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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 9GXA EM 4.01 2025-01-29 H3_H4_tetramer, H3_H4_tetramer 2 cenH3 canonical_H4 alphasat_native 112 CENP-A/H4 di-tetrasome assembled on alpha-satellite DNA. Ali-Ahmad, A., Mors, M., Carrer, M., Li, X., Bilokapic, S., Halic, M., Cascella, M., Sekulic, N. 10.1101/2024.12.31.630874 39803555 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 P49450, P62805 -
1 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 Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.563
2 7X57 EM 3.63 2022-11-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 121 Cryo-EM structure of human subnucleosome (closed form) Nozawa, K., Takizawa, Y., Pierrakeas, L., Sogawa-Fujiwara, C., Saikusa, K., Akashi, S., Luk, E., Kurumizaka, H. 10.1073/pnas.2206542119 36322721 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2022 P68431, P62805 0.37
3 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 Xenopus laevis 2023 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 P02281, P84233, P06897, P62799 0.489
4 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 Xenopus laevis 2023 ISWI one complex protein 3 Chromatin remodelers, ISWI P43596 P02281, P84233, P06897, P62799 0.502
5 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 Xenopus laevis 2022 Q9D2U9, A0A8X6EH29, P62806, C0HKE1 0.506
6 7E8I EM 3.10 2021-06-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Dai, L., Dai, Y., Han, J., Huang, Y., Wang, L., Huang, J., Zhou, Z. 10.1016/j.molcel.2021.05.010 34102105 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 BRCA1-associated RING domain protein 1, Polyubiquitin-B Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, Ubiquitin, DNA repair, Histone_ubiquitination_H2AK129_writer Q99728, P0CG47 P02281, P84233, P06897, P62799 0.456
7 6X5A EM 4.36 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. 10.1038/s41586-020-2749-z 32911481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P0C0S8, P62807, Q71DI3, P62805 0.265
8 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 Xenopus laevis 2020 P02281, P84233, P06897, P62799 0.504
9 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 Xenopus laevis 2020 P68431, P04908, P06899, P62805 -
10 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 Xenopus laevis 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, Ubiquitin, Spp1 Telomere-associated, Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated, Ubiquitin Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, P0CG47, Q6CRQ4 P84233, P62799, Q92133, P02281, Q6AZJ8 0.372
11 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 Xenopus laevis 2019 Swd3, Bre2, Histone-lysine N-methyltransferase, H3 lysine-4 specific, Swd1, Sdc1, H3 N-terminus, Spp1 Telomere-associated, Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q6CLY5, Q6CTQ1, Q6CIT4, Q6CXF3, Q6CPN6, Q6CRQ4 Q92133, P02281, Q6AZJ8, P62799 0.385
12 6M4G EM 2.80 2020-09-23 octamer 1 canonical_H3 canonical_H4 H2A.B canonical_H2B 601 93 Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Zhou, M., Dai, L., Li, C., Shi, L., Huang, Y., Guo, Z., Wu, F., Zhu, P., Zhou, Z. 10.15252/embj.2020105907 33073403 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P68431, P0C5Z0, Q16778, P62805 0.493
13 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 Xenopus laevis 2020 P68431, P04908, P06899, P62805 -
14 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 Xenopus laevis 2021 P68431, P04908, P06899, P62805 -
15 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 P68431, P06899, P04908, P07305, P62805 -
16 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 P68431, P06899, P04908, P07305, P62805 -
17 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 P68431, P06899, P04908, P07305, P62805 -
18 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 Q92522, P68431, P06899, P04908, P62805 -
19 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 Xenopus laevis 2019 P68431, P04908, P06899, P62805 -
20 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 Xenopus laevis 2019 Transcription regulatory protein SNF2 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P02281, P84233, P06897, P62799 0.349
21 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 Xenopus laevis 2019 Transcription regulatory protein SNF2 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P02281, P84233, P06897, P62799 0.261
22 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 Xenopus laevis 2018 Q9D2U9, P84244, P62806, C0HKE1 -
23 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 Xenopus laevis 2022 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 O60814, P04908, Q71DI3, P62805 0.514
24 7XT7 EM 4.20 2022-10-12 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated, DNA repair, FACT C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, F2QPX0, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P84243, P06899, P04908, P62805 0.207
25 5KGF EM 4.54 2016-07-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Wilson, M.D., Benlekbir, S., Fradet-Turcotte, A., Sherker, A., Julien, J.P., McEwan, A., Noordermeer, S.M., Sicheri, F., Rubinstein, J.L., Durocher, D. 10.1038/nature18951 27462807 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2016 Tumor suppressor p53-binding protein 1, Ubiquitin Histone_ubiquitination_H2AK15_reader, Telomere-associated, Histone PTM readers, Ubiquitin, DNA repair, Histone_methylation_H4K20_reader Q12888, P0CG47 P0C0S8, P84233, P62807, P62799 0.301
26 7XTD EM 3.90 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated, DNA repair, FACT C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P84243, P06899, P04908, P62805 0.221
