 8GUJ EM 2.80 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1-nucleosome complex (Model II) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM writers, Histone_ubiquitination_H2BK120_writer Q5VTR2, O75150 P62805, P0C0S8, P06899, P68431 0.532
30 8GUI EM 2.81 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1-nucleosome complex (Model I) Onishi, S., Uchiyama, K., Sato, K., Okada, C., Kobayashi, S., Hamada, K., Nishizawa, T., Nureki, O., Ogata, K., Sengoku, T. 10.1038/s41467-024-46910-8 38519511 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM writers, Histone_ubiquitination_H2BK120_writer Q5VTR2, O75150 P62805, P0C0S8, P06899, P68431 0.532
31 8G6S EM 3.47 2024-02-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2AK119ub-modified nucleosome ubiquitin position 2 Hicks, C.W., Rahman, S., Fields, J.K., Morgan, M.T., Wolberger, C. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P62799, Q6AZJ8 0.445
32 8G6Q EM 3.41 2024-02-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2AK119ub-modified nucleosome ubiquitin position 1 Hicks, C.W., Rahman, S., Fields, J.K., Morgan, M.T., Wolberger, C. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P62799, Q6AZJ8 0.434
33 8EVJ EM 4.10 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 138 CX3CR1 nucleosome bound PU.1 and C/EBPa Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 ScFv, Transcription factor PU.1 Transcription-associated, Transcription factors P17433 P62805, Q16778, Q16777, P68431 0.31
34 8EVI EM 2.64 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 143 CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Single-chain variable fragment, Transcription factor PU.1 Transcription-associated, Transcription factors P17433 P62805, Q16778, Q16777, P68431 0.559
35 8EVH EM 2.85 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 141 CX3CR1 nucleosome and wild type PU.1 complex Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Single-chain variable fragment, Transcription factor PU.1 Transcription-associated, Transcription factors P17433 P62805, Q16778, Q16777, P68431 0.509
36 8EVG EM 2.75 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 162bp CX3CR1 nucleosome (further classified with better nucleosome end) Tengfei, L., Ruifang, G., Yawen, B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Single-chain variable fragment P62805, Q16778, Q16777, P68431 0.531
37 7X3T EM 5.40 2023-09-20 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 339 Cryo-EM structure of ISW1a-dinucleosome Li, L., Chen, K., Sia, Y., Hu, P., Ye, Y., Chen, Z. 10.1038/s41594-023-01174-6 38177688 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 ISWI one complex protein 3, ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P43596, P38144 P02281, P84233, P06897, P62799 0.192
38 7VVZ EM 8.80 2022-08-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 180 NuA4 bound to the nucleosome Qu, K., Chen, K., Wang, H., Li, X., Chen, Z. 10.1038/s41586-022-05303-x 36198799 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Chromatin modification-related protein EAF1, Actin-related protein 4, Actin, Enhancer of polycomb-like protein 1, SWR1-complex protein 4, Transcription-associated protein 1, Histone acetyltransferase ESA1, Chromatin modification-related protein YNG2, Epl1 arginine anchor, Chromatin modification-related protein EAF6 Heterochromatin-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 Q06337, P80428, P60010, P43572, P53201, P38811, Q08649, P38806, P47128 P02281, P84233, P06897, P62799 0.108
39 6UPL EM 7.40 2019-12-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 79 Structure of FACT_subnucleosome complex 2 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Histone chaperones, FACT, DNA repair, DNA replication, Transcription-associated Q9Y5B9, Q08945 P62805, P62807, P68431, Q93077 0.173
40 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8C6L5 P62805, P0C0S8, P62807, Q71DI3 0.483
41 7LYC EM 2.94 2021-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 Ubiquitin, BRCA1-associated RING domain protein 1 E3 ubiquitin-protein ligation, Ubiquitin, DNA repair, Histone_ubiquitination_H2AK125_writer, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Transcription-associated, Histone PTM writers P0CG47, Q99728 P62805, P06899, P04908, P68431 0.566
42 7LYB EM 3.28 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 Isoform 7 of Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2 D3 E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK125_writer, DNA repair, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Transcription-associated, Histone PTM writers P38398, Q99728, P61077 P62805, P06899, P04908, P68431 0.458
43 7LYA EM 2.91 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P62805, P06899, P04908, P68431 0.59
44 7KBE EM 3.50 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction) Arimura, Y., Shih, R.M., Froom, R., Funabiki, H. 10.1016/j.molcel.2021.08.010 34478647 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P02281, Q6DKE3, P84233, P62799 0.445
45 7KBD EM 3.38 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) Arimura, Y., Shih, R.M., Froom, R., Funabiki, H. 10.1016/j.molcel.2021.08.010 34478647 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P02281, Q6DKE3, P84233, P62799 0.489
46 7K61 EM 2.85 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 197 Cryo-EM structure of 197bp nucleosome aided by scFv Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 scFv20 P62805, P06899, P04908, P68431 0.529
47 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8C6L5 P62805, P0C0S8, P62807, Q71DI3 0.474
48 7D1Z EM 3.15 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of SET8-nucleosome complex Ho, C.H., Takizawa, Y., Kobayashi, W., Arimura, Y., Kimura, H., Kurumizaka, H. 10.26508/lsa.202000919 33574035 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 Isoform 2 of N-lysine methyltransferase KMT5A Histone_methylation_H4K20_writer, Heterochromatin-associated, Transcription-associated, Nuclear division, Histone PTM writers Q9NQR1 P62805, P06899, P04908, P68431 0.514
49 7VVU EM 3.40 2022-08-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 180 NuA4 HAT module bound to the nucleosome Qu, K., Chen, K., Wang, H., Li, X., Chen, Z. 10.1038/s41586-022-05303-x 36198799 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Histone acetyltransferase ESA1, Enhancer of polycomb-like protein 1, Chromatin modification-related protein YNG2, Chromatin modification-related protein EAF6 Heterochromatin-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 Q08649, P43572, P38806, P47128 P02281, P84233, P06897, P62799 0.314
50 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8N884 P62805, P06899, P04908, P68431 0.225
51 6YOV EM 3.42 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 OCT4-SOX2-bound nucleosome - SHL+6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription-associated, Transcription factors P42212, P48431 P62805, P06899, P04908, P68431 0.35
52 6W5N EM 6.00 2021-03-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Lee, Y.T., Ayoub, A., Park, S.H., Sha, L., Xu, J., Mao, F., Zheng, W., Zhang, Y., Cho, U.S., Dou, Y. 10.1038/s41467-021-23268-9 34012049 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.167
53 6W5M EM 4.60 2021-03-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Lee, Y.T., Ayoub, A., Park, S.H., Sha, L., Xu, J., Mao, F., Zheng, W., Zhang, Y., Cho, U.S., Dou, Y. 10.1038/s41467-021-23268-9 34012049 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.177
54 6W5I EM 6.90 2021-03-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Lee, Y.T., Ayoub, A., Park, S.H., Sha, L., Xu, J., Mao, F., Zheng, W., Zhang, Y., Cho, U.S., Dou, Y. 10.1038/s41467-021-23268-9 34012049 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.135
55 6V92 EM 20.00 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 RSC-NCP Patel, A.B., Moore, C.M., Greber, B.J., Luo, J., Zukin, S.A., Ranish, J., Nogales, E. 10.7554/eLife.54449 31886770 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Actin-related protein 7, Actin-like protein ARP9, High temperature lethal protein 1, Chromatin structure-remodeling complex protein RSC14, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC4, Chromatin structure-remodeling complex protein RSC8, Chromatin structure-remodeling complex protein RSC6, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex protein RSC58, Regulator of Ty1 transposition protein 102, Chromatin structure-remodeling complex subunit SFH1, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC30 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers Q12406, Q05123, Q9URQ5, P38210, P32832, Q06488, Q06639, Q02206, P43609, P25632, Q03124, Q07979, P53330, Q06168, P32597, P38781 P62805, O60814, P04908, P68431 0.053
56 6V2K X-ray 2.60 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The nucleosome structure after H2A-H2B exchange Hirano, R., Arimura, Y., Kujirai, T., Shibata, M., Okuda, A., Morishima, K., Inoue, R., Sugiyama, M., Kurumizaka, H. 10.1038/s42003-021-01707-z 33580188 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, P06899, P04908, P68431 -
57 7NKX EM 2.90 2021-08-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 139 RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Chromo domain-containing protein 1, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Heterochromatin-associated, CHD, RNA polymerases, Transcription factors, Transcription-associated, Centromere-associated, Chromatin remodelers, SPT4-SPT5 complex P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P32657, P32914, P27692 P02281, P84233, P06897, P62799 0.444
58 7NKY EM 3.20 2021-07-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 148 RNA Polymerase II-Spt4/5-nucleosome-FACT structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, FACT complex subunit POB3, FACT complex subunit SPT16, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Heterochromatin-associated, Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, Centromere-associated, SPT4-SPT5 complex P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, Q04636, P32558, P32914, P27692 P02281, P84233, P06897, P62799 0.358
59 7NL0 EM 3.50 2021-08-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 131 Cryo-EM structure of the Lin28B nucleosome core particle Roberts, G.A., Ozkan, B., Gachulincova, I., O'Dwyer, M.R., Hall-Ponsele, E., Saxena, M., Robinson, P.J., Soufi, A. 10.1038/s41556-021-00727-5 34354236 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P62805, P06899, P04908, P68431 0.519
60 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 2022 Poly [ADP-ribose] polymerase 1 DNA repair, Histone PTM writers, Histone_PARylation_writer P09874 P62805, P06899, P04908, P68431 0.273
61 7VDV EM 3.40 2022-05-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 The overall structure of human chromatin remodeling PBAF-nucleosome complex Yuan, J.J., Chen, K.J., Zhang, W.B., Chen, Z.C. 10.1038/s41586-022-04658-5 35477757 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Isoform 2 of Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2, PHD finger protein 10, Isoform 2 of Bromodomain-containing protein 7, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Protein polybromo-1 Transcription-associated, PBAF (SWI/SNF), Chromatin remodelers, SWI/SNF P51532, O96019, P60709, Q68CP9, Q8WUB8, Q9NPI1, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q86U86 P02281, P84233, P06897, P62799 0.315
62 7VDT EM 2.80 2022-05-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 135 The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Yuan, J.J., Chen, K.J., Zhang, W.B., Chen, Z.C. 10.1038/s41586-022-04658-5 35477757 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Isoform 2 of Transcription activator BRG1 Transcription-associated, Chromatin remodelers, SWI/SNF P51532 P02281, P84233, P06897, P62799 0.549
63 7VA4 EM 14.00 2022-07-27 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 539 Telomeric tetranucleosome in open state Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, P68431 0.043
64 7V9S EM 11.00 2022-07-27 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 388 Telomeric trinucleosome in open state Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, P68431 0.093
65 7V9K EM 8.10 2022-07-27 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 539 Telomeric tetranucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, P68431 0.076
66 7V9J EM 8.00 2022-07-27 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 399 Telomeric trinucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, P68431 0.107
67 7V9C EM 4.50 2022-07-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 273 Telomeric Dinucleosome in open state Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, P68431 0.109
68 7V96 EM 3.92 2022-07-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 275 Telomeric Dinucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, P68431 0.4
69 7V90 EM 3.50 2022-07-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 Telomeric mononucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, P68431 0.459
70 7UND EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 131 Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Histone chaperones, RNA polymerases, Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, Transcription-associated, Histone PTM writers, PAF1C A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P02281, P84233, P62799, Q6AZJ8 0.216
71 7UNC EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 155 Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT5 Histone chaperones, RNA polymerases, Histone_methylation_H3K4_writer, Histone_ubiquitination_H2BK120_writer, Transcription factors, Transcription-associated, Histone PTM writers, PAF1C A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, O00267 P02281, P84233, P62799, Q6AZJ8 0.344
72 7U0J EM 2.70 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of 162bp LIN28b nucleosome Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Single-chain variable fragment P62805, Q16778, Q16777, P68431 0.568
73 7U0I EM 2.60 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of LIN28b nucleosome bound 2 OCT4 Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Single-chain variable fragment, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 P0AEX9 P62805, Q16778, Q16777, P68431 0.548
74 7U0G EM 2.60 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 133 structure of LIN28b nucleosome bound 3 OCT4 Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Maltodextrin-binding protein,POU domain, class 5, transcription factor 1, Single-chain variable fragment P0AEX9 P62805, Q16778, Q16777, P68431 0.531
75 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 2022 Poly [ADP-ribose] polymerase 1 DNA repair, Histone PTM writers, Histone_PARylation_writer P09874 P62805, P06899, P04908, P68431 0.425
76 8OSJ EM 6.20 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 128 Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription-associated, Transcription factors O08785, Q9WTL8 P62805, P06899, P04908, P68431 0.219
77 8OSK EM 3.60 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 124 Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription-associated, Transcription factors O08785, Q9WTL8 P62805, P06899, P04908, P68431 0.267
78 8OSL EM 4.90 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription-associated, Transcription factors O08785, Q9WTL8 P62805, P06899, P04908, P68431 0.177
79 1S32 X-ray 2.05 2004-05-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Molecular Recognition of the Nucleosomal 'Supergroove' Edayathumangalam, R.S., Weyermann, P., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1073/pnas.0401743101 15100411 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
80 3B6G X-ray 3.45 2007-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome core particle treated with oxaliplatin Wu, B., Droge, P., Davey, C.A. 10.1038/nchembio.2007.58 18157123 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2007 P02281, P84233, P06897, P62799 -
81 3B6F X-ray 3.45 2007-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome core particle treated with cisplatin Wu, B., Droge, P., Davey, C.A. 10.1038/nchembio.2007.58 18157123 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2007 P02281, P84233, P06897, P62799 -
82 2PYO X-ray 2.43 2007-11-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Drosophila nucleosome core Clapier, C.R., Chakravarthy, S., Petosa, C., Fernandez-Tornero, C., Luger, K., Muller, C.W. 10.1002/prot.21720 17957772 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2007 P02299, P02283, P84051, P84040 -
83 2NZD X-ray 2.65 2007-04-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing 145 bp of DNA Ong, M.S., Richmond, T.J., Davey, C.A. 10.1016/j.jmb.2007.02.062 17379244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2007 P02281, P84233, P06897, P62799 -
84 2NQB X-ray 2.30 2007-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Drosophila Nucleosome Structure Chakravarthy, S., Luger, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2007 P02299, P02283, P84051, P84040 -
85 2FJ7 X-ray 3.20 2006-09-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_A16 147 Crystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element Bao, Y., White, C.L., Luger, K. 10.1016/j.jmb.2006.06.051 16860337 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2006 P02281, P84233, P06897, P62799 -
86 1ZBB X-ray 9.00 2005-07-12 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 347 Structure of the 4_601_167 Tetranucleosome Schalch, T., Duda, S., Sargent, D.F., Richmond, T.J. 10.1038/nature03686 16001076 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2005 P02281, P84233, P06897, P62799 -
87 1KX5 X-ray 1.94 2002-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J. 10.1016/S0022-2836(02)00386-8 12079350 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2002 P02281, P84233, P06897, P62799 -
88 8OTS EM 3.30 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 OCT4 and MYC-MAX co-bound to a nucleosome Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Green fluorescent protein,POU domain, class 5, transcription factor 1, Myc proto-oncogene protein, Protein max Transcription-associated, Transcription factors P42212, P01106, P61244 P62805, P06899, P04908, P68431 0.404
89 1KX4 X-ray 2.60 2002-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 X-Ray Structure of the Nucleosome Core Particle, NCP146b, at 2.6 A Resolution Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J. 10.1016/S0022-2836(02)00386-8 12079350 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2002 P02281, P84233, P06897, P62799 -
90 1KX3 X-ray 2.00 2002-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J. 10.1016/S0022-2836(02)00386-8 12079350 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2002 P02281, P84233, P06897, P62799 -
91 8WHB EM 3.17 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 134 Structure of nucleosome core particle of Arabidopsis thaliana Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana 2024 P59259, O23629, P59226, Q9LD28 0.5
92 8WHA EM 4.05 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2 Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodeling Q9XFH4 P59259, O23629, P59226, Q9LD28 0.306
93 8WH9 EM 3.31 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of DDM1-nucleosome complex in ADP-BeFx state Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodeling Q9XFH4 P59259, O23629, P59226, Q9LD28 0.336