27 8V27 EM 3.34 2024-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2BK120ub-modified nucleosome ubiquitin position 3 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P06897, P62799 0.516
28 8UPF EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.464
29 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 Xenopus laevis 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Euchromatin-associated, Transcription factors, Transcription-associated Q01860 Q16777, P68431, Q16778, P62805 0.496
30 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 Xenopus laevis 2023 Leucine-rich repeat and WD repeat-containing protein 1, Origin recognition complex subunit 2 Heterochromatin-associated, DNA replication, ORC A0A140UHX1, Q75PQ8 P02281, P84233, P06897, P62799 0.497
31 8RUQ EM 2.29 2025-02-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Borealin N-terminus in complex with H3.T3p-nucleosome Ruza, R.R., Chung, C.W., Gold, D.B., Serena, M., Roberts, E., Gruneberg, U., Barr, F.A. 10.1101/2025.01.22.634029 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Borealin Q53HL2 P84233, P62799, P02281, A0A310TTQ1, Q6AZJ8 0.618
32 8QYV EM 3.50 2024-10-02 hexamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 118 SWR1-hexasome complex Jalal, A.S.B., Girvan, P., Chua, E.Y.D., Liu, L., Wang, S., McCormack, E.A., Skehan, M.T., Knight, C.L., Rueda, D.S., Wigley, D.B. 10.1016/j.molcel.2024.08.015 39226902 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, SWR1-complex protein 5, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 INO80, SRCAP (INO80), SWR1 (INO80), Chromatin remodelers, Euchromatin-associated, Transcription-associated Q05471, P38326, Q12509, Q03433, Q03940, Q12464, Q03388 P02293, P02309, P04911, P61830 0.324
33 8KD6 EM 3.07 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.311
34 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 Xenopus laevis 2023 P04908, P06899, Q71DI3, P62805 0.602
35 8IEJ EM 3.12 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 RNF20-RNF40/hRad6A-Ub/nucleosome complex Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.molcel.2023.08.001 37633270 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1B, E3 ubiquitin-protein ligase BRE1A, Ubiquitin-conjugating enzyme E2 A Histone PTM writers, Histone_ubiquitination_H2BK120_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair O75150, Q5VTR2, P49459 P62805, O60814, P04908, P68431 0.461
36 8IEG EM 3.44 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.molcel.2023.08.001 37633270 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1, Ubiquitin-conjugating enzyme E2 2 Telomere-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair Q07457, P06104 P62805, O60814, P04908, P68431 0.393
37 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 Xenopus laevis 2023 COMMD3 protein, Ring1B, Ubiquitin, UbcH5b Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer, Ubiquitin P35226, Q99496, P0CG47, P62837 O60814, P68431, P04908, P62805 0.516
38 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 Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Euchromatin-associated, Transcription factors, Transcription-associated Q01860 P02281, P84233, Q6AZJ8, P62799 0.233
39 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 Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Euchromatin-associated, Transcription factors, Transcription-associated Q01860 P02281, P84233, Q6AZJ8, P62799 0.199
40 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 Xenopus laevis 2023 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.434
41 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 Xenopus laevis 2023 Meiosis-specific protein HOP1 Nuclear division P20050 P02281, P84233, P06897, P62799 0.574
42 8BVW EM 4.00 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 206 RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta RNA polymerases, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated, DNA repair P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P02281, P84233, P06897, P62799 0.234
43 7ZSB EM 6.60 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 219 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta RNA polymerases, Transcription factors, Euchromatin-associated, Transcription-associated, DNA repair P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P02281, P84233, P06897, P62799 0.277
44 7ZS9 EM 3.10 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta RNA polymerases, Transcription factors, Euchromatin-associated, Transcription-associated, DNA repair P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P02281, P84233, P06897, P62799 0.34
45 7YOZ EM 4.30 2022-11-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 121 Cryo-EM structure of human subnucleosome (intermediate form) Nozawa, K., Takizawa, Y., Pierrakeas, L., Sogawa-Fujiwara, C., Saikusa, K., Akashi, S., Luk, E., Kurumizaka, H. 10.1073/pnas.2206542119 36322721 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2022 P68431, P62805 0.246
46 7YI5 EM 3.96 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.254
47 7Y5W EM 3.50 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 101 Cryo-EM structure of the left-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 P68431, P62805 0.35
48 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 Xenopus laevis 2018 Q9D2U9, P84244, P62806, C0HKE1 -
49 5GSU X-ray 3.10 2017-02-15 octamer 1 canonical_H3 canonical_H4 H2A.1 H2B.1 alphasat_146 146 Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B 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 Xenopus laevis 2017 Q96QV6, P68431, Q96A08, P62805 -
50 8VFY EM 2.89 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 171 Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Hepatocyte nuclear factor 3-alpha Transcription factors, Transcription-associated P55317 P68431, P04908, P06899, P62805 0.463
51 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 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 Chromatin remodelers, RSC (SWI/SNF), Cell cycle, Transcription-associated Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.086
52 8Q16 EM 3.60 2025-02-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 CryoEM structure of rice nucleosome containing a H4 variant chimera Gandhivel, V.H., Sotelo-Parrilla, P., Raju, S., Jha, S., Gireesh, A., Harshith, C.Y., Gut, F., Vinothkumar, K.R., Berger, F., Jeyaprakash, A.A., Shivaprasad, P.V. 10.1038/s41477-025-01974-2 40200022 Oryza Oryza Oryza Oryza Xenopus laevis 2025 A2WKP5, None, A2YMC6, A2Y533 0.441
53 8B0A EM 3.00 2023-09-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome Bacic, L., Gaullier, G., Mohapatra, J., Mao, G., Brackmann, K., Panfilov, M., Liszczak, G., Sabantsev, A., Deindl, S. 10.1038/s41467-024-45237-8 38307862 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.483
54 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 P68431, P06899, P04908, P07305, P62805 -
55 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 P10412, Q71DI3, P04908, P62805, O60814 0.105
56 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 Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.298
57 8VFX EM 2.65 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 158 Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 scFv P68431, P04908, P06899, P62805 0.559
58 9JO2 EM 3.00 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in Apo* state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.476
59 9JNX EM 3.00 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP*+ state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.497
60 9EOZ EM 3.10 2024-11-06 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 144 Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Ren, M., Gut, F., Fan, Y., Ma, J., Shan, X., Yikilmazsoy, A., Likhodeeva, M., Hopfner, K.P., Zhou, C. 10.1038/s41467-024-53811-3 39477986 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA repair, DNA modification O15527 P62807, P84243, Q93077, P62805 0.465
61 9J8N EM 7.14 2025-02-26 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 189 Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Horikoshi, N., Miyake, R., Sogawa-Fujiwara, C., Ogasawara, M., Takizawa, Y., Kurumizaka, H. 10.1038/s41467-025-56823-9 39929866 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Barrier-to-autointegration factor, Lamin-A/C O75531, P02545 P68431, P04908, P06899, P62805 0.164
62 9GD3 EM 3.00 2024-09-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. Engeholm, M., Roske, J.J., Oberbeckmann, E., Dienemann, C., Lidschreiber, M., Cramer, P., Farnung, L. 10.1016/j.molcel.2024.08.022 39270644 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Chromo domain-containing protein 1 CHD, Chromatin remodelers, Transcription-associated P32657 P02281, P84233, P06897, P62799 0.465
63 9E1W EM 3.20 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassC3 Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.578
64 9DWM EM 4.20 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 126 DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta P06746 P0C0S8, P62807, Q71DI3, P62805 0.31
65 9DWF EM 3.10 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 Nucleosome containing a 1-nt gap at SHL-4.5 Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P0C0S8, P62807, Q71DI3, P62805 0.526
66 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., Sui, F., Gu, F., Li, W., Yu, Z., Wang, Q., He, S., Wang, L., Xu, Y. 10.1038/s41421-023-00640-1 38331872 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 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 INO80, SRCAP (INO80), Chromatin remodelers, Histone_acetylation_reader, Histone chaperones, Cell cycle, Euchromatin-associated, Transcription-associated, Histone PTM readers Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62807, P68431, Q93077, P62805 0.218
67 8VWV EM 3.60 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA repair, DNA modification O15527 P0C0S8, P62807, Q71DI3, P62805 0.359
68 8U13 EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5 P68431, P04908, P62807, P62805 0.381
69 8TOF EM 2.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 176 Rpd3S bound to an H3K36Cme3 modified nucleosome Markert, J.W., Vos, S.M., Farnung, L. 10.1038/s41467-023-43968-8 38065958 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Rco1, histone N-terminal tail Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P06897, P02302, P62799 0.464
70 8TAS EM 4.10 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 193 PRC2 monomer bound to nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Histone PTM writers, Histone chaperones, Polycomb, Transcription-associated, Heterochromatin-associated, Histone_methylation_H3K27_writer Q15022, Q15910, O75530, Q09028, Q6ZN18 P02281, P84233, P06897, P62799 0.259
71 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 Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Telomere-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Transcription-associated Q07457 P02281, P84233, P06897, P62799 0.503
72 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 Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Telomere-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Transcription-associated Q07457 P02281, P84233, P06897, P62799 0.52