94 8WH8 EM 3.60 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 125 Structure of DDM1-nucleosome complex in ADP state Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodeling Q9XFH4 P59259, O23629, P59226, Q9LD28 0.403
95 8WH5 EM 3.58 2024-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Structure of DDM1-nucleosome complex in the apo state Liu, Y., Zhang, Z., Hu, H., Chen, W., Zhang, F., Wang, Q., Wang, C., Yan, K., Du, J. 10.1038/s41477-024-01640-z 38413824 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodeling Q9XFH4 P59259, O23629, P59226, Q9LD28 -
96 3C1B X-ray 2.20 2008-10-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure Lu, X., Simon, M.D., Chodaparambil, J.V., Hansen, J.C., Shokat, K.M., Luger, K. 10.1038/nsmb.1489 18794842 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus (Silurana) tropicalis 2008 Q28D68, P84233, P06897, P62799 -
97 3KUY X-ray 2.90 2010-01-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent Davey, G.E., Wu, B., Dong, Y., Surana, U., Davey, C.A. 10.1093/nar/gkp1174 20026584 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P06897, P62799 -
98 3LJA X-ray 2.75 2010-04-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome Wu, B., Davey, C.A. 10.1016/j.jmb.2010.03.038 20350553 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P06897, P62799 -
99 3LZ0 X-ray 2.50 2010-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1) Vasudevan, D., Chua, E.Y., Davey, C.A. 10.1016/j.jmb.2010.08.039 20800598 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P62799, Q6AZJ8 -
100 3UT9 X-ray 2.20 2012-04-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L) Chua, E.Y.D., Vasudevan, D., Davey, G.E., Wu, B., Davey, C.A. 10.1093/nar/gks261 22453276 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
101 3TU4 X-ray 3.00 2011-11-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Armache, K.J., Garlick, J.D., Canzio, D., Narlikar, G.J., Kingston, R.E. 10.1126/science.1210915 22096199 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2011 Regulatory protein SIR3 Transcription-associated P06701 P02281, P84233, P06897, P62799 -
102 3REL X-ray 2.70 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Triamminechloroplatinum(II) Chloride Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
103 3REK X-ray 2.60 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
104 3REJ X-ray 2.55 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
105 3REI X-ray 2.65 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
106 3REH X-ray 2.50 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
107 3O62 X-ray 3.22 2011-01-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link Todd, R.C., Lippard, S.J. 10.1016/j.chembiol.2010.10.018 21168769 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2011 P02281, P84233, P06897, P62799 -
108 3MVD X-ray 2.90 2010-08-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle Makde, R.D., England, J.R., Yennawar, H.P., Tan, S. 10.1038/nature09321 20739938 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Regulator of chromosome condensation Nuclear division P25171 P02281, P84233, P62799, Q6AZJ8 -
109 3MNN X-ray 2.50 2011-04-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Wu, B., Ong, M.S., Groessl, M., Adhireksan, Z., Hartinger, C.G., Dyson, P.J., Davey, C.A. 10.1002/chem.201100298 21344528 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2011 P02281, P84233, P06897, P62799 -
110 3MGS X-ray 3.15 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Cesium ions to the Nucleosome Core particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P62799, Q6AZJ8 -
111 7YWX EM 12.00 2022-05-18 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 162 Structure of the human CCAN CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein S, Centromere protein T, Centromere protein U, Centromere protein W, Centromere protein X, Centromere protein C Kinetochore, DNA repair, Fanconi anemia core complex, CENP-A NAC/CAD, Transcription-associated, Centromere-associated, Nuclear division Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q8N2Z9, Q96BT3, Q71F23, Q5EE01, A8MT69, Q03188 P62805, P62807, P49450, Q93077 0.054
112 3MGQ X-ray 2.65 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Nickel ions to the Nucleosome Core Particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P62799, Q6AZJ8 -
113 3MGP X-ray 2.44 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Cobalt ions to the Nucleosome Core Particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P62799, Q6AZJ8 -
114 3LZ1 X-ray 2.50 2010-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2) Vasudevan, D., Chua, E.Y., Davey, C.A. 10.1016/j.jmb.2010.08.039 20800598 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P62799, Q6AZJ8 -
115 8HE5 EM 6.95 2023-07-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, DNA repair protein Transcription-associated, Transcription factors, RNA polymerases, DNA repair C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R198 P62805, P06899, P04908, P68431 0.105
116 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8C6L5 P62805, P84243, P62807, Q93077 0.533
117 3AZH X-ray 3.49 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
118 8SNA EM 4.00 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.405
119 8SN8 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.443
120 8SN7 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.445
121 8SN6 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.434
122 8SN5 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.41
123 8SN4 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.439
124 8SN3 EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.429
125 8SN2 EM 3.60 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.452
126 8SN1 EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.526
127 8SN0 EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.547
128 8SMZ EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.535
129 8SMY EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.544
130 8SMX EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.549
131 8SMW EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.526
132 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 2023 Telomeric repeat-binding factor 1 Shelterin, DNA repair, Telomere-associated P54274 P62805, P62807, P68431, Q93077 0.579
133 8OX0 EM 2.52 2023-08-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 Structure of apo 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 2023 P62805, P62807, P68431, Q93077 0.607
134 8SN9 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077, P0CG47 P62805, P06899, P04908, P68431 0.424
135 8SPS EM 3.00 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P62805, Q16778, Q16777, P68431 0.434
136 3AZG X-ray 2.40 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
137 8SPU EM 2.80 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of ESRRB nucleosome bound OCT4 at site c Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P62805, Q16778, Q16777, P68431 0.496
138 3AZF X-ray 2.70 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
139 3AZE X-ray 3.00 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
140 3AYW X-ray 2.90 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
141 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 2024 DNA repair protein RAD51 homolog 1 Q06609 P62805, P06899, P04908, P68431 0.199
142 8X1C EM 3.20 2024-03-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of nucleosome-bound SRCAP-C in the ADP-bound state Yu, J., Wang, Q., Yu, Z., Li, W., Wang, L., Xu, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2, Actin, cytoplasmic 1, Actin-like protein 6A, DNA methyltransferase 1-associated protein 1, YEATS domain-containing protein 4 Transcription-associated, SWI/SNF, Chromatin remodelers, INO80 Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, P62807, P68431, Q93077 0.297
143 8X19 EM 3.20 2024-03-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state Yu, J., Wang, Q., Yu, Z., Li, W., Wang, L., Xu, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2, Actin, cytoplasmic 1, Actin-like protein 6A, DNA methyltransferase 1-associated protein 1, YEATS domain-containing protein 4 Transcription-associated, SWI/SNF, Chromatin remodelers, INO80 Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, P62807, P68431, Q93077 0.292
144 8X15 EM 3.20 2024-03-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 137 Structure of nucleosome-bound SRCAP-C in the apo state Yu, J., Wang, Q., Yu, Z., Li, W., Wang, L., Xu, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Helicase SRCAP, Vacuolar protein sorting-associated protein 72 homolog, Actin-related protein 6, Zinc finger HIT domain-containing protein 1, RuvB-like 1, RuvB-like 2, Actin, cytoplasmic 1, N-terminally processed, Actin-like protein 6A, DNA methyltransferase 1-associated protein 1, YEATS domain-containing protein 4 Transcription-associated, SWI/SNF, Chromatin remodelers, INO80 Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62805, P62807, P68431, Q93077 0.218
145 8UPF EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.464
146 8U14 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Transcription-associated, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P61077 P62805, P06899, P04908, P68431 0.352
147 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 2024 E3 ubiquitin-protein ligase RNF168 Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5 P62805, P62807, P04908, P68431 0.381
148 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 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P0CG47 P62805, P62807, P04908, P68431 0.438
149 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 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P0CG47 P62805, P62807, P04908, P68431 0.455
150 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 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, E3 ubiquitin-protein ligation, DNA repair, Ubiquitin, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK13_writer Q8IYW5, P0CG47 P62805, P62807, P04908, P68431 0.432
151 8TOF EM 2.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 176 Rpd3S bound to an H3K36Cme3 modified nucleosome Markert, J.W., Vos, S.M., Farnung, L. 10.1038/s41467-023-43968-8 38065958 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Rco1, histone N-terminal tail Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P22579, P32561, Q12432, Q04779 P02281, P02302, P06897, P62799 0.464
152 8SYP EM 2.60 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 Genomic CX3CR1 nucleosome Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Single-chain variable fragment P62805, Q16778, Q16777, P68431 0.559
153 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 2020 Poly [ADP-ribose] polymerase 2 DNA repair, Histone PTM writers, Histone_PARylation_writer Q9UGN5 P62805, P06899, P04908, P68431 0.092
154 6UPK EM 4.90 2019-12-11 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 72 Structure of FACT_subnucleosome complex 1 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Histone chaperones, FACT, DNA repair, DNA replication, Transcription-associated Q9Y5B9, Q08945 P62805, P62807, P68431, Q93077 0.203
155 3UTB X-ray 2.20 2012-04-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b) Chua, E.Y.D., Vasudevan, D., Davey, G.E., Wu, B., Davey, C.A. 10.1093/nar/gks261 22453276 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
156 6A5R EM 8.70 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 136 RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.11
157 6J4Y EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.235
158 6J4X EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.233
159 6J4W EM 7.90 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 171 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, F2QTN1, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.123
160 6IR9 EM 3.80 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.264
161 6INQ EM 6.90 2019-04-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 125 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.149
162 6A5U EM 7.60 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.14
163 6A5T EM 6.70 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.151
164 6A5P EM 7.00 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 168 RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.138
165 8YTI X-ray 2.70 2024-04-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.10 601L 169 Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Adhireksan, Z., Sharma, D., Qiuye, B., Lee, P.L., Padavattan, S., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 P06899, P04908, P68431, P62805, Q92522 -
166 6A5O EM 9.90 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 178 RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.083
167 6A5L EM 5.60 2018-10-03 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S.I., Kurumizaka, H. 10.1126/science.aau9904 30287617 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.182
168 5XM0 X-ray 2.87 2018-03-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4 Harada, A., Maehara, K., Ono, Y., Taguchi, H., Yoshioka, K., Kitajima, Y., Xie, Y., Sato, Y., Iwasaki, T., Nogami, J., Okada, S., Komatsu, T., Semba, Y., Takemoto, T., Kimura, H., Kurumizaka, H., Ohkawa, Y. 10.1038/s41467-018-03845-1 29643389 Mus musculus Mus musculus Mus musculus Mus musculus 2018 Q9D2U9, P84244, C0HKE1, P62806 -
169 5X7X X-ray 2.18 2017-04-19 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Taguchi, H., Xie, Y., Horikoshi, N., Maehara, K., Harada, A., Nogami, J., Sato, K., Arimura, Y., Osakabe, A., Kujirai, T., Iwasaki, T., Semba, Y., Tachibana, T., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1021/acs.biochem.6b01098 28374988 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 P62805, P06899, P84243, P04908 -
170 5B32 X-ray 2.35 2016-08-03 octamer 1 H3.3 canonical_H4 H2A.Z,canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Horikoshi, N., Arimura, Y., Taguchi, H., Kurumizaka, H. 10.1098/rsob.160127 27358293 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P06899, P0C0S5, P84243, P04908, P62805 -
171 3WTP X-ray 2.67 2014-12-03 octamer 1 H3.3,cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Arimura, Y., Shirayama, K., Horikoshi, N., Fujita, R., Taguchi, H., Kagawa, W., Fukagawa, T., Almouzni, G., Kurumizaka, H. 10.1038/srep07115 25408271 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2014 P06899, P84243, P04908, P49450, P62805 -
172 3AV2 X-ray 2.80 2011-06-01 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The human nucleosome structure containing the histone variant H3.3 Tachiwana, H., Osakabe, A., Shiga, T., Miya, Y., Kimura, H., Kagawa, W., Kurumizaka, H. 10.1107/S0907444911014818 21636898 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P84243, P04908 -
173 6J4Z EM 4.10 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Spt5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.244
174 6J50 EM 4.70 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.195
175 6J51 EM 4.20 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.23
176 6R0C EM 4.20 2019-09-25 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B Human-D02 142 Human-D02 Nucleosome Core Particle with biotin-streptavidin label Wilson, M.D., Renault, L., Maskell, D.P., Ghoneim, M., Pye, V.E., Nans, A., Rueda, D.S., Cherepanov, P., Costa, A. 10.1038/s41467-019-12007-w 31519882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, P0C0S8, P84243, P62807 0.373
177 8PKJ EM 2.50 2024-02-28 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of the nucleosome containing Nr5a2 motif at SHL+5.5 Kobayashi, W., Sappler, A.H., Bollschweiler, D., Kummecke, M., Basquin, J., Arslantas, E.N., Ruangroengkulrith, S., Hornberger, R., Duderstadt, K., Tachibana, K. 10.1038/s41594-024-01239-0 38409506 Mus musculus Mus musculus Mus musculus Mus musculus 2024 A0A7L1D652, A0A2J8S4Y0, A0A3Q2Z0K7, B2RVF0 0.6
178 8PKI EM 2.58 2024-02-28 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 137 Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 Kobayashi, W., Sappler, A.H., Bollschweiler, D., Kummecke, M., Basquin, J., Arslantas, E.N., Ruangroengkulrith, S., Hornberger, R., Duderstadt, K., Tachibana, K. 10.1038/s41594-024-01239-0 38409506 Mus musculus Mus musculus Mus musculus Mus musculus 2024 Nuclear receptor subfamily 5 group A member 2 O00482 Q6ZWY9, B2RVF0, P84244, P62806 0.572
179 8JH4 EM 3.20 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 178 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.313
180 8JH3 EM 3.70 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P62805, P06899, P84243, P04908 0.255
181 8JH2 EM 5.70 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.145
182 7XTI EM 3.90 2022-10-12 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 85 RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.223
183 7XTD EM 3.90 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.221
184 7XT7 EM 4.20 2022-10-12 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, F2QPX0, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.207
185 7XSZ EM 3.40 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 155 RNA polymerase II elongation complex transcribing a nucleosome (EC115) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.248
186 7XSX EM 3.80 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 108 RNA polymerase II elongation complex transcribing a nucleosome (EC49) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, FACT, DNA repair, Transcription factors, DNA replication, Transcription-associated, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.227
187 7XSE EM 3.60 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 134 RNA polymerase II elongation complex transcribing a nucleosome (EC42) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P62805, P06899, P84243, P04908 0.238
188 7WBX EM 4.00 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 150 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.298
189 7WBW EM 7.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.137
190 7WBV EM 4.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Transcription factors, RNA polymerases, SPT4-SPT5 complex C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P62805, P06899, P84243, P04908 0.267
191 6RNY EM 3.90 2019-09-25 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B Human-D02 128 PFV intasome - nucleosome strand transfer complex Wilson, M.D., Renault, L., Maskell, D.P., Ghoneim, M., Pye, V.E., Nans, A., Rueda, D.S., Cherepanov, P., Costa, A. 10.1038/s41467-019-12007-w 31519882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 Integrase Viral, DNA integration P14350 P62805, P0C0S8, P84243, P62807 0.349
192 7KBF EM 4.42 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.8 601L 172 H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) Arimura, Y., Shih, R.M., Froom, R., Funabiki, H. 10.1016/j.molcel.2021.08.010 34478647 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P02281, Q6DKE3, P15308, P62799, P84233 0.29
193 7K60 EM 3.12 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.10 601 197 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 scFv20 P06899, P04908, P68431, P62805, Q92522 0.435
194 6T93 EM 3.49 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Nucleosome with OCT4-SOX2 motif at SHL-6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, P06899, P04908, P68431 0.419
195 7XX6 X-ray 3.39 2023-05-31 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601L 169 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P06899, P07305, P04908, P68431, P62805 -