73 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 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 Chromatin remodelers, RSC (SWI/SNF), Cell cycle, Transcription-associated Q06168, P43609, P32832, Q03124, P25632, Q07979, Q9URQ5, Q02206, P32597, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.081
74 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 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 Chromatin remodelers, RSC (SWI/SNF), Cell cycle, Transcription-associated Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P84233, P06897, A0A1L8G0X3, P62799 0.062
75 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
76 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 Xenopus laevis 2011 P49450, P06899, P04908, P62805 -
77 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 Xenopus laevis 2016 P04908, P06899, Q71DI3, P62805 -
78 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 Xenopus laevis 2013 P02281, P84233, P06897, P62799 -
79 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 Xenopus laevis 2013 P02281, P84233, P06897, P62799 -
80 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 Xenopus laevis 2014 P84243, P06899, P49450, P04908, P62805 -
81 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 Xenopus laevis 2010 P02281, P84233, Q6AZJ8, P62799 -
82 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 Xenopus laevis 2007 P02281, P84233, P06897, P62799 -
83 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 Xenopus laevis 2005 O60814, P68431, P04908, P62805 -
84 1U35 X-ray 3.00 2005-09-27 octamer 1 canonical_H3 canonical_H4 macroH2A canonical_H2B alphasat_146 145 Crystal structure of the nucleosome core particle containing the histone domain of macroH2A Chakravarthy, S., Gundimella, S.K., Caron, C., Perche, P.Y., Pehrson, J.R., Khochbin, S., Luger, K. 10.1128/MCB.25.17.7616-7624.2005 16107708 Mus musculus Mus musculus Homo sapiens Mus musculus Xenopus laevis 2005 Q9D2U9, P68433, P62806, O75367 -
85 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
86 6UPK EM 4.90 2019-12-11 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 72 Structure of FACT_subnucleosome complex 1 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Histone chaperones, DNA replication, Transcription-associated, DNA repair, FACT Q9Y5B9, Q08945 P62807, P68431, Q93077, P62805 0.203
87 6UPH EM 2.70 2019-11-06 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 119 Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution Migl, D., Kschonsak, M., Arthur, C.P., Khin, Y., Harrison, S.C., Ciferri, C., Dimitrova, Y.N. 10.1016/j.str.2019.12.002 32004465 Saccharomyces cerevisiae Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Xenopus laevis 2019 Q6CK59, Q6CK60, P36012, Q6CMU6 0.623
88 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 Xenopus laevis 2020 P68431, P04908, P06899, P62805 -
89 7K78 EM 3.10 2021-03-31 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 116 antibody and nucleosome complex Guan, R., Lian, T., Zhou, B.R., He, E., Wu, C., Singleton, M., Bai, Y. 10.1038/s41467-021-21985-9 33741944 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2021 scFv P02293, P02309, P04911, None 0.556
90 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 Xenopus laevis 2010 P02281, P84233, Q6AZJ8, P62799 -
91 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 Xenopus laevis 2017 Q9D2U9, P68433, P62806, C0HKE1 -
92 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q03164, Q15291, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.31
93 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 Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
94 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 Xenopus laevis 2002 P02281, P84233, P06897, P62799 -
95 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 Xenopus laevis 2023 Lysine-specific demethylase 2A Heterochromatin-associated, Histone_demethylation_H3K36, Centromere-associated, Histone PTM erasers Q9Y2K7 P0C0S8, P62807, Q71DI3, P62805 0.42
96 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 Xenopus laevis 2016 Guanine nucleotide exchange factor SRM1, N-lysine methyltransferase SETD8 Histone_methylation_H4K20_writer, Histone PTM writers, Cell cycle, Transcription-associated, Heterochromatin-associated, Nuclear division P21827, Q9NQR1 P02281, P84233, P06897, P62799 -
97 7YWX EM 12.00 2022-05-18 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B 162 Structure of the human CCAN CENP-A alpha-satellite complex Yatskevich, S., Muir, K.W., Bellini, D., Zhang, Z., Yang, J., Tischer, T., Predin, M., Dendooven, T., McLaughlin, S.H., Barford, D. 10.1126/science.abn3810 35420891 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein S, Centromere protein T, Centromere protein U, Centromere protein W, Centromere protein X, Centromere protein C Fanconi anemia core complex, CENP-A NAC/CAD, DNA repair, Cell cycle, Transcription-associated, Centromere-associated, Nuclear division, Kinetochore Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q8N2Z9, Q96BT3, Q71F23, Q5EE01, A8MT69, Q03188 P62807, P49450, Q93077, P62805 0.054
98 8V28 EM 3.36 2024-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2BK120ub-modified nucleosome ubiquitin position 4 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P06897, P62799 0.505
99 8VFZ EM 4.10 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 171 Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Hepatocyte nuclear factor 3-alpha Transcription factors, Transcription-associated P55317 P68431, P04908, P06899, P62805 0.27
100 8SN7 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.445
101 7JOA EM 3.30 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 2:1 cGAS-nucleosome complex Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q. 10.1126/science.abd0609 32913000 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P0C0S8, P62807, Q71DI3, P62805 0.474
102 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 Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-36 specific Histone PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated P46995 P02281, P84233, Q6AZJ8, P62799 0.473
103 7DBH EM 3.60 2022-01-19 octamer 1 canonical_H3,H3.3 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 Xenopus laevis 2022 Q9D2U9, A0A8X6EH29, P62806, C0HKE1 0.391
104 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 Xenopus laevis 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription factors, Transcription-associated P42212, P48431 P68431, P04908, P06899, P62805 0.35
105 6XJD EM 6.80 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Two mouse cGAS catalytic domain binding to human assembled nucleosome Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. 10.1038/s41586-020-2749-z 32911481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P0C0S8, P62807, Q71DI3, P62805 0.196
106 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 Xenopus laevis 2020 Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102 Chromatin remodelers, RSC (SWI/SNF), Cell cycle, Transcription-associated P32597, Q12406, Q05123, P53330 Q92133, P02281, P06897, P62799 -
107 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 Xenopus laevis 2019 Integrase Viral, DNA integration P14350 P84243, P62807, P0C0S8, P62805 0.349
108 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, F5H388 P02281, P84233, P06897, P62799 0.371
109 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P02281, P84233, P06897, P62799 0.551
110 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 Xenopus laevis 2019 Centromere protein C, Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188, Q96H22 P49450, Q93077, Q5QNW6, P62805 0.401
111 6JOU X-ray 2.17 2020-03-25 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 Crystal structure of the human nucleosome containing H2A.Z.1 S42R Horikoshi, N., Kujirai, T., Sato, K., Kimura, H., Kurumizaka, H. 10.1016/j.bbrc.2019.06.012 31186139 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P68431, P06899, P0C0S5, P62805 -
112 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 Xenopus laevis 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.195
113 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 Xenopus laevis 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.235
114 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 Xenopus laevis 2018 Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q96H22 P62807, P49450, Q93077, P62805 0.39
115 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 Xenopus laevis 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 Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P84243, P06899, P04908, P62805 0.083
116 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 Xenopus laevis 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 Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P84243, P06899, P04908, P62805 0.182
117 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 Xenopus laevis 2019 P68431, P04908, P06899, P62805 -
118 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 P84233, P22844, P06897, P62799, P02281 -
119 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 Xenopus laevis 2017 PFV GAG peptide Viral, DNA integration P14349 P02281, P84233, P06897, P62799 -
120 5GT0 X-ray 2.82 2017-02-15 octamer 1 canonical_H3 canonical_H4 H2A.1 canonical_H2B alphasat_146 146 Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a 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 Xenopus laevis 2017 Q96QV6, P68431, P62807, P62805 -
121 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 Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
122 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
123 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 Xenopus laevis 2021 Histone-lysine N-methyltransferase SETD2 Histone PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated Q9BYW2 P20671, P06899, Q6PI79, P62799 0.509
124 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 P10412, Q71DI3, P04908, P62805, O60814 0.177
125 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
126 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 P10412, Q71DI3, P04908, P62805, O60814 0.208
127 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 Xenopus laevis 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Euchromatin-associated, Transcription factors, Transcription-associated Q01860 Q16777, P68431, Q16778, P62805 0.434
128 8SN9 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.424
129 8SN8 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.443
130 8Q3X X-ray 2.30 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Batchelor, L.K., De Falco, L., Dyson, P.J., Davey, C.A. 10.1039/d4ra01617c 38495982 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 LANA peptide Viral Q9QR71 O60814, P68431, P04908, P62805 -
131 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 Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer P35226, Q99496 P84040, P84051, P02299, P02283 0.511
132 8KCC EM 3.10 2024-06-26 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 150 Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2 Zhang, H., Gu, Z., Zeng, Y., Zhang, Y. 10.1016/j.str.2024.05.013 38870940 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9FFC0, Q9FJE8, P59259, P59226 0.387