196 7PEZ EM 7.90 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 182 Nucleosome 4 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.203
197 7PEX EM 5.10 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 177 Nucleosome 2 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.267
198 7PEU EM 7.20 2022-08-03 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 520 Trinucleosome of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.138
199 7PET EM 9.50 2022-08-03 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 698 The 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.105
200 7K5Y EM 2.76 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 197 Cryo-EM structure of a chromatosome containing human linker histone H1.4 Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 scFv20 P06899, P04908, P68431, P10412, P62805 0.527
201 5WCU X-ray 5.53 2018-10-31 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H5 601 164 Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Zhou, B.R., Jiang, J., Ghirlando, R., Norouzi, D., Sathish Yadav, K.N., Feng, H., Wang, R., Zhang, P., Zhurkin, V., Bai, Y. 10.1016/j.jmb.2018.06.020 29959925 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Gallus gallus 2018 P02283, P84051, P02299, P02259, P84040 -
202 4QLC X-ray 3.50 2015-07-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H5 601 166 Crystal structure of chromatosome at 3.5 angstrom resolution Zhou, B.R., Jiang, J., Feng, H., Ghirlando, R., Xiao, T.S., Bai, Y. 10.1016/j.molcel.2015.06.025 26212454 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Gallus gallus 2015 P02283, P84051, P02299, P02259, P84040 -
203 7K5X EM 2.93 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601 197 Cryo-EM structure of a chromatosome containing human linker histone H1.0 Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 scFv20 P06899, P07305, P04908, P68431, P62805 0.489
204 6L9Z X-ray 2.50 2021-02-17 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.10 601_modified 338 338 bp di-nucleosome assembled with linker histone H1.X Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P06899, P04908, P68431, P62805, Q92522 -
205 7DBP EM 4.50 2020-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601 175 Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Wang, S., Vogirala, V.K., Soman, A., Berezhnoy, N.V., Liu, Z.B., Wong, A.S.W., Korolev, N., Su, C.J., Sandin, S., Nordenskiold, L. 10.1038/s41598-020-79654-8 33432055 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P07305, O60814, P04908, P68431, P62805 0.246
206 7COW X-ray 2.86 2021-08-11 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 353 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P06899, P07305, P04908, P68431, P62805 -
207 6LAB X-ray 3.20 2021-02-17 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601L 169 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P06899, P07305, P04908, P68431, P62805 -
208 6LA9 X-ray 3.70 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 349 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A. 10.1038/s41467-020-18533-2 32958761 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P06899, P07305, P04908, P68431, P62805 -
209 6LA8 X-ray 3.40 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 349 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A. 10.1038/s41467-020-18533-2 32958761 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P06899, P07305, P04908, P68431, P62805 -
210 6LA2 X-ray 3.89 2021-02-17 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 343 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P06899, P07305, P04908, P68431, P62805 -
211 7XVM X-ray 2.84 2023-05-24 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H5 601L 169 Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Gallus gallus 2023 P06899, P04908, P68431, P62805, P02259 -
212 7PF0 EM 11.00 2022-08-03 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 541 Trinucleosome of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.101
213 7PF2 EM 5.10 2022-08-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 339 Nucleosome stack of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.217
214 7PF3 EM 4.00 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Nucleosome 4 of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.351
215 7PF5 EM 3.80 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Nucleosome 2 of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.329
216 7K63 EM 3.03 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 197 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Zhou, B.R., Feng, H., Kale, S., Fox, T., Khant, H., de Val, N., Ghirlando, R., Panchenko, A.R., Bai, Y. 10.1016/j.molcel.2020.10.038 33238161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 scFv20 P06899, P04908, P68431, P10412, P62805 0.492
217 7XX5 X-ray 3.19 2023-05-31 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B generic_H1 601L 169 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P06899, P16402, P04908, P68431, P62805 -
218 8H0W EM 4.60 2022-12-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.2 601 196 RNA polymerase II transcribing a chromatosome (type II) Hirano, R., Ehara, H., Kujirai, T., Uejima, T., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1038/s41467-022-35003-z 36435862 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P04908, P68431, P16403, P62805 0.16
219 8H0V EM 3.80 2022-12-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.2 601 201 RNA polymerase II transcribing a chromatosome (type I) Hirano, R., Ehara, H., Kujirai, T., Uejima, T., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1038/s41467-022-35003-z 36435862 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Transcription-associated, RNA polymerases C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P06899, P04908, P68431, P16403, P62805 0.228
220 8H1T EM 3.00 2023-02-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Ge, W., Yu, C., Li, J., Yu, Z., Li, X., Zhang, Y., Liu, C.P., Li, Y., Tian, C., Zhang, X., Li, G., Zhu, B., Xu, R.M. 10.1038/s41586-023-05841-y 36991118 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Ubiquitin carboxyl-terminal hydrolase BAP1, Ubiquitin, Polycomb group protein ASXL1 Histone PTM erasers, Ubiquitin, Polycomb, Histone_deubiquitination_H2AK119, Transcription-associated Q92560, P0CG47, Q8IXJ9 Q16778, P20671, P68431, P10412, P62805 0.435
221 7PFX EM 4.30 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 177 Nucleosome 3 of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.269
222 7PFW EM 5.20 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Nucleosome 2 of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.264
223 7PFV EM 4.40 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 177 Nucleosome 1 of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.268
224 7PFU EM 5.00 2022-08-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 354 Nucleosome stack of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.236
225 7PFT EM 9.80 2022-08-03 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 591 Trinucleosome of the 4x207 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.109
226 7PFE EM 4.40 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 177 Nucleosome 2 of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.302
227 7PFD EM 4.40 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 172 Nucleosome 1 of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.208
228 7PFC EM 6.40 2022-08-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 344 Nucleosome stack of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.177
229 7PFA EM 9.70 2022-08-03 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 561 Trinucleosome of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.084
230 7PF6 EM 4.00 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 167 Nucleosome 1 of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Q71DI3, O60814, P04908, P10412, P62805 0.27
231 1EQZ X-ray 2.50 2000-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION Harp, J.M., Hanson, B.L., Timm, D.E., Bunick, G.J. 10.1107/S0907444900011847 11092917 Gallus gallus Gallus gallus Gallus gallus Gallus gallus 2000 P84229, P62801, P02263, P0C1H5 -
232 2CV5 X-ray 2.50 2005-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of human nucleosome core particle Tsunaka, Y., Kajimura, N., Tate, S., Morikawa, K. 10.1093/nar/gki663 15951514 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2005 P62805, O60814, P04908, P68431 -
233 2F8N X-ray 2.90 2006-05-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A,macroH2A canonical_H2B alphasat_146 145 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Chakravarthy, S., Luger, K. 0 Xenopus laevis Xenopus laevis Mus musculus,Homo sapiens Mus musculus,Xenopus laevis 2006 P02281, Q9D2U9, Q8CGP6, P62799, P84233, O75367 -
234 6HTS EM 4.80 2018-11-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Cryo-EM structure of the human INO80 complex bound to nucleosome Ayala, R., Willhoft, O., Aramayo, R.J., Wilkinson, M., McCormack, E.A., Ocloo, L., Wigley, D.B., Zhang, X. 10.1038/s41586-018-0021-6 29643506 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit B INO80, DNA repair, DNA replication, Transcription-associated, Chromatin remodelers Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q9C086 P62805, P06899, P04908, P68431 0.181
235 6L49 EM 18.90 2019-12-04 octamer, octamer, octamer 3 cenH3,canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 485 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Takizawa, Y., Ho, C.H., Tachiwana, H., Matsunami, H., Kobayashi, W., Suzuki, M., Arimura, Y., Hori, T., Fukagawa, T., Ohi, M.D., Wolf, M., Kurumizaka, H. 10.1016/j.str.2019.10.016 31711756 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P06899, P04908, P49450, P68431, P62805 0.071
236 6KW5 EM 10.13 2020-09-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The ClassC RSC-Nucleosome Complex Ye, Y.P., Wu, H., Chen, K.J., Verma, N., Cairns, B., Gao, N., Chen, Z.C. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromatin structure-remodeling complex protein RSC58, Chromatin structure-remodeling complex protein RSC30, Chromatin structure-remodeling complex protein RSC8, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC6, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex subunit RSC4, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P84233, P06897, P62799, A0A1L8G0X3 0.062
237 6KW3 EM 7.13 2019-11-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The ClassA RSC-Nucleosome Complex Ye, Y., Wu, H., Chen, K., Clapier, C.R., Verma, N., Zhang, W., Deng, H., Cairns, B.R., Gao, N., Chen, Z. 10.1126/science.aay0033 31672915 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Chromatin structure-remodeling complex protein RSC58, Chromatin structure-remodeling complex protein RSC30, Chromatin structure-remodeling complex protein RSC8, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC6, Nuclear protein STH1/NPS1, Chromatin structure-remodeling complex protein RSC3, Chromatin structure-remodeling complex subunit RSC2, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex subunit RSC4, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.086
238 6JR1 X-ray 2.40 2019-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the human nucleosome phased with 16 selenium atoms Saotome, M., Horikoshi, N., Urano, K., Kujirai, T., Yuzurihara, H., Kurumizaka, H., Kagawa, W. 10.1107/S2059798319012713 31588924 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, P06899, P04908, P68431 -
239 6JR0 X-ray 2.50 2019-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the human nucleosome phased with 12 selenium atoms Saotome, M., Horikoshi, N., Urano, K., Kujirai, T., Yuzurihara, H., Kurumizaka, H., Kagawa, W. 10.1107/S2059798319012713 31588924 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, P06899, P04908, P68431 -
240 6J99 EM 4.10 2019-02-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Yao, T., Jing, W., Hu, Z., Tan, M., Cao, M., Wang, Q., Li, Y., Yuan, G., Lei, M., Huang, J. 10.1038/s41422-019-0146-7 30770869 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, P62979 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.132
241 6I84 EM 4.40 2019-01-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 169 Structure of transcribing RNA polymerase II-nucleosome complex Farnung, L., Vos, S.M., Cramer, P. 10.1038/s41467-018-07870-y 30575770 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4 Transcription-associated, RNA polymerases P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422 P02281, P84233, P06897, P62799 0.241
242 6HKT X-ray 9.70 2018-10-31 octamer, octamer, octamer, octamer, octamer, octamer 6 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 1122 Structure of an H1-bound 6-nucleosome array Garcia-Saez, I., Menoni, H., Boopathi, R., Shukla, M.S., Soueidan, L., Noirclerc-Savoye, M., Le Roy, A., Skoufias, D.A., Bednar, J., Hamiche, A., Angelov, D., Petosa, C., Dimitrov, S. 10.1016/j.molcel.2018.09.027 30392928 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 P62805, P06899, P04908, P68431 -
243 3AFA X-ray 2.50 2010-05-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The human nucleosome structure Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H. 10.1073/pnas.1003064107 20498094 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2010 P62805, P06899, P04908, P68431 -
244 6DZT EM 2.99 2019-05-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of nucleosome in complex with a single chain antibody fragment Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2019 scFv P02299, P02283, P84051, P84040 0.589
245 5Y0D X-ray 1.99 2018-07-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of the human nucleosome containing the H2B E76K mutant Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T., Kurumizaka, H. 10.1093/nar/gky661 30053102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 P62805, P06899, P04908, P68431 -
246 5Y0C X-ray 2.09 2018-07-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of the human nucleosome at 2.09 angstrom resolution Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T., Kurumizaka, H. 10.1093/nar/gky661 30053102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 P62805, P06899, P04908, P68431 -
247 5XF5 X-ray 2.82 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 P62805, P06899, P04908, P68431 -
248 5XF4 X-ray 2.87 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 P62805, P06899, P04908, P68431 -
249 5XF3 X-ray 2.60 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 P62805, P06899, P04908, P68431 -
250 5X0X EM 3.97 2017-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome Liu, X., Li, M., Xia, X., Li, X., Chen, Z. 10.1038/nature22036 28424519 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.372
251 6L4A EM 12.30 2019-12-04 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 485 H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Takizawa, Y., Ho, C.H., Tachiwana, H., Matsunami, H., Kobayashi, W., Suzuki, M., Arimura, Y., Hori, T., Fukagawa, T., Ohi, M.D., Wolf, M., Kurumizaka, H. 10.1016/j.str.2019.10.016 31711756 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, P06899, P04908, P68431 0.085
252 6LER X-ray 3.00 2021-03-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 169 169 bp nucleosome harboring non-identical cohesive DNA termini. Adhireksan, Z., Sharma, D., Lee, P.L., Bao, Q., Padavattan, S., Shum, W.K., Davey, G.E., Davey, C.A. 10.1093/nar/gkab070 33590100 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 P62805, P06899, P04908, P68431 -
253 6M3V X-ray 4.60 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 355 355 bp di-nucleosome harboring cohesive DNA termini Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A. 10.1038/s41467-020-18533-2 32958761 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, P06899, P04908, P68431 -
254 6M44 X-ray 3.81 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 355 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Adhireksan, Z., Sharma, D., Lee, P.L., Davey, C.A. 10.1038/s41467-020-18533-2 32958761 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, P06899, P04908, P68431 -
255 6T90 EM 3.05 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 141 OCT4-SOX2-bound nucleosome - SHL-6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription-associated, Transcription factors P42212, P48431 P62805, P06899, P04908, P68431 0.451
256 6RYU EM 4.00 2020-07-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Nucleosome-CHD4 complex structure (two CHD4 copies) Farnung, L., Ochmann, M., Cramer, P. 10.7554/eLife.56178 32543371 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 4,CHD4,Chromodomain-helicase-DNA-binding protein 4 NuRD (CHD), Chromatin remodelers Q14839 P02281, P84233, P06897, P62799 0.342
257 6RYR EM 3.10 2020-07-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Nucleosome-CHD4 complex structure (single CHD4 copy) Farnung, L., Ochmann, M., Cramer, P. 10.7554/eLife.56178 32543371 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 4,Chromodomain-helicase-DNA-binding protein 4,Chromodomain-helicase-DNA-binding protein 4 NuRD (CHD), Chromatin remodelers Q14839 P02281, P84233, P06897, P62799 0.52
258 6R94 EM 3.50 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP_THF2(-3) 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 2019 P62805, P06899, P04908, P68431 0.363
259 6R93 EM 4.00 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Cryo-EM structure of NCP-6-4PP 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 2019 P62805, P06899, P04908, P68431 0.352
260 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 2019 DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, DCX complex, UV-DDB complex Q16531, Q92466 P62805, P06899, P04908, P68431 0.22
261 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 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, DCX complex, UV-DDB complex Q16531, Q92466 P62805, P06899, P04908, P68431 0.212
262 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 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, DCX complex, UV-DDB complex Q16531, Q92466 P62805, P06899, P04908, P68431 0.278
263 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 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, DCX complex, UV-DDB complex Q16531, Q92466 P62805, P06899, P04908, P68431 0.307
264 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 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, DCX complex, UV-DDB complex Q16531, Q92466 P62805, P06899, P04908, P68431 0.313
265 6PWX EM 4.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of RbBP5 bound to the nucleosome Park, S.H., Ayoub, A., Lee, Y.T., Xu, J., Kim, H., Zheng, W., Zhang, B., Sha, L., An, S., Zhang, Y., Cianfrocco, M.A., Su, M., Dou, Y., Cho, U.S. 10.1038/s41467-019-13550-2 31804488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Retinoblastoma-binding protein 5 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291 P02281, P84233, P06897, P62799 0.332
266 6PWW EM 4.40 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Park, S.H., Ayoub, A., Lee, Y.T., Xu, J., Kim, H., Zheng, W., Zhang, B., Sha, L., An, S., Zhang, Y., Cianfrocco, M.A., Su, M., Dou, Y., Cho, U.S. 10.1038/s41467-019-13550-2 31804488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164 P02281, P84233, P06897, P62799 0.26
267 6PWF EM 4.07 2019-08-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome Chittori, S., Hong, J., Bai, Y., Subramaniam, S. 10.1093/nar/gkz670 31402386 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2019 chromatin remodeling factor ISWI Chromatin remodelers, ISWI G0S9L5 P02299, P02283, P84051, P84040 0.39
268 6PWE EM 3.95 2019-08-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of nucleosome core particle Chittori, S., Hong, J., Bai, Y., Subramaniam, S. 10.1093/nar/gkz670 31402386 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2019 P02299, P02283, P84051, P84040 0.409
269 6NE3 EM 3.90 2019-07-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2 Armache, J.P., Gamarra, N., Johnson, S.L., Leonard, J.D., Wu, S., Narlikar, G.J., Cheng, Y. 10.7554/eLife.46057 31210637 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Transcription-associated, Heterochromatin-associated, Chromatin remodelers, ISWI O60264 P02281, P84233, P06897, P62799 0.42
270 5O9G EM 4.80 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 162 Structure of nucleosome-Chd1 complex Farnung, L., Vos, S.M., Wigge, C., Cramer, P. 10.1038/nature24046 29019976 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Chromo domain-containing protein 1 Transcription-associated, CHD, Chromatin remodelers P32657 P02281, P84233, P06897, P62799 0.018
271 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 2016 Tumor suppressor p53-binding protein 1, Ubiquitin Ubiquitin, DNA repair, Telomere-associated, Histone PTM readers, Histone_ubiquitination_H2AK15_reader, Histone_methylation_H4K20_reader Q12888, P0CG47 P0C0S8, P84233, P62807, P62799 0.301
272 5JRG X-ray 2.50 2017-03-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 144 Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Osakabe, A., Arimura, Y., Matsumoto, S., Horikoshi, N., Sugasawa, K., Kurumizaka, H. 10.1038/srep41783 28139742 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 P62805, P06899, P04908, P68431 -
273 4ZUX X-ray 3.82 2016-02-24 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Morgan, M.T., Haj-Yahya, M., Ringel, A.E., Bandi, P., Brik, A., Wolberger, C. 10.1126/science.aac5681 26912860 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 Ubiquitin carboxyl-terminal hydrolase 8, Transcription and mRNA export factor SUS1, SAGA-associated factor 11, Polyubiquitin-B, SAGA-associated factor 73 Histone PTM erasers, Ubiquitin, SAGA, Transcription-associated, Histone_deubiquitination P50102, Q6WNK7, Q03067, P0CG47, P53165 P02281, P84233, P06897, P62799 -
274 4YM5 X-ray 4.00 2015-12-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 143 Crystal structure of the human nucleosome containing 6-4PP (inside) Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H. 10.1038/srep16330 26573481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
275 4LD9 X-ray 3.31 2013-08-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Arnaudo, N., Fernandez, I.S., McLaughlin, S.H., Peak-Chew, S.Y., Rhodes, D., Martino, F. 10.1038/nsmb.2641 23934150 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 Regulatory protein SIR3 Transcription-associated P06701 P02281, P84233, P06897, P62799 -
276 4KGC X-ray 2.69 2014-03-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM Adhireksan, Z., Davey, G.E., Campomanes, P., Groessl, M., Clavel, C.M., Yu, H., Nazarov, A.A., Yeo, C.H., Ang, W.H., Droge, P., Rothlisberger, U., Dyson, P.J., Davey, C.A. 10.1038/ncomms4462 24637564 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2014 P02281, P84233, P62799, Q6AZJ8 -
277 3WKJ X-ray 2.80 2014-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 145 The nucleosome containing human TSH2B Urahama, T., Horikoshi, N., Osakabe, A., Tachiwana, H., Kurumizaka, H. 10.1107/S2053230X14004695 24699735 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2014 P62805, P04908, P68431, Q96A08 -
278 3W99 X-ray 3.00 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2013 P62805, P06899, P04908, P68431 -
279 3W97 X-ray 3.20 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2013 P62805, P06899, P04908, P68431 -
280 3W96 X-ray 3.00 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2013 P62805, P06899, P04908, P68431 -
281 3LEL X-ray 2.95 2010-05-19 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 147 Structural Insight into the Sequence-Dependence of Nucleosome Positioning Wu, B., Mohideen, K., Vasudevan, D., Davey, C.A. 10.1016/j.str.2010.01.015 20399189 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P62799, Q6AZJ8 -
282 3AZN X-ray 3.00 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
283 3AZM X-ray 2.89 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
284 3AZL X-ray 2.70 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
285 3AZK X-ray 3.20 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
286 3AZJ X-ray 2.89 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
287 3AZI X-ray 2.70 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P68431 -
288 3AV1 X-ray 2.50 2011-06-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The human nucleosome structure containing the histone variant H3.2 Tachiwana, H., Osakabe, A., Shiga, T., Miya, Y., Kimura, H., Kagawa, W., Kurumizaka, H. 10.1107/S0907444911014818 21636898 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, Q71DI3 -
289 4YM6 X-ray 3.51 2015-12-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 144 Crystal structure of the human nucleosome containing 6-4PP (outside) Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H. 10.1038/srep16330 26573481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
290 5AV5 X-ray 2.40 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
291 5GTC X-ray 2.70 2017-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Amamoto, Y., Aoi, Y., Nagashima, N., Suto, H., Yoshidome, D., Arimura, Y., Osakabe, A., Kato, D., Kurumizaka, H., Kawashima, S.A., Yamatsugu, K., Kanai, M. 10.1021/jacs.7b02138 28534629 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 LANA peptide Viral Q9QR71 P62805, P06899, P04908, P68431 -
292 5AV6 X-ray 2.20 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
293 5GSE X-ray 3.14 2017-05-03 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 244 Crystal structure of unusual nucleosome Kato, D., Osakabe, A., Arimura, Y., Mizukami, Y., Horikoshi, N., Saikusa, K., Akashi, S., Nishimura, Y., Park, S.Y., Nogami, J., Maehara, K., Ohkawa, Y., Matsumoto, A., Kono, H., Inoue, R., Sugiyama, M., Kurumizaka, H. 10.1126/science.aak9867 28408607 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 P62805, P06899, P04908, P68431 -
294 5E5A X-ray 2.81 2016-02-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle Fang, Q., Chen, P., Wang, M., Fang, J., Yang, N., Li, G., Xu, R.M. 10.7554/eLife.11911 26812545 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 C-terminal domain of Regulatory protein IE1 Viral P03169 P02281, P84233, P06897, P62799 -
295 5CPK X-ray 2.63 2015-10-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_2L 139 Nucleosome containing methylated Sat2L DNA Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H. 10.1098/rsob.150128 26446621 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
296 5CPJ X-ray 3.15 2015-10-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_2R 140 Nucleosome containing methylated Sat2R DNA Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H. 10.1098/rsob.150128 26446621 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
297 5CPI X-ray 2.90 2015-10-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_2R 146 Nucleosome containing unmethylated Sat2R DNA Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H. 10.1098/rsob.150128 26446621 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
298 5B31 X-ray 2.20 2016-08-03 octamer 1 canonical_H3 canonical_H4 H2A.Z,canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Horikoshi, N., Arimura, Y., Taguchi, H., Kurumizaka, H. 10.1098/rsob.160127 27358293 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P06899, P0C0S5, P04908, P68431, P62805 -
299 5B2J X-ray 2.60 2016-06-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146_4CpG 142 Human nucleosome containing CpG methylated DNA Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S. 10.1002/2211-5463.12064 27419055 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P62805, P06899, P04908, P68431 -
300 5B2I X-ray 3.00 2016-06-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146_4CpG 146 Human nucleosome containing CpG unmethylated DNA Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S. 10.1002/2211-5463.12064 27419055 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P62805, P06899, P04908, P68431 -
301 5B24 X-ray 3.60 2016-03-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 144 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Horikoshi, N., Tachiwana, H., Kagawa, W., Osakabe, A., Matsumoto, S., Iwai, S., Sugasawa, K., Kurumizaka, H. 10.1016/j.bbrc.2016.01.170 26837048 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P62805, P06899, P04908, P68431 -
302 5B1M X-ray 2.34 2017-02-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The mouse nucleosome structure containing H3.1 Ueda, J., Harada, A., Urahama, T., Machida, S., Maehara, K., Hada, M., Makino, Y., Nogami, J., Horikoshi, N., Osakabe, A., Taguchi, H., Tanaka, H., Tachiwana, H., Yao, T., Yamada, M., Iwamoto, T., Isotani, A., Ikawa, M., Tachibana, T., Okada, Y., Kimura, H., Ohkawa, Y., Kurumizaka, H., Yamagata, K. 10.1016/j.celrep.2016.12.065 28099840 Mus musculus Mus musculus Mus musculus Mus musculus 2017 Q9D2U9, C0HKE1, P62806, P68433 -
303 5B0Z X-ray 1.99 2016-01-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Suzuki, Y., Horikoshi, N., Kato, D., Kurumizaka, H. 10.1016/j.bbrc.2015.12.041 26694698 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P62805, P06899, P04908, Q71DI3 -
304 5AVC X-ray 2.40 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
305 5AVB X-ray 2.40 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
306 5AV9 X-ray 2.20 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
307 5AV8 X-ray 2.20 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P06899, P04908, P68431 -
308 3UTA X-ray 2.07 2012-04-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) Chua, E.Y.D., Vasudevan, D., Davey, G.E., Wu, B., Davey, C.A. 10.1093/nar/gks261 22453276 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
309 3MGR X-ray 2.30 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Rubidium ions to the Nucleosome Core Particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P62799, Q6AZJ8 -
310 3X1S X-ray 2.80 2015-09-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the nucleosome core particle Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bbrc.2015.07.070 26188507 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2015 P62805, P04908, P68431, P33778 -
311 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 2022 DNA-(apurinic or apyrimidinic site) endonuclease DNA repair P27695 P62805, P0C0S8, P62807, Q71DI3 0.415
312 1P3F X-ray 2.90 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
313 1P3B X-ray 3.00 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
314 8JLD EM 2.48 2023-10-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Ehara, H., Sekine, S.I., Hayashi, G., Takizawa, Y., Kurumizaka, H. 10.1093/nar/gkad754 37718728 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P62805, P06899, P04908, Q71DI3 0.579
315 8JLB EM 2.36 2023-10-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Ehara, H., Sekine, S.I., Hayashi, G., Takizawa, Y., Kurumizaka, H. 10.1093/nar/gkad754 37718728 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P62805, P06899, P04908, Q71DI3 0.602
316 7U53 EM 4.00 2022-09-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Nucleosome core particle with AP-site at SHL0 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 2022 P62805, P0C0S8, P62807, Q71DI3 0.385
317 7U52 EM 3.40 2022-09-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 nucleosome core particle with AP-site at SHL-6.5 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 2022 P62805, P0C0S8, P62807, Q71DI3 0.454
318 7U51 EM 3.10 2022-09-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 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 2022 P62805, P0C0S8, P62807, Q71DI3 0.537
319 7JZV EM 3.90 2021-02-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Witus, S.R., Burrell, A.L., Farrell, D.P., Kang, J., Wang, M., Hansen, J.M., Pravat, A., Tuttle, L.M., Stewart, M.D., Brzovic, P.S., Chatterjee, C., Zhao, W., DiMaio, F., Kollman, J.M., Klevit, R.E. 10.1038/s41594-020-00556-4 33589814 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 BRCA1,Ubiquitin-conjugating enzyme E2 D3, BRCA1-associated RING domain protein 1 E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK125_writer, DNA repair, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Transcription-associated, Histone PTM writers P38398, Q99728 P62805, Q6FI13, O60814, Q71DI3 0.313
320 8V4Y EM 2.80 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1) Chio, U.S., Palovcak, E., Smith, A.A.A., Autzen, H., Munoz, E.N., Yu, Z., Wang, F., Agard, D.A., Armache, J.P., Narlikar, G.J., Cheng, Y. 10.1038/s41467-024-46178-y 38472177 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Transcription-associated, Heterochromatin-associated, Chromatin remodelers, ISWI O60264 P02281, P84233, P06897, P62799 0.53
321 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8C6L5 P62805, P0C0S8, P62807, Q71DI3 0.196
322 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8C6L5 P62805, P0C0S8, P62807, Q71DI3 0.265
323 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8C6L5 P62805, P0C0S8, P62807, Q71DI3 0.54
324 6VEN EM 3.37 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Yeast COMPASS in complex with a ubiquitinated nucleosome Worden, E.J., Zhang, X., Wolberger, C. 10.7554/eLife.53199 31922488 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Ubiquitin, COMPASS component SWD3, COMPASS component SWD1, Histone-lysine N-methyltransferase, H3 lysine-4 specific, COMPASS component BRE2, COMPASS component SDC1, COMPASS component SPP1 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Telomere-associated, Transcription-associated, Histone PTM writers P0CG48, P38123, P39706, P38827, P43132, Q03323, Q03012 P02281, P84233, P06897, P62799 0.449
325 6NQA EM 3.54 2019-02-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C. 10.1016/j.cell.2019.02.002 30765112 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, P0CG48 P02281, P84233, P06897, P62799 0.436
326 6NJ9 EM 2.96 2019-02-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C. 10.1016/j.cell.2019.02.002 30765112 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, P0CG47 P02281, P84233, P06897, P62799 0.551
327 8V7L EM 2.90 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 140 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 2) Chio, U.S., Palovcak, E., Smith, A.A.A., Autzen, H., Munoz, E.N., Yu, Z., Wang, F., Agard, D.A., Armache, J.P., Narlikar, G.J., Cheng, Y. 10.1038/s41467-024-46178-y 38472177 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Transcription-associated, Heterochromatin-associated, Chromatin remodelers, ISWI O60264 P02281, P84233, P06897, P62799 0.456
328 1P3G X-ray 2.70 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
329 1P3I X-ray 2.30 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
330 1P3O X-ray 2.75 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
331 1P3P X-ray 2.70 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
332 7DBH EM 3.60 2022-01-19 octamer 1 H3.3,canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 126 The mouse nucleosome structure containing H3mm18 Hirai, S., Tomimatsu, K., Miyawaki-Kuwakado, A., Takizawa, Y., Komatsu, T., Tachibana, T., Fukushima, Y., Takeda, Y., Negishi, L., Kujirai, T., Koyama, M., Ohkawa, Y., Kurumizaka, H. 10.1093/nar/gkab1137 34929737 Mus musculus Mus musculus Mus musculus Mus musculus 2022 C0HKE1, None, Q9D2U9, P62806 0.391
333 8KB5 EM 2.26 2023-10-18 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Cryo-EM structure of the human nucleosome containing H3.8 Hirai, S., Kujirai, T., Akatsu, M., Ogasawara, M., Ehara, H., Sekine, S.I., Ohkawa, Y., Takizawa, Y., Kurumizaka, H. 10.1093/jb/mvad069 37757444 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P62805, P06899, P84243, P04908 0.655
334 4Z5T X-ray 2.80 2016-02-10 octamer 1 H3.5 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The nucleosome containing human H3.5 Urahama, T., Harada, A., Maehara, K., Horikoshi, N., Sato, K., Sato, Y., Shiraishi, K., Sugino, N., Osakabe, A., Tachiwana, H., Kagawa, W., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1186/s13072-016-0051-y 26779285 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P62805, P06899, Q6NXT2, P04908 -
335 1P3M X-ray 2.90 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
336 1P3L X-ray 2.40 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
337 1P34 X-ray 2.70 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
338 7UV9 EM 3.20 2023-02-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate Spangler, C.J., Skrajna, A., Foley, C.A., Nguyen, A., Budziszewski, G.R., Azzam, D.N., Arteaga, E.C., Simmons, H.C., Smith, C.B., Wesley, N.A., Wilkerson, E.M., McPherson, J.E., Kireev, D., James, L.I., Frye, S.V., Goldfarb, D., McGinty, R.K. 10.1038/s41589-023-01256-y 36797403 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Lysine-specific demethylase 2A Heterochromatin-associated, Histone PTM erasers, Centromere-associated, Histone_demethylation_H3K36 Q9Y2K7 P62805, P0C0S8, P62807, Q71DI3 0.42
339 1P3K X-ray 2.90 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
340 1P3A X-ray 3.00 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
341 7CRR EM 3.48 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 Native NSD3 bound to 187-bp nucleosome Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis 2020 Histone-lysine N-methyltransferase NSD3 Transcription-associated, Histone_methylation_H3K27_writer, Histone_methylation_H3K4_writer, Histone PTM writers Q9BZ95 P02281, Q92133, P06897, P62799 0.464
342 7CRQ EM 3.15 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis 2020 Histone-lysine N-methyltransferase NSD3 Transcription-associated, Histone_methylation_H3K27_writer, Histone_methylation_H3K4_writer, Histone PTM writers Q9BZ95 P02281, Q92133, P06897, P62799 0.507
343 7CRP EM 3.20 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode) Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis 2020 Histone-lysine N-methyltransferase NSD3 Transcription-associated, Histone_methylation_H3K27_writer, Histone_methylation_H3K4_writer, Histone PTM writers Q9BZ95 P02281, Q92133, P06897, P62799 0.542
344 7CRO EM 3.75 2020-10-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 168 NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP Li, W., Tian, W., Yuan, G., Deng, P., Sengupta, D., Cheng, Z., Cao, Y., Ren, J., Qin, Y., Zhou, Y., Jia, Y., Gozani, O., Patel, D.J., Wang, Z. 10.1038/s41586-020-03069-8 33361816 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis 2020 Histone-lysine N-methyltransferase NSD2 Transcription-associated, Euchromatin-associated, Histone_methylation_H3K36_writer, Histone PTM writers O96028 P02281, Q92133, P06897, P62799 0.448
345 5ONW X-ray 2.80 2017-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 146 X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C Frouws, T.D., Barth, P.D., Richmond, T.J. 10.1016/j.jmb.2017.10.029 29113904 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