133 8KCB EM 3.17 2024-06-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 126 Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2 Zhang, H., Gu, Z., Zeng, Y., Zhang, Y. 10.1016/j.str.2024.05.013 38870940 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9FFC0, P59259, Q9LD28, P59226 0.38
134 8J91 EM 2.90 2024-07-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 113 Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones Osakabe, A., Takizawa, Y., Horikoshi, N., Hatazawa, S., Negishi, L., Sato, S., Berger, F., Kakutani, T., Kurumizaka, H. 10.1038/s41467-024-49465-w 38992002 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 Q9LHQ5, O23629, P59259, P59226 0.545
135 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 Xenopus laevis 2023 SSX1 Histone_ubiquitination_H2AK119_reader, Histone PTM readers, Transcription-associated Q16384 O60814, P04908, Q71DI3, P62805 0.532
136 8HAK EM 4.50 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.214
137 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 Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.186
138 7ZSA EM 4.00 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta RNA polymerases, Transcription factors, Euchromatin-associated, Transcription-associated, DNA repair P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P02281, P84233, P06897, P62799 0.342
139 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 P68431, P02259, P06899, P04908, P62805 -
140 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 Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.55
141 7XFJ EM 3.00 2023-11-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-3-methyladenine glycosylase DNA repair, DNA modification P29372 P02281, P84233, P06897, P62799 0.466
142 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 Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.569
143 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 Xenopus laevis 2022 P0C0S8, P62807, Q71DI3, P62805 0.454
144 7SSA EM 3.20 2023-04-05 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 137 Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome Donovan, B.T., Chen, H., Eek, P., Meng, Z., Jipa, C., Tan, S., Bai, L., Poirier, M.G. 10.1016/j.molcel.2023.03.006 36996811 Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2023 Centromere-binding protein 1 Transcription-associated P17106 P02293, P84233, P04911, P62799 0.449
145 7SCZ EM 3.50 2022-01-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to multiple BRCTs Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 DNA repair, Histone PTM writers, Histone_PARylation_writer P09874 P68431, P04908, P06899, P62805 0.425
146 7SCY EM 4.10 2022-01-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nuc147 bound to single BRCT Rudolph, J., Muthurajan, U.M., Palacio, M., Mahadevan, J., Roberts, G., Erbse, A.H., Dyer, P.N., Luger, K. 10.1016/j.molcel.2021.11.014 34919819 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Poly [ADP-ribose] polymerase 1 DNA repair, Histone PTM writers, Histone_PARylation_writer P09874 P68431, P04908, P06899, P62805 0.273
147 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 Xenopus laevis 2022 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 P62807, P49450, Q93077, P62805 0.571
148 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 Xenopus laevis 2016 P68431, P04908, P06899, P62805 -
149 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
150 8VLR EM 2.60 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 136 Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Shen, X.Y., Chen, C.X., Wang, Y., Zheng, W., Zheng, J.H., Jones, A.E., Zhu, B., Zhang, H., Lyons, C., Rijal, A., Moley, J.A., Cao, G.S., Liu, K., Winn, R., McGinty, R.K., Zhang, K., Wang, H.B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Q96A08, P68431, P04908, P62805 0.602
151 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 Q92522, P68431, P06899, P04908, P62805 0.435
152 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 P02299, P02259, P84040, P84051, P02283 -
153 6KW4 EM 7.55 2019-11-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 The ClassB 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 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 Chromatin remodelers, RSC (SWI/SNF), Cell cycle, Transcription-associated Q07979, P38781, P43609, Q9URQ5, P32832, Q06168, P25632, P32597, Q06639, Q06488, Q03124, Q02206, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.099
154 5B33 X-ray 2.92 2016-08-03 octamer 1 H3.3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the H2AZ 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 Xenopus laevis 2016 P84243, P0C0S5, P06899, P62805 -
155 5B31 X-ray 2.20 2016-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A,H2A.Z 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 Xenopus laevis 2016 P68431, P06899, P0C0S5, P04908, P62805 -
156 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 Xenopus laevis 2002 P02281, P84233, P06897, P62799 -
157 8X7J EM 3.39 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair P61077, Q8IYW5, P62979 O60814, P04908, Q71DI3, P62805 0.391
158 7U50 EM 3.40 2022-09-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Weaver, T.M., Hoitsma, N.M., Spencer, J.J., Gakhar, L., Schnicker, N.J., Freudenthal, B.D. 10.1038/s41467-022-33057-7 36104361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-(apurinic or apyrimidinic site) endonuclease DNA repair P27695 P0C0S8, P62807, Q71DI3, P62805 0.415
159 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 Xenopus laevis 2018 P02281, P06897, P02302, P62799 0.196
160 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 Xenopus laevis 2018 P02281, P84233, P06897, P62799 0.235
161 8X7K EM 3.27 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair P61077, Q8IYW5 O60814, P04908, Q71DI3, P62805 0.423
162 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 Xenopus laevis 2007 P02281, P84233, P06897, P62799 -
163 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
164 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 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 RSC (SWI/SNF), Chromatin remodelers, SWI/SNF, Transcription-associated P22082, P09547, P18480, P32591, P53628, P18888, Q12406, Q05123, P53330 P02281, P84233, P06897, P62799 0.122
165 9QAJ EM 2.95 2025-04-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of the nucleosome-bound human BCL7A Martin, F., Kazrani, A.A., Lafouge, J., Diaz-Jimenez, D.M., Siebert, S., Fabbro-Burtschell, L., Maillard, E., Lapouge, K., Mertens, H.D.T., Sauter, C., Leitner, A., Ochsenbein, F., Blais, A., Bergamin, E. 10.1093/nar/gkaf273 40207634 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Isoform 2 of B-cell CLL/lymphoma 7 protein family member A Q4VC05 P02281, P84233, Q6AZJ8, P62799 0.493
166 9LJ2 EM 2.98 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, P62799, Q6AZJ8 0.458
167 9LIU EM 2.70 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome double-bound complex in ATP-ATP state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.487
168 9JO5 EM 2.80 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP-B state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.482
169 9EH1 EM 3.10 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerase I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, Superkiller complex protein 8, N-terminally processed, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Histone PTM writers, Histone_methylation_H3K36_writer, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Euchromatin-associated, Transcription-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q96ST2, Q6PD62, Q92541, B7Z4W0, Q9GZS3, A0A2R8YHB3, P63272, Q9BYW2 P02281, P06897, A0A310TTQ1, P62799 0.237
170 9DWL EM 3.90 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 Nucleosome containing a 1-nt gap at SHL-5.5 Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P0C0S8, P62807, Q71DI3, P62805 0.366
171 9DGG EM 2.98 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 ncPRC1RYBP bound to unmodified nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2 Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer P35226, Q99496 P02281, P84233, P06897, P62799 0.47
172 8YV8 EM 3.00 2024-07-31 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Wassing, I.E., Nishiyama, A., Shikimachi, R., Jia, Q., Kikuchi, A., Hiruta, M., Sugimura, K., Hong, X., Chiba, Y., Peng, J., Jenness, C., Nakanishi, M., Zhao, L., Arita, K., Funabiki, H. 10.1126/sciadv.adp5753 39178260 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Cell division cycle-associated protein 7 Methylated DNA binding Q9BWT1 O60814, P68431, P04908, P62805 0.524
173 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 Xenopus laevis 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 Chromatin remodelers, RSC (SWI/SNF), Cell cycle, Transcription-associated Q12406, Q05123, Q9URQ5, P38210, P32832, Q06488, Q06639, Q02206, P43609, P25632, Q03124, Q07979, P53330, Q06168, P32597, P38781 O60814, P68431, P04908, P62805 0.053
174 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 Xenopus laevis 2020 scFv20 P68431, P04908, P06899, P62805 0.529
175 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
176 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 Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.177
177 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
178 4JJN X-ray 3.09 2013-05-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome Wang, F., Li, G., Altaf, M., Lu, C., Currie, M.A., Johnson, A., Moazed, D. 10.1073/pnas.1300126110 23650358 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2013 Regulatory protein SIR3 Transcription-associated P06701 P02294, P02309, P61830, P04912 -
179 3X1U X-ray 3.25 2015-09-23 octamer 1 canonical_H3 canonical_H4 H2A.1 canonical_H2B alphasat_146 146 Crystal structure of nucleosome core particle in the presence of histone variants 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 Mus musculus Homo sapiens Xenopus laevis 2015 P33778, P68431, Q8CGP4, P62805 -
180 3X1T X-ray 2.81 2015-09-23 octamer 1 canonical_H3 canonical_H4 H2A.1 H2B.1 alphasat_146 146 Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bbrc.2015.07.070 26188507 Homo sapiens Homo sapiens Mus musculus Mus musculus Xenopus laevis 2015 P68431, P70696, Q8CGP4, P62805 -
181 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 Xenopus laevis 2015 P33778, P68431, P04908, P62805 -
182 3WAA X-ray 3.20 2013-12-18 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The nucleosome containing human H2A.Z.2 Horikoshi, N., Sato, K., Shimada, K., Arimura, Y., Osakabe, A., Tachiwana, H., Hayashi-Takanaka, Y., Iwasaki, W., Kagawa, W., Harata, M., Kimura, H., Kurumizaka, H. 10.1107/S090744491302252X 24311584 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P68431, P06899, Q71UI9, P62805 -
183 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 Xenopus laevis 2013 P68431, P04908, P06899, P62805 -
184 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 Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
185 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
186 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
187 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