346 5ONG X-ray 2.80 2017-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 146 X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Frouws, T.D., Barth, P.D., Richmond, T.J. 10.1016/j.jmb.2017.10.029 29113904 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
347 8V6V EM 2.80 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of doubly-bound SNF2h-nucleosome complex Chio, U.S., Palovcak, E., Smith, A.A.A., Autzen, H., Munoz, E.N., Yu, Z., Wang, F., Agard, D.A., Armache, J.P., Narlikar, G.J., Cheng, Y. 10.1038/s41467-024-46178-y 38472177 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Transcription-associated, Heterochromatin-associated, Chromatin remodelers, ISWI O60264 P02281, P84233, P06897, P62799 0.477
348 8PEP EM 3.33 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.399
349 7PEY EM 4.50 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 171 Nucleosome 3 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, Q71DI3 0.281
350 3A6N X-ray 2.70 2010-05-26 octamer 1 TS_H3.4 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 The nucleosome containing a testis-specific histone variant, human H3T Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H. 10.1073/pnas.1003064107 20498094 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2010 P62805, P06899, P04908, Q16695 -
351 7ZS9 EM 3.10 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P02281, P84233, P06897, P62799 0.34
352 7TN2 EM 2.30 2022-03-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A Cryo-EM maps Nodelman, I.M., Das, S., Faustino, A.M., Fried, S.D., Bowman, G.D., Armache, J.P. 10.1038/s41594-021-00719-x 35173352 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Chromo domain-containing protein 1 Transcription-associated, CHD, Chromatin remodelers P32657 P02281, P84233, P06897, P62799 -
353 7SWY EM 2.60 2022-03-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 2.6 A structure of a 40-601[TA-rich+1]-40 nucleosome Nodelman, I.M., Das, S., Faustino, A.M., Fried, S.D., Bowman, G.D., Armache, J.P. 10.1038/s41594-021-00719-x 35173352 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 P02281, P84233, P06897, P62799 -
354 6S01 EM 3.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Wang, H., Farnung, L., Dienemann, C., Cramer, P. 10.1038/s41594-019-0345-4 31819277 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.529
355 5OMX X-ray 2.32 2017-11-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 X-ray Structure of the H2A-N38C Nucleosome Core Particle Frouws, T.D., Barth, P.D., Richmond, T.J. 10.1016/j.jmb.2017.10.029 29113904 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
356 5B1L X-ray 2.35 2017-02-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 The mouse nucleosome structure containing H3t Ueda, J., Harada, A., Urahama, T., Machida, S., Maehara, K., Hada, M., Makino, Y., Nogami, J., Horikoshi, N., Osakabe, A., Taguchi, H., Tanaka, H., Tachiwana, H., Yao, T., Yamada, M., Iwamoto, T., Isotani, A., Ikawa, M., Tachibana, T., Okada, Y., Kimura, H., Ohkawa, Y., Kurumizaka, H., Yamagata, K. 10.1016/j.celrep.2016.12.065 28099840 Mus musculus Mus musculus Mus musculus Mus musculus 2017 Q9D2U9, C0HKE1, P62806, P68433 -
357 3C1C X-ray 3.15 2008-10-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure Lu, X., Simon, M.D., Chodaparambil, J.V., Hansen, J.C., Shokat, K.M., Luger, K. 10.1038/nsmb.1489 18794842 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus (Silurana) tropicalis 2008 Q28D68, P84233, P06897, P62799 -
358 1ZLA X-ray 2.90 2006-02-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bound to the nucleosomal core Barbera, A.J., Chodaparambil, J.V., Kelley-Clarke, B., Joukov, V., Walter, J.C., Luger, K., Kaye, K.M. 10.1126/science.1120541 16469929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2006 latent nuclear antigen Viral Q9DUM3 P02281, P84233, P06897, P62799 -
359 8PEO EM 2.69 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.548
360 1M1A X-ray 2.65 2003-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1016/S0022-2836(02)01407-9 12559907 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2003 P02281, P02302, P06897, P62799 -
361 1M19 X-ray 2.30 2003-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1016/S0022-2836(02)01407-9 12559907 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2003 P02281, P02302, P06897, P62799 -
362 1M18 X-ray 2.45 2003-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1016/S0022-2836(02)01407-9 12559907 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2003 P02281, P02302, P06897, P62799 -
363 8UX1 EM 2.50 2023-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle Huang, S.K., Rubinstein, J.L., Kay, L.E. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2023 GTP-binding nuclear protein Ran, Regulator of chromosome condensation P62826, P18754 P02299, P02283, P84051, P84040 0.609
364 8DU4 EM 3.55 2022-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Rahman, S., Hoffmann, N.A., Worden, E.J., Smith, M.L., Namitz, K.E.W., Knutson, B.A., Cosgrove, M.S., Wolberger, C. 10.1073/pnas.2205691119 36095189 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 WD repeat-containing protein 5, Retinoblastoma-binding protein 5, Polyubiquitin-B COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers P61964, Q15291, P0CG47 P02281, P02302, P06897, P62799 0.237
365 7UD5 EM 4.25 2022-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Rahman, S., Hoffmann, N.A., Worden, E.J., Smith, M.L., Namitz, K.E.W., Knutson, B.A., Cosgrove, M.S., Wolberger, C. 10.1073/pnas.2205691119 36095189 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 cDNA FLJ56846, highly similar to Zinc finger protein HRX, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2, Retinoblastoma-binding protein 5, Polyubiquitin-B, Protein dpy-30 homolog COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers B4DIJ7, P61964, Q9UBL3, Q15291, P0CG47, Q9C005 P02281, P84233, P06897, P62799 0.263
366 7PFF EM 4.30 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 167 Nucleosome 3 of the 4x197 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, Q71DI3 0.221
367 7ZSA EM 4.00 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P02281, P84233, P06897, P62799 0.342
368 7ZSB EM 6.60 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 219 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription-associated, Transcription factors, DNA repair, RNA polymerases P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P02281, P84233, P06897, P62799 0.277
369 8CBN EM 3.34 2023-12-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.392
370 8CBQ EM 4.00 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.304
371 8PC6 EM 3.04 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.484
372 8PC5 EM 3.02 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Transcription-associated, Transcription factors, Histone_methylation_H3K36_reader, Histone PTM readers O75475 P02281, P84233, P06897, P62799 0.521
373 8KD7 EM 3.09 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.324
374 8KD6 EM 3.07 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.311
375 8KD5 EM 2.90 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.378
376 8KD4 EM 2.93 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.373
377 8JHO EM 7.60 2023-09-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 340 Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.067
378 8IHT EM 3.72 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Rpd3S bound to the nucleosome Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. 10.1038/s41422-023-00884-2 37845487 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, RCO1 isoform 1, Chromatin modification-related protein EAF3 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Transcription-associated P22579, P32561, A0A8H4BXB0, A0A8H4F719 A0A310TTQ1, A0A8J0U496, Q6AZJ8, A0A8J1LTD2 0.345
379 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 2024 Rco1-ABR, Chromatin modification-related protein EAF3 A0A8H4F719 A0A310TTQ1, A0A8J0U496, Q6AZJ8, A0A8J1LTD2 0.434
380 8HY0 EM 3.10 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.463
381 8HXZ EM 3.40 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Cryo-EM structure of Eaf3 CHD in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 DNA repair, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 Q12432 P02281, P84233, P06897, P62799 0.326
382 8HXY EM 3.10 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.44
383 8G57 EM 3.07 2023-04-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Structure of nucleosome-bound Sirtuin 6 deacetylase Chio, U.S., Rechiche, O., Bryll, A.R., Zhu, J., Leith, E.M., Feldman, J.L., Peterson, C.L., Tan, S., Armache, J.P. 10.1126/sciadv.adf7586 37058572 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens 2023 NAD-dependent protein deacylase sirtuin-6 Histone PTM erasers, Histone_deacetylation, Histone_deacetylation_H3K9, DNA repair, Transcription-associated Q8N6T7 P06899, P84233, P04908, P62799 0.493
384 8F86 EM 3.10 2023-04-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 SIRT6 bound to an H3K9Ac nucleosome Wang, Z.A., Markert, J.W., Whedon, S.D., Yapa Abeywardana, M., Lee, K., Jiang, H., Suarez, C., Lin, H., Farnung, L., Cole, P.A. 10.1021/jacs.2c13512 36930461 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Histone PTM erasers, Histone_deacetylation, Histone_deacetylation_H3K9, DNA repair, Transcription-associated Q8N6T7 P02281, P84233, P06897, P62799 0.434
385 8CEO EM 3.60 2023-03-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Schilbach, S., Wang, H., Dienemann, C., Cramer, P. 10.1073/pnas.2220542120 37014863 Xenopus laevis Xenopus laevis Xenopus laevis Saccharomyces cerevisiae 2023 General transcription and DNA repair factor IIH helicase subunit XPD, TFB1 isoform 1, RNA polymerase II transcription factor B subunit 2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, TOA1 isoform 1, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta, Mediator of RNA polymerase II transcription subunit 6, Mediator of RNA polymerase II transcription subunit 8, Mediator of RNA polymerase II transcription subunit 11, Mediator of RNA polymerase II transcription subunit 17, Mediator of RNA polymerase II transcription subunit 18, Mediator of RNA polymerase II transcription subunit 20, Mediator of RNA polymerase II transcription subunit 22, Mediator of RNA polymerase II transcription subunit 4, Mediator of RNA polymerase II transcription subunit 7, Mediator of RNA polymerase II transcription subunit 9, Mediator of RNA polymerase II transcription subunit 10, Mediator of RNA polymerase II transcription subunit 14, Mediator of RNA polymerase II transcription subunit 19, Mediator of RNA polymerase II transcription subunit 21, Mediator of RNA polymerase II transcription subunit 31, Mediator of RNA polymerase II transcription subunit 1 RNA polymerases, DNA repair, Mediator, Transcription factors, Transcription-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145, P38782, P38304, Q99278, P32569, P32585, P34162, P32570, Q12343, Q08278, P33308, Q06213, P19263, P25046, P47822, P38633, Q12321 P02281, P84233, P06897, P62799 0.222
386 7VBM EM 3.40 2022-01-19 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 126 The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv Hirai, S., Tomimatsu, K., Miyawaki-Kuwakado, A., Takizawa, Y., Komatsu, T., Tachibana, T., Fukushima, Y., Takeda, Y., Negishi, L., Kujirai, T., Koyama, M., Ohkawa, Y., Kurumizaka, H. 10.1093/nar/gkab1137 34929737 Mus musculus Mus musculus Mus musculus Mus musculus 2022 C0HKE1, None, Q9D2U9, P62806 0.506
387 5ZBX X-ray 2.58 2019-02-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Arimura, Y., Tachiwana, H., Takagi, H., Hori, T., Kimura, H., Fukagawa, T., Kurumizaka, H. 10.1038/s41467-019-08314-x 30718488 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, P06899, P04908, P68431 -
388 1AOI X-ray 2.80 1998-09-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J. 10.1038/38444 9305837 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 1998 P02281, P02302, P06897, P62799 -
389 6KE9 X-ray 2.22 2020-04-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Soman, A., Liew, C.W., Teo, H.L., Berezhnoy, N.V., Olieric, V., Korolev, N., Rhodes, D., Nordenskiold, L. 10.1093/nar/gkaa289 32374876 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, O60814, P04908, P68431 -
390 3AN2 X-ray 3.60 2011-07-20 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_4_palindorm 121 The structure of the centromeric nucleosome containing CENP-A Tachiwana, H., Kagawa, W., Shiga, T., Osakabe, A., Miya, Y., Saito, K., Hayashi-Takanaka, Y., Oda, T., Sato, M., Park, S.-Y., Kimura, H., Kurumizaka, H. 10.1038/nature10258 21743476 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2011 P62805, P06899, P04908, P49450 -
391 8COM EM 3.30 2023-07-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 Structure of the Nucleosome Core Particle from Trypanosoma brucei Deak, G., Wapenaar, H., Sandoval, G., Chen, R., Taylor, M.R.D., Burdett, H., Watson, J.A., Tuijtel, M.W., Webb, S., Wilson, M.D. 10.1093/nar/gkad577 37427792 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 Trypanosoma brucei brucei TREU927 2023 Q57YA3, Q389T1, Q4GYX7, Q57Z31 0.439
392 6KXV X-ray 3.63 2020-07-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of a nucleosome containing Leishmania histone H3 Dacher, M., Tachiwana, H., Horikoshi, N., Kujirai, T., Taguchi, H., Kimura, H., Kurumizaka, H. 10.1093/nar/gkz1040 31722422 Leishmania major Homo sapiens Homo sapiens Homo sapiens 2020 P62805, P06899, Q4QHB5, P04908 -
393 4X23 X-ray 3.50 2014-12-10 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Kato, H., Jiang, J.S., Zhou, B.R., Rozendaal, M., Feng, H., Ghirlando, R., Xiao, T.S., Straight, A.F., Bai, Y. 10.1126/science.1235532 23723239 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2014 CENP-C Kinetochore, Centromere-associated, Nuclear division Q66LH7 P02299, P02283, P84051, P84040 -
394 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8N884 P62805, O60814, Q16777, Q71DI3 0.43
395 6LE9 X-ray 2.60 2020-04-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Soman, A., Liew, C.W., Teo, H.L., Berezhnoy, N.V., Olieric, V., Korolev, N., Rhodes, D., Nordenskiold, L. 10.1093/nar/gkaa289 32374876 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, O60814, P04908, P68431 -
396 6L9H X-ray 2.60 2020-04-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Soman, A., Liew, C.W., Teo, H.L., Berezhnoy, N.V., Olieric, V., Korolev, N., Rhodes, D., Nordenskiold, L. 10.1093/nar/gkaa289 32374876 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, O60814, P04908, P68431 -
397 8OTT EM 3.30 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 MYC-MAX bound to a nucleosome at SHL+5.8 Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Myc proto-oncogene protein, Protein max Transcription-associated, Transcription factors P01106, P61244 P62805, P06899, P04908, P68431 0.411
398 5AY8 X-ray 2.80 2016-04-06 octamer 1 H3.Y canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal structure of human nucleosome containing H3.Y Kujirai, T., Horikoshi, N., Sato, K., Maehara, K., Machida, S., Osakabe, A., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1093/nar/gkw202 27016736 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P0DPK2, P06899, P04908, P62805 -
399 8HR1 EM 3.02 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom Tong, Z., Ai, H., Xu, Z., He, K., Chu, G.C., Shi, Q., Deng, Z., Xue, Q., Sun, M., Du, Y., Liang, L., Li, J.B., Pan, M., Liu, L. 10.1038/s41594-023-01141-1 38177667 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 SSX1 Q16384 P62805, O60814, P04908, Q71DI3 0.532
400 8HQY EM 3.05 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 136 Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom Tong, Z., Ai, H., Xu, Z., He, K., Chu, G.C., Shi, Q., Deng, Z., Xue, Q., Sun, M., Du, Y., Liang, L., Li, J.B., Pan, M., Liu, L. 10.1038/s41594-023-01141-1 38177667 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Protein SSX2, Polyubiquitin-B (Fragment) Transcription-associated, Ubiquitin, Histone_ubiquitination_H2AK119_reader, Histone PTM readers Q16385, P0CG47 P62805, O60814, P04908, Q71DI3 0.47
401 8GRQ EM 3.87 2023-04-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.chempr.2023.01.012 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK125_writer, DNA repair, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Transcription-associated, Histone PTM writers P38398, Q99728, P61077 P62805, O60814, P04908, Q71DI3 0.352
402 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8N884 O60814, P62805, Q6FI13, Q71DI3 0.195
403 5MLU X-ray 2.80 2017-05-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Crystal structure of the PFV GAG CBS bound to a mononucleosome Lesbats, P., Serrao, E., Maskell, D.P., Pye, V.E., O'Reilly, N., Lindemann, D., Engelman, A.N., Cherepanov, P. 10.1073/pnas.1621159114 28490494 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 PFV GAG peptide Viral, DNA integration P14349 P02281, P84233, P06897, P62799 -
404 7XCT EM 2.72 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, P0CG47 P62805, O60814, P04908, Q71DI3 0.514
405 7XCR EM 2.57 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, P0CG47 P62805, O60814, P04908, Q71DI3 0.571
406 6BUZ EM 3.92 2017-12-20 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N Chittori, S., Hong, J., Saunders, H., Feng, H., Ghirlando, R., Kelly, A.E., Bai, Y., Subramaniam, S. 10.1126/science.aar2781 29269420 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 Maltose-binding periplasmic protein, Centromere protein N chimera P0AEX9 P62805, P06899, P04908, P49450 0.372
407 6C0W EM 4.00 2018-01-17 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 139 Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A Pentakota, S., Zhou, K., Smith, C., Maffini, S., Petrovic, A., Morgan, G.P., Weir, J.R., Vetter, I.R., Musacchio, A., Luger, K. 10.7554/eLife.33442 29280735 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 Centromere protein N Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q96H22 P62805, P62807, P49450, Q93077 0.39
408 6E0C EM 2.63 2019-05-22 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 scFv P62805, P06899, P04908, P49450 0.59
409 6E0P EM 2.60 2019-05-22 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 145 Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 scFv P62805, P06899, P04908, P49450 0.57
410 7U4D EM 8.10 2022-03-30 octamer, octamer 2 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 139 CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and 601 DNA sequence Zhou, K., Gebala, M., Woods, D., Sundararajan, K., Edwards, G., Krzizike, D., Wereszczynski, J., Straight, A.F., Luger, K. 10.1038/s41594-022-00758-y 35422519 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Centromere protein N Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q96H22 P62805, P62807, P49450, Q93077 0.114
411 7U47 EM 7.50 2022-03-16 octamer, octamer 2 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and palindromic alpha satellite DNA sequence Zhou, K., Gebala, M., Woods, D., Sundararajan, K., Edwards, G., Krzizike, D., Wereszczynski, J., Straight, A.F., Luger, K. 10.1038/s41594-022-00758-y 35422519 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Centromere protein N Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q96H22 P62805, P62807, P49450, Q93077 0.179
412 7U46 EM 2.68 2022-03-16 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with CENP-N Zhou, K., Gebala, M., Woods, D., Sundararajan, K., Edwards, G., Krzizike, D., Wereszczynski, J., Straight, A.F., Luger, K. 10.1038/s41594-022-00758-y 35422519 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Centromere protein N Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q96H22 P62805, P62807, P49450, Q93077 0.559
413 7R5R EM 2.44 2022-04-27 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 133 Structure of the human CCAN CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Centromere protein C Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q03188 P62805, P62807, P49450, Q93077 0.571
414 7PII EM 2.68 2022-05-25 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 122 Structure of the human CCAN CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Centromere protein C Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q03188 P62805, P62807, P49450, Q93077 0.573
415 7D20 EM 3.00 2021-02-10 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 136 Cryo-EM structure of SET8-CENP-A-nucleosome complex Ho, C.H., Takizawa, Y., Kobayashi, W., Arimura, Y., Kimura, H., Kurumizaka, H. 10.26508/lsa.202000919 33574035 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 Isoform 2 of N-lysine methyltransferase KMT5A Histone_methylation_H4K20_writer, Heterochromatin-associated, Transcription-associated, Nuclear division, Histone PTM writers Q9NQR1 P62805, P06899, P04908, P49450 0.446
416 6TEM EM 3.90 2020-04-08 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 130 CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM Boopathi, R., Danev, R., Khoshouei, M., Kale, S., Nahata, S., Ramos, L., Angelov, D., Dimitrov, S., Hamiche, A., Petosa, C., Bednar, J. 10.1093/nar/gkaa246 32313946 Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2020 P02281, P62799, P06897, P49450 -
417 6SEG EM 3.10 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class1: CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, Q6FI13, P62807, P49450 0.512
418 6SEF EM 3.70 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2C : CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 Centromere protein C Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q03188 P62805, Q6FI13, P62807, P49450 0.372
419 6SEE EM 4.20 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2A : CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 Centromere protein C Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q03188 P62805, Q6FI13, P62807, P49450 0.309
420 6SE6 EM 3.50 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2 : CENP-A nucleosome in complex with CENP-C central region Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 Centromere protein C Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q03188 P62805, Q6FI13, P62807, P49450 0.416
421 6SE0 EM 3.80 2019-08-14 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class 1 : CENP-A nucleosome Ali-Ahmad, A., Bilokapic, S., Schafer, I.B., Halic, M., Sekulic, N. 10.15252/embr.201948913 31475439 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, Q6FI13, P62807, P49450 0.328
422 6O1D EM 3.40 2019-05-22 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 145 Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA Zhou, B.R., Yadav, K.N.S., Borgnia, M., Hong, J., Cao, B., Olins, A.L., Olins, D.E., Bai, Y., Zhang, P. 10.1038/s41467-019-10247-4 31127102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, P06899, P04908, P49450 0.482
423 6MUP EM 3.50 2019-07-24 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 147 CENP-A nucleosome bound by two copies of CENP-C(CD) and two copies CENP-N(NT) Allu, P.K., Dawicki-McKenna, J.M., Van Eeuwen, T., Slavin, M., Braitbard, M., Xu, C., Kalisman, N., Murakami, K., Black, B.E. 10.1016/j.cub.2019.06.062 31353180 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 Centromere protein C, Centromere protein N Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q03188, Q96H22 Q5QNW6, P62805, P49450, Q93077 0.401
424 6MUO EM 3.60 2019-07-24 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 147 CENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT) Allu, P.K., Dawicki-McKenna, J.M., Van Eeuwen, T., Slavin, M., Braitbard, M., Xu, C., Kalisman, N., Murakami, K., Black, B.E. 10.1016/j.cub.2019.06.062 31353180 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 Centromere protein C, Centromere protein N Kinetochore, Centromere-associated, Nuclear division, CENP-A NAC/CAD Q03188, Q96H22 Q5QNW6, P62805, P49450, Q93077 0.369
425 7K6Q EM 3.10 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1 bound to the H4K16ac nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Truong, D.M., Lee, R., Armache, J.P., Boeke, J.D., Armache, K.J. 10.1126/science.abc6663 33479126 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Telomere-associated, Histone PTM writers, Ubiquitin Q04089, P0CG48 P02281, P84233, P06897, P62799 0.489
426 7K6P EM 3.20 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Active state Dot1 bound to the unacetylated H4 nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Truong, D.M., Lee, R., Armache, J.P., Boeke, J.D., Armache, K.J. 10.1126/science.abc6663 33479126 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Histone_methylation_H3K79_writer, Telomere-associated, Histone PTM writers, Ubiquitin Q04089, P0CG48 P02281, P84233, P06897, P62799 0.473
427 3KWQ X-ray 3.50 2010-05-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Watanabe, S., Resch, M., Lilyestrom, W., Clark, N., Hansen, J.C., Peterson, C., Luger, K. 10.1016/j.bbagrm.2010.01.009 20100606 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P06897, P62799 -
428 8IEG EM 3.44 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.molcel.2023.08.001 37633270 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 E3 ubiquitin-protein ligase BRE1, Ubiquitin-conjugating enzyme E2 2 E3 ubiquitin-protein ligation, DNA repair, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457, P06104 P62805, O60814, P04908, P68431 0.393
429 7XD1 EM 3.20 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 cryo-EM structure of unmodified nucleosome Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, P68431 0.558
430 7XD0 EM 3.48 2022-04-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 cryo-EM structure of H2BK34ub nucleosome Ai, H., Sun, M., Liu, A., Sun, Z., Liu, T., Cao, L., Liang, L., Qu, Q., Li, Z., Deng, Z., Tong, Z., Chu, G., Tian, X., Deng, H., Zhao, S., Li, J.B., Lou, Z., Liu, L. 10.1038/s41589-022-01067-7 35739357 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Ubiquitin-60S ribosomal protein L40 Ubiquitin P62987 P62805, Q2M2T1, P04908, Q71DI3 0.457
431 7KTQ EM 3.30 2021-02-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Nucleosome from a dimeric PRC2 bound to a nucleosome Grau, D., Zhang, Y., Lee, C.H., Valencia-Sanchez, M., Zhang, J., Wang, M., Holder, M., Svetlov, V., Tan, D., Nudler, E., Reinberg, D., Walz, T., Armache, K.J. 10.1038/s41467-020-20775-z 33514705 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P02281, P84233, P62799, Q6AZJ8 0.494
432 6R1T EM 4.02 2019-04-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 1, free nuclesome Marabelli, C., Marrocco, B., Pilotto, S., Chittori, S., Picaud, S., Marchese, S., Ciossani, G., Forneris, F., Filippakopoulos, P., Schoehn, G., Rhodes, D., Subramaniam, S., Mattevi, A. 10.1016/j.celrep.2019.03.061 30970244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 P02281, P84233, P06897, P62799 0.339
433 6FQ8 EM 4.80 2018-04-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Class 3 : translocated nucleosome Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41467-018-03677-z 29626188 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2018 P02281, P02302, P06897, P62799 0.196
434 6FQ6 EM 4.00 2018-04-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Class 2 : distorted nucleosome Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41467-018-03677-z 29626188 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2018 P02281, P84233, P06897, P62799 0.235
435 6FQ5 EM 3.80 2018-04-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Class 1 : canonical nucleosome Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41467-018-03677-z 29626188 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2018 P02281, P84233, P06897, P62799 0.301
436 7EA5 EM 3.30 2021-07-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Yeast Set2 bound to a nucleosome containing oncohistone mutations Liu, Y., Zhang, Y., Xue, H., Cao, M., Bai, G., Mu, Z., Yao, Y., Sun, S., Fang, D., Huang, J. 10.1038/s41421-021-00261-6 33972509 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-36 specific Transcription-associated, Histone_methylation_H3K36_writer, Histone PTM writers P46995 P02281, P84233, P62799, Q6AZJ8 0.473
437 7EA8 EM 3.10 2021-07-14 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 122 Human SETD2 bound to a nucleosome containing oncohistone mutations Liu, Y., Zhang, Y., Xue, H., Cao, M., Bai, G., Mu, Z., Yao, Y., Sun, S., Fang, D., Huang, J. 10.1038/s41421-021-00261-6 33972509 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 Histone-lysine N-methyltransferase SETD2 Transcription-associated, Heterochromatin-associated, Histone PTM writers, Histone_methylation_H3K36_writer Q9BYW2 Q6PI79, P06899, P62799, P20671 0.509
438 7Y7I EM 3.42 2022-07-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 chicken KNL2 in complex with the CENP-A nucleosome Jiang, H., Ariyoshi, M., Watanabe, R., Makino, F., Namba, K., Fukagawa, T. 10.1101/2022.06.24.497480 0 Gallus gallus Homo sapiens Homo sapiens Homo sapiens 2022 Myb-like domain-containing protein F1NE16 P62805, P06899, P04908, P68431 0.454
439 7BY0 EM 4.50 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C Ariyoshi, M., Makino, F., Watanabe, R., Nakagawa, R., Kato, T., Namba, K., Arimura, Y., Fujita, R., Kurumizaka, H., Okumura, E.I., Hara, M., Fukagawa, T. 10.15252/embj.2020105671 33463726 Gallus gallus Homo sapiens Homo sapiens Homo sapiens 2021 Maltose Binding Protein tag, linker,CENP-C P0AEX9 P84229, P62805, P06899, P04908 0.297
440 7BXT EM 4.20 2021-02-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain Ariyoshi, M., Makino, F., Watanabe, R., Nakagawa, R., Kato, T., Namba, K., Arimura, Y., Fujita, R., Kurumizaka, H., Okumura, E.I., Hara, M., Fukagawa, T. 10.15252/embj.2020105671 33463726 Gallus gallus Homo sapiens Homo sapiens Homo sapiens 2021 CENP-C, Maltodextrin-binding protein,Centromere protein N Kinetochore, Centromere-associated, Nuclear division O57392, P0AEX9 P84229, P62805, Q16778, P04908 0.387
441 8JLA EM 3.44 2023-10-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 156 Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Oishi, T., Hatazawa, S., Kujirai, T., Kato, J., Kobayashi, Y., Ogasawara, M., Akatsu, M., Ehara, H., Sekine, S.I., Hayashi, G., Takizawa, Y., Kurumizaka, H. 10.1093/nar/gkad754 37718728 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P62805, P06899, P04908, P68431 0.453
442 3W98 X-ray 3.42 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2013 P62805, P06899, P04908, P68431 -
443 5Z23 X-ray 2.73 2019-02-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Arimura, Y., Tachiwana, H., Takagi, H., Hori, T., Kimura, H., Fukagawa, T., Kurumizaka, H. 10.1038/s41467-019-08314-x 30718488 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, P06899, P04908, P68431 -
444 8GRM EM 3.05 2023-04-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.chempr.2023.01.012 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 COMMD3 protein, Ring1B, Ubiquitin, UbcH5b E3 ubiquitin-protein ligation, Ubiquitin, Polycomb, Histone_ubiquitination_H2AK119_writer, Transcription-associated, Histone PTM writers P35226, Q99496, P0CG47, P62837 P62805, O60814, P04908, P68431 0.516
445 8IEJ EM 3.12 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 RNF20-RNF40/hRad6A-Ub/nucleosome complex Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.molcel.2023.08.001 37633270 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 E3 ubiquitin-protein ligase BRE1B, E3 ubiquitin-protein ligase BRE1A, Ubiquitin-conjugating enzyme E2 A E3 ubiquitin-protein ligation, DNA repair, Histone_ubiquitination_H2BK120_writer, Transcription-associated, Histone PTM writers O75150, Q5VTR2, P49459 P62805, O60814, P04908, P68431 0.461
446 7XYF EM 4.30 2023-12-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome Nan, Z., Tao, J., Yangao, H. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2023 ATP-dependent helicase fft3 Heterochromatin-associated, Chromatin remodeling O42861 P02299, P02283, P84051, P84040 0.272
447 8WG5 EM 3.05 2023-12-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Ai, H.S., He, Z.Z., Deng, Z.H., Liu, L. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Ubiquitin carboxyl-terminal hydrolase 16, Ubiquitin B Transcription-associated, Histone_deubiquitination_H2AK119, Ubiquitin Q9Y5T5, P0CG47 P62805, O60814, P04908, P68431 0.306
448 6Z6P EM 4.43 2021-02-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 HDAC-PC-Nuc Lee, J.H., Bollschweiler, D., Schafer, T., Huber, R. 10.1126/sciadv.abd4413 33523989 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Histone deacetylase HDA1, HDA1 complex subunit 3,HDA1 complex subunit 3, HDA1 complex subunit 2 Transcription-associated, Histone PTM erasers, Histone_deacetylation, HDA1 P53973, Q06623, Q06629 P02281, P06897, Q6AZJ8, P62799, P84233 0.189
449 6JMA EM 6.80 2019-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 114 cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Jang, S., Kang, C., Yang, H.S., Jung, T., Hebert, H., Chung, K.Y., Kim, S.J., Hohng, S., Song, J.J. 10.1101/gad.323790.118 30923167 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, P0CG47 P02281, P84233, P62799, Q6AZJ8 0.144
450 6JM9 EM 7.30 2019-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 123 cryo-EM structure of DOT1L bound to unmodified nucleosome Jang, S., Kang, C., Yang, H.S., Jung, T., Hebert, H., Chung, K.Y., Kim, S.J., Hohng, S., Song, J.J. 10.1101/gad.323790.118 30923167 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3 P02281, P84233, P62799, Q6AZJ8 0.132
451 6IY3 EM 3.67 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B MMTV 147 Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.399
452 6IY2 EM 3.47 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B MMTV 147 Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.427
453 6FTX EM 4.50 2018-08-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 159 Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome Sundaramoorthy, R., Hughes, A.L., El-Mkami, H., Norman, D.G., Ferreira, H., Owen-Hughes, T. 10.7554/eLife.35720 30079888 Petromyzon marinus,Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis 2018 Polyubiquitin-B, Chromatin-remodeling ATPase Transcription-associated, Ubiquitin, CHD, Chromatin remodelers P0CG47, P32657 Q28D68, P06897, S4RAZ3, P62799, P02302 0.23
454 8OL1 EM 3.50 2024-02-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Xu, P., Liu, Y., Liu, C., Guey, B., Li, L., Melenec, P., Ricci, J., Ablasser, A. 10.1038/s41586-024-07112-w 38418882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Cyclic GMP-AMP synthase, SPRY domain-containing SOCS box protein 3, Elongin-C, Elongin-B Antiviral defense, Synthesis of second messengers, E3 ubiquitin-protein ligation, DNA repair, Transcription factors, Transcription-associated, 2'3'-cGAMP Q8N884, Q6PJ21, Q15369, Q15370 Q71DI3, Q99878, Q99877, Q96KK5, P62805, Q93079 0.4
455 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8N884 P62805, P06899, P04908, P68431 0.152
456 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 2020 Cyclic GMP-AMP synthase DNA repair, Antiviral defense, 2'3'-cGAMP, Synthesis of second messengers Q8N884 P62805, P06899, P04908, P68431 0.371
457 6JXD X-ray 2.25 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 147 Human nucleosome core particle with cohesive end DNA termini Sharma, D., De Falco, L., Padavattan, S., Rao, C., Geifman-Shochat, S., Liu, C.F., Davey, C.A. 10.1038/s41467-019-13641-0 31848352 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, P06899, P04908, P68431 -
458 6IQ4 X-ray 2.25 2019-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Batchelor, L.K., De Falco, L., von Erlach, T., Sharma, D., Adhireksan, Z., Roethlisberger, U., Davey, C.A., Dyson, P.J. 10.1002/anie.201906423 31478581 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2019 P62805, P06899, P04908, P68431 -
459 6IPU X-ray 1.99 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Human nucleosome core particle containing 145 bp of DNA Sharma, D., De Falco, L., Padavattan, S., Rao, C., Geifman-Shochat, S., Liu, C.F., Davey, C.A. 10.1038/s41467-019-13641-0 31848352 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, P06899, P04908, P68431 -
460 4Z66 X-ray 2.50 2015-10-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Chatterjee, N., North, J.A., Dechassa, M.L., Manohar, M., Prasad, R., Luger, K., Ottesen, J.J., Poirier, M.G., Bartholomew, B. 10.1128/MCB.00441-15 26416878 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
461 4YS3 X-ray 3.00 2015-10-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Chatterjee, N., North, J.A., Dechassa, M.L., Manohar, M., Prasad, R., Luger, K., Ottesen, J.J., Poirier, M.G., Bartholomew, B. 10.1128/MCB.00441-15 26416878 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
462 4XZQ X-ray 2.40 2015-10-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Chatterjee, N., North, J.A., Dechassa, M.L., Manohar, M., Prasad, R., Luger, K., Ottesen, J.J., Poirier, M.G., Bartholomew, B. 10.1128/MCB.00441-15 26416878 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
463 7PF4 EM 4.00 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 167 Nucleosome 3 of the 4x187 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, Q71DI3 0.274
464 5F99 X-ray 2.63 2016-02-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B MMTV 147 X-ray Structure of the MMTV-A Nucleosome Core Particle Frouws, T.D., Duda, S.C., Richmond, T.J. 10.1073/pnas.1524607113 26787910 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
465 7PEW EM 4.60 2022-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 176 Nucleosome 1 of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, Q71DI3 0.29
466 6R25 EM 4.61 2019-04-24 octamer 1 H3.3,canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3 Marabelli, C., Marrocco, B., Pilotto, S., Chittori, S., Picaud, S., Marchese, S., Ciossani, G., Forneris, F., Filippakopoulos, P., Schoehn, G., Rhodes, D., Subramaniam, S., Mattevi, A. 10.1016/j.celrep.2019.03.061 30970244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Lysine-specific histone demethylase 1B, NPAC Histone PTM erasers, Histone_demethylation_H3K4, Histone PTM readers, Transcription-associated, Histone_methylation_H3K36_reader Q8NB78, Q49A26 P02281, P84233, P06897, P62799 0.186
467 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 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
468 6WZ9 EM 2.80 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 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 2020 P02281, P84233, P06897, P62799 0.508
469 6WZ5 EM 2.20 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 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 2020 P02281, P84233, P06897, P62799 0.504
470 6VZ4 EM 3.90 2020-12-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state Baker, R.W., Reimer, J.M., Carman, P.J., Turegun, B., Arakawa, T., Dominguez, R., Leschziner, A.E. 10.1038/s41594-020-00528-8 33288924 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers P32597, Q12406, Q05123, P53330 P02281, Q92133, P06897, P62799 -
471 6UXW EM 8.96 2020-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 SWI/SNF nucleosome complex with ADP-BeFx Han, Y., Reyes, A.A., Malik, S., He, Y. 10.1038/s41586-020-2087-1 32188938 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Transcription regulatory protein SNF2, SWI/SNF chromatin-remodeling complex subunit SWI1, SWI/SNF chromatin-remodeling complex subunit SNF5, SWI/SNF complex subunit SWI3, Transcription regulatory protein SNF12, Transcription regulatory protein SNF6, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers, SWI/SNF P22082, P09547, P18480, P32591, P53628, P18888, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.122
472 6TDA EM 15.00 2020-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Wagner, F.R., Dienemann, C., Wang, H., Stutzer, A., Tegunov, D., Urlaub, H., Cramer, P. 10.1038/s41586-020-2088-0 32188943 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromatin structure-remodeling complex subunit SFH1, Chromatin structure-remodeling complex protein RSC8, Chromatin structure-remodeling complex subunit RSC7, Chromatin structure-remodeling complex subunit RSC9, Chromatin structure-remodeling complex protein RSC6, Chromatin structure-remodeling complex protein RSC58, High temperature lethal protein 1, Chromatin structure-remodeling complex subunit RSC4, Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers Q06168, P43609, P32832, Q03124, P25632, Q07979, Q9URQ5, Q02206, P32597, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.081
473 6T9L EM 3.60 2020-01-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 SAGA DUB module bound to a ubiqitinated nucleosome Wang, H., Dienemann, C., Stutzer, A., Urlaub, H., Cheung, A.C.M., Cramer, P. 10.1038/s41586-020-1933-5 31969703 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Ubiquitin carboxyl-terminal hydrolase 8, Transcription and mRNA export factor SUS1, SAGA-associated factor 11, SAGA-associated factor 73, Polyubiquitin-C Histone PTM erasers, Ubiquitin, SAGA, Transcription-associated, Histone_deubiquitination P50102, Q6WNK7, Q03067, P53165, P0CG48 P02281, P84233, P06897, P62799 0.394
474 6R1U EM 4.36 2019-04-24 octamer 1 H3.3,canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Marabelli, C., Marrocco, B., Pilotto, S., Chittori, S., Picaud, S., Marchese, S., Ciossani, G., Forneris, F., Filippakopoulos, P., Schoehn, G., Rhodes, D., Subramaniam, S., Mattevi, A. 10.1016/j.celrep.2019.03.061 30970244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Lysine-specific histone demethylase 1B, Putative oxidoreductase GLYR1 Histone PTM erasers, Histone_demethylation_H3K4, Histone PTM readers, Transcription-associated, Histone_methylation_H3K36_reader Q8NB78, Q49A26 P02281, P84233, P06897, P62799 0.198
475 8CWW EM 2.74 2023-06-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of S. cerevisiae Hop1 CBR bound to a nucleosome Milano, C.R., Ur, S.N., Gu, Y., Zhang, J., Allison, R., Brown, G., Neale, M.J., Tromer, E.C., Corbett, K.D., Hochwagen, A. 10.1038/s44318-024-00034-3 38332377 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Meiosis-specific protein HOP1 Nuclear division P20050 P02281, P84233, P06897, P62799 0.574
476 6PX3 EM 4.10 2019-08-28 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Set2 bound to nucleosome Bilokapic, S., Halic, M. 10.1038/s41467-019-11726-4 31439846 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Xenopus laevis 2019 Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone-lysine N-methyltransferase Transcription-associated, Ubiquitin, Histone_methylation_H3K36_writer, Histone PTM writers P0CH09, G0S676 P02281, P02302, P62799, P0CH09 0.261
477 6PX1 EM 3.30 2019-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Set2 bound to nucleosome Bilokapic, S., Halic, M. 10.1038/s41467-019-11726-4 31439846 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Xenopus laevis 2019 P02281, P02302, P62799, P0CH09 0.49
478 6PA7 EM 2.94 2020-06-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 166 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Xu, T.H., Liu, M., Zhou, X.E., Liang, G., Zhao, G., Xu, H.E., Melcher, K., Jones, P.A. 10.1038/s41586-020-2747-1 32968275 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 DNA (cytosine-5)-methyltransferase 3A, DNA (cytosine-5)-methyltransferase 3B Transcription-associated, DNA modification Q9Y6K1, Q9UBC3 P02281, P84233, P06897, P62799 0.403
479 6OM3 X-ray 3.30 2019-07-10 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle De Ioannes, P., Leon, V.A., Kuang, Z., Wang, M., Boeke, J.D., Hochwagen, A., Armache, K.J. 10.1038/s41467-019-10609-y 31263106 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Origin recognition complex subunit 1 Transcription-associated, ORC, DNA replication P54784 P02281, P84233, P06897, P62799 -
480 6O96 EM 3.50 2019-04-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Vasilyev, N., Chen, R., Nudler, E., Armache, J.-P., Armache, K.J. 10.1016/j.molcel.2019.03.029 30981630 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Polyubiquitin-B Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, P0CG47 P02281, P84233, P06897, P62799 0.38
481 6NZO EM 3.80 2019-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Set2 bound to nucleosome Bilokapic, S., Halic, M. 10.1038/s41467-019-11726-4 31439846 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Xenopus laevis 2019 Histone-lysine N-methyltransferase Transcription-associated, Histone_methylation_H3K36_writer, Histone PTM writers G0S676 P02281, P02302, P62799, P0CH09 0.364
482 6NOG EM 3.90 2019-02-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C. 10.1016/j.cell.2019.02.002 30765112 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, J3QS39 P02281, P84233, P06897, P62799 0.356
483 7AT8 EM 4.40 2020-12-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Finogenova, K., Bonnet, J., Poepsel, S., Schafer, I.B., Finkl, K., Schmid, K., Litz, C., Strauss, M., Benda, C., Muller, J. 10.7554/eLife.61964 33211010 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2, Polycomb protein SUZ12 Histone_methylation_H3K27_writer, Histone_methylation_H3K9_writer, Polycomb, Transcription-associated, Histone PTM writers Q15910, Q15022 P02281, P84233, P06897, P62799 0.29
484 7BWD EM 4.32 2021-04-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Dot1L-H2BK34ub Nucleosome Complex Liu, L., Lou, Z.Y., Ai, H.S., Cao, L. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, P62979 P62805, O60814, P04908, P68431 0.332
485 7E8I EM 3.10 2021-06-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Dai, L., Dai, Y., Han, J., Huang, Y., Wang, L., Huang, J., Zhou, Z. 10.1016/j.molcel.2021.05.010 34102105 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 BRCA1-associated RING domain protein 1, Polyubiquitin-B E3 ubiquitin-protein ligation, Histone_ubiquitination_H2AK125_writer, DNA repair, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK129_writer, Ubiquitin, Transcription-associated, Histone PTM writers Q99728, P0CG47 P02281, P84233, P06897, P62799 0.456
486 7EG6 EM 3.10 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Snf5 Finger Helix bound to the nucleosome He, Z.Y., Chen, K.J., Ye, Y.P., Chen, Z.C. 10.1038/s41421-021-00262-5 33907182 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 SWI/SNF chromatin-remodeling complex subunit SNF5 Transcription-associated, Chromatin remodelers, SWI/SNF P18480 P02281, P84233, P06897, P62799 0.513
487 8ATF EM 3.45 2022-12-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Nucleosome-bound Ino80 ATPase Kunert, F., Metzner, F.J., Jung, J., Hopfler, M., Woike, S., Schall, K., Kostrewa, D., Moldt, M., Chen, J.X., Bantele, S., Pfander, B., Eustermann, S., Hopfner, K.P. 10.1126/sciadv.add3189 36490333 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Ino80 ATPase, PAPA-1 domain-containing protein Chromatin remodelers, INO80 G0RY01 P62805, P0C0S8, P62807, Q71DI3 0.474
488 7YI1 EM 2.80 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 DNA repair, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 Q12432 P02281, P84233, P06897, P62799 0.572
489 7Y8R EM 4.40 2022-12-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 165 The nucleosome-bound human PBAF complex Wang, L., Yu, J., Yu, Z., Wang, Q., Li, W., Ren, Y., Chen, Z., He, S., Xu, Y. 10.1038/s41467-022-34859-5 36496390 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Transcription activator BRG1, ACTB protein (Fragment), Actin-like protein 6A, AT-rich interactive domain-containing protein 2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, PHD finger protein 10, Bromodomain-containing protein 7, Protein polybromo-1 Transcription-associated, PBAF (SWI/SNF), Chromatin remodelers, SWI/SNF P51532, P60709, O96019, Q68CP9, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q8WUB8, Q9NPI1, Q86U86 P62805, P62807, P68431, Q93077 0.172
490 7XYG EM 5.40 2023-12-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome Nan, Z., Tao, J., Yangao, H. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2023 ATP-dependent helicase fft3 Heterochromatin-associated, Chromatin remodeling O42861 P02299, P02283, P84051, P84040 0.219
491 7XPX EM 3.20 2022-06-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 145 Cryo-EM structure of the histone methyltransferase SET8 bound to H4K20Ecx-nucleosome Shi, L., Huang, L., Long, H., Song, A., Zhou, Z. 10.1096/fj.202101821R 35532550 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 N-lysine methyltransferase KMT5A Histone_methylation_H4K20_writer, Heterochromatin-associated, Transcription-associated, Nuclear division, Histone PTM writers Q9NQR1 P02281, P84233, P06897, P62799 0.475
492 7PEV EM 6.00 2022-08-03 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 347 Nucleosome stack of the 4x177 nucleosome array containing H1 Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S., Cramer, P. 10.1038/s41594-022-00768-w 35581345 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 P62805, O60814, P04908, Q71DI3 0.224
493 7TAN EM 3.00 2022-05-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of VRK1 C-terminal tail bound to nucleosome core particle Budziszewski, G.R., Zhao, Y., Spangler, C.J., Kedziora, K.M., Williams, M.R., Azzam, D.N., Skrajna, A., Koyama, Y., Cesmat, A.P., Simmons, H.C., Arteaga, E.C., Strauss, J.D., Kireev, D., McGinty, R.K. 10.1093/nar/gkac198 35390161 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Serine/threonine-protein kinase VRK1 Histone_phosphorylation_H3T3_writer, Nuclear division, Histone PTM writers Q99986 P62805, P0C0S8, P62807, Q71DI3 0.56
494 7OHC EM 2.50 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 P02281, P84233, P06897, P62799 0.587
495 7OHB EM 3.40 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 TBP-nucleosome complex Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein Transcription-associated, Transcription factors P13393 P02281, P84233, P06897, P62799 0.435
496 7OHA EM 2.90 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 122 nucleosome with TBP and TFIIA bound at SHL +2 Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription-associated, Transcription factors P13393, P32773, P32774 P02281, P84233, P06897, P62799 0.516
497 7OH9 EM 3.00 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome with TBP and TFIIA bound at SHL -6 Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription-associated, Transcription factors P13393, P32773, P32774 P02281, P84233, P06897, P62799 0.49
498 7MBN EM NaN 2021-12-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Ayoub, A., Park, S.H., Lee, Y.T., Cho, U.S., Dou, Y. 10.1021/acs.biochem.1c00603 34928138 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.217
499 7MBM EM NaN 2021-12-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Ayoub, A., Park, S.H., Lee, Y.T., Cho, U.S., Dou, Y. 10.1021/acs.biochem.1c00603 34928138 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, Histone_methylation_H3K4_writer, COMPASS, Histone PTM writers Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.198
500 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 2021 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.567
501 7EGP EM 6.90 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 166 The structure of SWI/SNF-nucleosome complex He, Z.Y., Chen, K.J., Ye, Y.P., Chen, Z.C. 10.1038/s41421-021-00262-5 33907182 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 Transcription regulatory protein SNF2, SWI/SNF chromatin-remodeling complex subunit SWI1, SWI/SNF chromatin-remodeling complex subunit SNF5, SWI/SNF complex subunit SWI3, Transcription regulatory protein SNF12, Transcription regulatory protein SNF6, SWI/SNF global transcription activator complex subunit SWP82, Regulator of Ty1 transposition protein 102, Actin-related protein 7, Actin-like protein ARP9 Transcription-associated, RSC (SWI/SNF), Chromatin remodelers, SWI/SNF P22082, P09547, P18480, P32591, P53628, P18888, P43554, P53330, Q12406, Q05123 P02281, P84233, P62799, Q6AZJ8 0.105
502 6NN6 EM 3.90 2019-02-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of Dot1L-H2BK120ub nucleosome complex Anderson, C.J., Baird, M.R., Hsu, A., Barbour, E.H., Koyama, Y., Borgnia, M.J., McGinty, R.K. 10.1016/j.celrep.2019.01.058 30759380 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone_ubiquitination_H2BK120_reader, Histone_methylation_H3K79_writer, Histone PTM writers Q8TEK3, F5H388 P02281, P84233, P06897, P62799 0.371
503 6KIZ EM 4.50 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-NCP complex, binding mode2 Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers Q03164, Q15291, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.31
504 6KIX EM 4.10 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-NCP complex, binding mode1 Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Transcription-associated, COMPASS, Histone_methylation_H3K4_writer, Histone PTM writers Q03164, Q15291, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.338
505 5X0Y EM 4.69 2017-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome Liu, X., Li, M., Xia, X., Li, X., Chen, Z. 10.1038/nature22036 28424519 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.315
506 5OXV X-ray 6.72 2017-10-11 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 311 Structure of the 4_601_157 tetranucleosome (C2 form) Ekundayo, B., Richmond, T.J., Schalch, T. 10.1016/j.jmb.2017.09.002 28893533 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
507 5HQ2 X-ray 4.50 2016-03-23 split_octasome 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 73 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Girish, T.S., McGinty, R.K., Tan, S. 10.1016/j.jmb.2016.02.025 26953260 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 Guanine nucleotide exchange factor SRM1, N-lysine methyltransferase SETD8 Histone_methylation_H4K20_writer, Heterochromatin-associated, Transcription-associated, Nuclear division, Histone PTM writers P21827, Q9NQR1 P02281, P84233, P06897, P62799 -
508 5GT3 X-ray 2.91 2017-02-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 146 Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b Padavattan, S., Thiruselvam, V., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bpc.2016.11.013 27992841 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 Q96A08, P62805, P68431, P20671 -
509 5DNN X-ray 2.80 2016-09-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes Adhireksan, Z., Palermo, G., Riedel, T., Ma, Z., Muhammad, R., Rothlisberger, U., Dyson, P.J., Davey, C.A. 10.1038/ncomms14860 28358030 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
510 5DNM X-ray 2.81 2016-09-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex Adhireksan, Z., Palermo, G., Riedel, T., Ma, Z., Muhammad, R., Rothlisberger, U., Dyson, P.J., Davey, C.A. 10.1038/ncomms14860 28358030 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
511 5CP6 X-ray 2.60 2016-06-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] Ma, Z., Palermo, G., Adhireksan, Z., Murray, B.S., von Erlach, T., Dyson, P.J., Rothlisberger, U., Davey, C.A. 10.1002/anie.201602145 27184539 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
512 4XUJ X-ray 3.18 2016-01-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound Hanif, M., Meier, S.M., Adhireksan, Z., Henke, H., Martic, S., Labib, M., Kandioller, W., Jakupec, M.A., Kraatz, H.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
513 4WU9 X-ray 2.60 2015-09-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of cisPtNAP-NCP145 Chua, E.Y., Davey, G.E., Chin, C.F., Droge, P., Ang, W.H., Davey, C.A. 10.1093/nar/gkv356 25916851 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
514 4WU8 X-ray 2.45 2015-09-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of trPtNAP-NCP145 Chua, E.Y., Davey, G.E., Chin, C.F., Droge, P., Ang, W.H., Davey, C.A. 10.1093/nar/gkv356 25916851 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
515 4R8P X-ray 3.28 2014-11-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle McGinty, R.K., Henrici, R.C., Tan, S. 10.1038/nature13890 25355358 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2014 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 E3 ubiquitin-protein ligation, Polycomb, Histone_ubiquitination_H2AK119_writer, Transcription-associated, Histone PTM writers P35226, Q99496 P02281, P84233, P06897, P62799 -
516 4J8X X-ray 2.87 2013-05-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P02281, P84233, P06897, P62799 -
517 4J8W X-ray 2.41 2013-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P02281, P84233, P06897, P62799 -
518 4J8V X-ray 2.58 2013-05-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P02281, P84233, P06897, P62799 -
519 4J8U X-ray 2.38 2013-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P02281, P84233, P06897, P62799 -
520 3X1V X-ray 2.92 2015-09-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 146 Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bbrc.2015.07.070 26188507 Homo sapiens Homo sapiens Homo sapiens Mus musculus 2015 P62805, P70696, P04908, P68431 -
521 5OY7 X-ray 5.77 2017-09-20 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 619 Structure of the 4_601_157 tetranucleosome (P1 form) Ekundayo, B., Richmond, T.J., Schalch, T. 10.1016/j.jmb.2017.09.002 28893533 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
522 5XF6 X-ray 2.63 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
523 6KIW EM 4.00 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2C, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q8NEZ4, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.33
524 5XM1 X-ray 3.45 2018-03-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4 Harada, A., Maehara, K., Ono, Y., Taguchi, H., Yoshioka, K., Kitajima, Y., Xie, Y., Sato, Y., Iwasaki, T., Nogami, J., Okada, S., Komatsu, T., Semba, Y., Takemoto, T., Kimura, H., Kurumizaka, H., Ohkawa, Y. 10.1038/s41467-018-03845-1 29643389 Mus musculus Mus musculus Mus musculus Mus musculus 2018 Q9D2U9, P84244, C0HKE1, P62806 -
525 6KIV EM 4.00 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q03164, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.343
526 6KIU EM 3.20 2019-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Xue, H., Yao, T., Cao, M., Zhu, G., Li, Y., Yuan, G., Chen, Y., Lei, M., Huang, J. 10.1038/s41586-019-1528-1 31485071 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, Ubiquitin, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Transcription-associated, Histone PTM writers Q03164, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.461
527 6K1P EM 3.87 2019-05-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The complex of ISWI-nucleosome in the ADP.BeF-bound state Yan, L., Wu, H., Li, X., Gao, N., Chen, Z. 10.1038/s41594-019-0199-9 30872815 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.42
528 6JYL EM 3.37 2019-05-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state Yan, L., Wu, H., Li, X., Gao, N., Chen, Z. 10.1038/s41594-019-0199-9 30872815 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.452
529 6IRO EM 3.40 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 the crosslinked complex of ISWI-nucleosome in the ADP-bound state Yan, L., Wu, H., Li, X., Gao, N., Chen, Z. 10.1038/s41594-019-0199-9 30872815 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 Transcription-associated, Chromatin remodelers, ISWI P38144 P02281, P84233, P06897, P62799 0.435
530 6G0L EM 10.00 2018-08-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 176 Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome Sundaramoorthy, R., Hughes, A.L., El-Mkami, H., Norman, D.G., Ferreira, H., Owen-Hughes, T. 10.7554/eLife.35720 30079888 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2018 Chromo domain-containing protein 1 Transcription-associated, CHD, Chromatin remodelers P32657 Q92133, P06897, P62799, A0A1L8G0X3 0.095
531 6FML EM 4.34 2018-04-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 CryoEM Structure INO80core Nucleosome complex Eustermann, S., Schall, K., Kostrewa, D., Lakomek, K., Strauss, M., Moldt, M., Hopfner, K.P. 10.1038/s41586-018-0029-y 29643509 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2018 RuvB-like helicase, Ino80, les2, Ies6, Actin related protein 5 Kinetochore, Nuclear division, Chromatin remodelers, INO80 G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62805, P0C0S8, P62807, Q71DI3 0.33
532 6ESI EM 6.30 2017-12-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Nucleosome breathing : Class 4 Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41594-017-0005-5 29323273 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P62799, Q6AZJ8 0.167
533 6ESH EM 5.10 2017-12-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 137 Nucleosome breathing : Class 3 Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41594-017-0005-5 29323273 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P62799, Q6AZJ8 0.209
534 6ESG EM 5.40 2017-12-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 141 Nucleosome breathing : Class 2 Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41594-017-0005-5 29323273 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P62799, Q6AZJ8 0.198
535 6ESF EM 3.70 2017-12-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nucleosome : Class 1 Bilokapic, S., Strauss, M., Halic, M. 10.1038/s41594-017-0005-5 29323273 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P84233, P62799, Q6AZJ8 0.378
536 5Z3V EM 4.22 2019-05-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P62799, Q6AZJ8 0.356
537 5Z3U EM 4.31 2019-05-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P62799, Q6AZJ8 0.372
538 5Z3O EM 3.62 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex in ADP state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.349
539 5Z3L EM 4.31 2019-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Snf2-nucleosome complex in apo state Li, M., Xia, X., Tian, Y., Jia, Q., Liu, X., Lu, Y., Li, M., Li, X., Chen, Z. 10.1038/s41586-019-1029-2 30867599 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Transcription regulatory protein SNF2 Transcription-associated, Chromatin remodelers, SWI/SNF P22082 P02281, P84233, P06897, P62799 0.261
540 8AV6 EM 4.68 2022-12-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 CryoEM structure of INO80 core nucleosome complex in closed grappler conformation Kunert, F., Metzner, F.J., Jung, J., Hopfler, M., Woike, S., Schall, K., Kostrewa, D., Moldt, M., Chen, J.X., Bantele, S., Pfander, B., Eustermann, S., Hopfner, K.P. 10.1126/sciadv.add3189 36490333 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 RuvB-like helicase, Ino80, PAPA-1 domain-containing protein, YL1_C domain-containing protein, DASH complex subunit DAD4 Kinetochore, Nuclear division, Chromatin remodelers, INO80 G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62805, P0C0S8, P62807, Q71DI3 -
541 7W9V EM 3.95 2022-07-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L., Kutateladze, T.G., Kurumizaka, H. 10.1016/j.isci.2022.104563 35754730 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2022 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.307
542 5NL0 X-ray 5.40 2017-05-17 octamer, hemisome 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0-B 601L 193 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Bednar, J., Garcia-Saez, I., Boopathi, R., Cutter, A.R., Papai, G., Reymer, A., Syed, S.H., Lone, I.N., Tonchev, O., Crucifix, C., Menoni, H., Papin, C., Skoufias, D.A., Kurumizaka, H., Lavery, R., Hamiche, A., Hayes, J.J., Schultz, P., Angelov, D., Petosa, C., Dimitrov, S. 10.1016/j.molcel.2017.04.012 28475873 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P06897, P62799, P22844, P84233 -
543 6T7A EM 3.70 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Transcription factor SOX-11 Transcription-associated, Transcription factors P35716 P62805, O60814, P04908, Q71DI3 0.37
544 8OOP EM 2.70 2023-07-26 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 110 CryoEM Structure INO80core Hexasome complex composite model state2 Zhang, M., Jungblut, A., Kunert, F., Hauptmann, L., Hoffmann, T., Kolesnikova, O., Metzner, F., Moldt, M., Weis, F., DiMaio, F., Hopfner, K.P., Eustermann, S. 10.1126/science.adf6287 37384673 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 RuvB-like protein 1, RuvB-like protein 2, Chromatin-remodeling ATPase Ino80, Ino eighty subunit 2, Chromatin-remodeling complex subunit IES6, Actin-related protein 5 Kinetochore, Nuclear division, Chromatin remodelers, INO80 G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62805, P62807, P68431, Q93077 0.554
545 8OOS EM 3.29 2023-07-26 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 110 CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2 Zhang, M., Jungblut, A., Kunert, F., Hauptmann, L., Hoffmann, T., Kolesnikova, O., Metzner, F., Moldt, M., Weis, F., DiMaio, F., Hopfner, K.P., Eustermann, S. 10.1126/science.adf6287 37384673 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Chromatin-remodeling ATPase Ino80 P62805, P62807, P68431, Q93077 0.494
546 8PP6 EM 3.18 2024-04-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 human RYBP-PRC1 bound to H2AK118ub1 nucleosome Ciapponi, M., Karlukova, E., Schkolziger, S., Benda, C., Muller, J. 10.1038/s41594-024-01258-x 38528151 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2024 RING1 and YY1-binding protein, Ubiquitin-40S ribosomal protein S27a (Fragment) Q8N488, J3QTR3 P02283, A0A0B4KFZ9, P84051, A0A7L0PXJ3 0.465
547 8PP7 EM 2.91 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 human RYBP-PRC1 bound to mononucleosome Ciapponi, M., Karlukova, E., Schkolziger, S., Benda, C., Muller, J. 10.1038/s41594-024-01258-x 38528151 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 E3 ubiquitin-protein ligation, Polycomb, Histone_ubiquitination_H2AK119_writer, Transcription-associated, Histone PTM writers P35226, Q99496 P02283, A0A0B4KFZ9, P84051, A0A7L0PXJ3 0.511
548 8SIY EM 2.90 2023-08-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome Sahu, S., Ekundayo, B.E., Kumar, A., Bleichert, F. 10.15252/embj.2023114654 37551430 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Leucine-rich repeat and WD repeat-containing protein 1, Origin recognition complex subunit 2 Heterochromatin-associated, ORC, DNA replication A0A140UHX1, Q75PQ8 P02281, P84233, P06897, P62799 0.497
549 5B40 X-ray 3.33 2016-06-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Machida, S., Sekine, S., Nishiyama, Y., Horikoshi, N., Kurumizaka, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P62805, P06899, P04908, Q71DI3 -
550 8T3T EM 3.21 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state3 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 E3 ubiquitin-protein ligation, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457 P02281, P84233, P06897, P62799 0.535
551 8T3W EM 3.25 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state2 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 E3 ubiquitin-protein ligation, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457 P02281, P84233, P06897, P62799 0.52
552 8T3Y EM 3.47 2023-10-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of Bre1-nucleosome complex - state1 Zhao, F., Hicks, C.W., Wolberger, C. 10.1038/s41594-023-01137-x 37872231 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 E3 ubiquitin-protein ligation, Telomere-associated, Histone_ubiquitination_H2BK123_writer, Transcription-associated, Histone PTM writers Q07457 P02281, P84233, P06897, P62799 0.503
553 8G6H EM 3.06 2024-02-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Hicks, C.W., Rahman, S., Fields, J.K., Morgan, M.T., Wolberger, C. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.552
554 8T9H EM 3.37 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 99 Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Abini-Agbomson, S., Armache, K.-J. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Transcription-associated, Histone_methylation_H4K20_writer, Heterochromatin-associated, Histone PTM writers Q4FZB7 P02281, P84233, P06897, P62799 0.393
555 8G6G EM 2.93 2024-02-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Hicks, C.W., Rahman, S., Fields, J.K., Morgan, M.T., Wolberger, C. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.575
556 8EUJ EM 3.36 2023-07-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class2 of the INO80-Nucleosome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus Xenopus Xenopus Xenopus 2023 P62798, A0A310TTQ1, Q6AZJ8, A0A1B8Y854 0.322
557 8EUE EM 3.48 2023-07-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Class1 of the INO80-Nucleosome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus Xenopus Xenopus Xenopus 2023 P02281, P84233, P06897, P62799 0.356
558 3KXB X-ray 3.20 2010-06-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Watanabe, S., Resch, M., Lilyestrom, W., Clark, N., Hansen, J.C., Peterson, C., Luger, K. 10.1016/j.bbagrm.2010.01.009 20100606 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P84233, P62799, Q6AZJ8 -
559 8EU2 EM 2.93 2023-07-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Class3 of the INO80-Hexasome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.434
560 5B0Y X-ray 2.56 2016-01-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Suzuki, Y., Horikoshi, N., Kato, D., Kurumizaka, H. 10.1016/j.bbrc.2015.12.041 26694698 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2016 P62805, P06899, P04908, Q71DI3 -
561 8ETV EM 3.16 2023-07-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Class2 of the INO80-Hexasome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, P02302, P62799, Q6AZJ8 0.387
562 8ETT EM 6.68 2023-07-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Class1 of the INO80-Hexasome complex Wu, H., Munoz, E.N., Hsieh, L.J., Chio, U.S., Gourdet, M.A., Narlikar, G.J., Cheng, Y. 10.1126/science.adf4197 37384669 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.186
563 5GXQ X-ray 2.85 2017-04-19 octamer 1 H3.6 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing H3.6 Taguchi, H., Xie, Y., Horikoshi, N., Maehara, K., Harada, A., Nogami, J., Sato, K., Arimura, Y., Osakabe, A., Kujirai, T., Iwasaki, T., Semba, Y., Tachibana, T., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1021/acs.biochem.6b01098 28374988 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2017 P62805, P06899, P04908, A0A1X8XL64 -
564 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 2023 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.483
565 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 2020 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.625
566 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 2021 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.282
567 6T79 EM 3.20 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 145 Structure of a human nucleosome at 3.2 A resolution Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 P62805, O60814, P04908, Q71DI3 0.47
568 8OOA EM 3.18 2023-07-26 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 102 CryoEM Structure INO80core Hexasome complex Hexasome refinement state1 Zhang, M., Jungblut, A., Kunert, F., Hauptmann, L., Hoffmann, T., Kolesnikova, O., Metzner, F., Moldt, M., Weis, F., DiMaio, F., Hopfner, K.P., Eustermann, S. 10.1126/science.adf6287 37384673 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 P62805, P62807, P68431, Q93077 0.525
569 6T7B EM 5.10 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of human Sox2 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Transcription factor SOX-2 Transcription-associated, Transcription factors P48431 P62805, O60814, P04908, Q71DI3 0.217
570 8HAL EM 4.40 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 151 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 CREB-binding protein Transcription-associated, Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P62805, P06899, P04908, P68431 0.195
571 8CZE EM 2.58 2023-06-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of a Xenopus Nucleosome with Widom 601 DNA Milano, C.R., Ur, S.N., Gu, Y., Zhang, J., Allison, R., Brown, G., Neale, M.J., Tromer, E.C., Corbett, K.D., Hochwagen, A. 10.1038/s44318-024-00034-3 38332377 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.598
572 8G86 EM 2.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 145 Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome) Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis laevis Xenopus laevis Xenopus laevis 2023 P02281, P84233, P62799, Q6AZJ8 0.606
573 8G88 EM 2.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 168 Human Oct4 bound to nucleosome with human nMatn1 sequence Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P02281, P84233, P62799, Q6AZJ8 0.199
574 8G8B EM 4.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 168 Nucleosome with human nMatn1 sequence in complex with Human Oct4 Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P02281, P84233, P62799, Q6AZJ8 0.233
575 7E8D EM 2.80 2021-11-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 172 NSD2 E1099K mutant bound to nucleosome Sato, K., Kumar, A., Hamada, K., Okada, C., Oguni, A., Machiyama, A., Sakuraba, S., Nishizawa, T., Nureki, O., Kono, H., Ogata, K., Sengoku, T. 10.1038/s41467-021-26913-5 34782608 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2021 Histone-lysine N-methyltransferase NSD2 Transcription-associated, Euchromatin-associated, Histone_methylation_H3K36_writer, Histone PTM writers O96028 P62805, P0C0S8, P06899, P68431 0.556
576 8G8G EM 3.20 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 174 Interaction of H3 tail in LIN28B nucleosome with Oct4 Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription-associated, Transcription factors Q01860 P02281, P84233, P62799, Q6AZJ8 0.218
577 8HAG EM 3.20 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.29
578 8HAH EM 3.90 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 164 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.159
579 6VYP X-ray 4.99 2020-05-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 191 Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Kim, S.A., Zhu, J., Yennawar, N., Eek, P., Tan, S. 10.1016/j.molcel.2020.04.019 32396821 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Lysine-specific histone demethylase 1A, REST corepressor 1 Transcription-associated, Histone PTM erasers, Histone_demethylation_H3K9, Histone_demethylation_H3K4 O60341, Q9UKL0 P02281, P84233, P06897, P62799 -
580 8HAJ EM 4.80 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 164 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.2
581 8HAK EM 4.50 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.214
582 8HAI EM 4.70 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 Histone acetyltransferase p300 DNA repair, p300, Histone_acetylation_writer, Transcription-associated, Histone PTM writers Q09472 P62805, P06899, P04908, P68431 0.212
583 6UH5 EM 3.50 2019-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structural basis of COMPASS eCM recognition of the H2Bub nucleosome Hsu, P.L., Shi, H., Leonen, C., Kang, J., Chatterjee, C., Zheng, N. 10.1016/j.molcel.2019.10.013 31733991 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, Ubiquitin, Spp1 COMPASS, Ubiquitin, Histone_methylation_H3K4_writer, Telomere-associated, Transcription-associated, Histone PTM writers Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, P0CG47, Q6CRQ4 P02281, Q6AZJ8, Q92133, P62799, P84233 0.372
584 8OO7 EM 2.80 2023-07-26 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 113 CryoEM Structure INO80core Hexasome complex composite model state1 Zhang, M., Jungblut, A., Kunert, F., Hauptmann, L., Hoffmann, T., Kolesnikova, O., Metzner, F., Moldt, M., Weis, F., DiMaio, F., Hopfner, K.P., Eustermann, S. 10.1126/science.adf6287 37384673 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 RuvB-like protein 1, RuvB-like protein 2, Chromatin-remodeling ATPase Ino80, Ino eighty subunit 2, Chromatin-remodeling complex subunit IES6, Actin-related protein 5 Kinetochore, Nuclear division, Chromatin remodelers, INO80 G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62805, P62807, P68431, Q93077 0.556
585 6T7C EM 4.00 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Transcription factor SOX-11 Transcription-associated, Transcription factors P35716 P62805, O60814, P04908, Q71DI3 0.355
586 6T7D EM 4.40 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 117 Structure of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2020 Transcription factor SOX-11 Transcription-associated, Transcription factors P35716 P62805, O60814, P04908, Q71DI3 0.323
587 6UGM EM 3.70 2019-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structural basis of COMPASS eCM recognition of an unmodified nucleosome Hsu, P.L., Shi, H., Leonen, C., Kang, J., Chatterjee, C., Zheng, N. 10.1016/j.molcel.2019.10.013 31733991 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, H3 N-terminus, Spp1 COMPASS, Histone_methylation_H3K4_writer, Telomere-associated, Transcription-associated, Histone PTM writers Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, Q6CRQ4 P02281, Q92133, P62799, Q6AZJ8 0.385
588 8HAM EM 4.50 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 165 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 CREB-binding protein Transcription-associated, Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P62805, P06899, P04908, P68431 0.242
589 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 2020 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.516
590 8HAN EM 4.20 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2023 CREB-binding protein Transcription-associated, Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer Q92793 P62805, P06899, P04908, P68431 0.209
591 8KD2 EM 3.02 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 174 Rpd3S in complex with 187bp nucleosome Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Histone PTM erasers, Histone_deacetylation, Rpd3, DNA repair, Telomere-associated, Histone_acetylation_writer, Transcription-associated, Histone PTM writers, NuA4 P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.35