188 2F8N X-ray 2.90 2006-05-23 octamer 1 canonical_H3 canonical_H4 macroH2A,canonical_H2A canonical_H2B alphasat_146 145 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Chakravarthy, S., Luger, K. 0 Xenopus laevis Xenopus laevis Homo sapiens,Mus musculus Xenopus laevis Xenopus laevis 2006 P84233, P62799, Q8CGP6, O75367, P02281, Q9D2U9 -
189 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 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 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Euchromatin-associated, Ubiquitin B4DIJ7, P61964, Q9UBL3, Q15291, P0CG47, Q9C005 P02281, P84233, P06897, P62799 0.263
190 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 Xenopus laevis 2022 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 O60814, P04908, Q71DI3, P62805 0.571
191 6LTJ EM 3.70 2020-02-12 octamer 1 H3.3 canonical_H4 H2A.X canonical_H2B 601 119 Structure of nucleosome-bound human BAF complex He, S., Wu, Z., Tian, Y., Yu, Z., Yu, J., Wang, X., Li, J., Liu, B., Xu, Y. 10.1126/science.aaz9761 32001526 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4 Chromatin remodelers, SWI/SNF, Cell cycle, Transcription-associated P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785 P02281, P06897, Q6PI79, P62799 0.007
192 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 Xenopus laevis 2010 P02281, P84233, Q6AZJ8, P62799 -
193 7JO9 EM 3.30 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 1:1 cGAS-nucleosome complex Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q. 10.1126/science.abd0609 32913000 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P0C0S8, P62807, Q71DI3, P62805 0.483
194 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
195 9E1V EM 3.10 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassC2 Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.586
196 9E1U EM 3.10 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassC1 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1101/2024.12.31.630910 39803580 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.595
197 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 Xenopus laevis 2022 Serine/threonine-protein kinase VRK1 Nuclear division, Histone PTM writers, Cell cycle, Histone_phosphorylation_H3T3_writer Q99986 P0C0S8, P62807, Q71DI3, P62805 0.56
198 8SVF EM 3.20 2023-08-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 BAP1/ASXL1 bound to the H2AK119Ub Nucleosome Thomas, J.F., Valencia-Sanchez, M.I., Tamburri, S., Gloor, S.L., Rustichelli, S., Godinez-Lopez, V., De Ioannes, P., Lee, R., Abini-Agbomson, S., Gretarsson, K., Burg, J.M., Hickman, A.R., Sun, L., Gopinath, S., Taylor, H.F., Sun, Z.W., Ezell, R.J., Vaidya, A., Meiners, M.J., Cheek, M.A., Rice, W.J., Svetlov, V., Nudler, E., Lu, C., Keogh, M.C., Pasini, D., Armache, K.J. 10.1126/sciadv.adg9832 37556531 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Ubiquitin carboxyl-terminal hydrolase BAP1, Polycomb group protein ASXL1, Ubiquitin Histone_deubiquitination_H2AK119, Polycomb, Transcription-associated, Heterochromatin-associated, Histone PTM erasers, Ubiquitin Q92560, Q8IXJ9, P0CG48 P02281, P84233, P06897, P62799 0.383
199 8QKT X-ray 3.26 2023-10-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 167 Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment Ma, Z., Davey, C.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 P68431, P06899, A0A2Y9FT95, H2QSF5, A0A8C1JQV0 -
200 9B2T EM 2.99 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Haspin bound to nucleosome in position 2 Hicks, C.W., Gliech, C.R., Zhang, X., Rahman, S., Vasquez, S., Holland, A.J., Wolberger, C. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Serine/threonine-protein kinase haspin Q8TF76 P02281, P84233, P06897, P62799 0.502
201 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 Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.267
202 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 Xenopus laevis 2022 O60814, P68431, P04908, P62805 0.107
203 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 Xenopus laevis 2022 Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q96H22 P62807, P49450, Q93077, P62805 0.114
204 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 Xenopus laevis 2022 Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q96H22 P62807, P49450, Q93077, P62805 0.179
205 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 Xenopus laevis 2022 Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q96H22 P62807, P49450, Q93077, P62805 0.559
206 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 Xenopus laevis 2021 Q6DKE3, P02281, P84233, P62799 0.489
207 7K7G EM 4.20 2021-03-31 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601_modified 123 nucleosome and Gal4 complex Guan, R., Lian, T., Zhou, B.R., He, E., Wu, C., Singleton, M., Bai, Y. 10.1038/s41467-021-21985-9 33741944 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2021 Centromere DNA-binding protein complex CBF3 subunit B Nuclear division, CBF3, Centromere-associated, Kinetochore P40969 P02293, P02309, P04911, P61830 0.3
208 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 Xenopus laevis 2021 Isoform 2 of N-lysine methyltransferase KMT5A Histone_methylation_H4K20_writer, Histone PTM writers, Cell cycle, Transcription-associated, Heterochromatin-associated, Nuclear division Q9NQR1 P49450, P06899, P04908, P62805 0.446
209 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 Xenopus laevis 2021 Isoform 2 of N-lysine methyltransferase KMT5A Histone_methylation_H4K20_writer, Histone PTM writers, Cell cycle, Transcription-associated, Heterochromatin-associated, Nuclear division Q9NQR1 P68431, P04908, P06899, P62805 0.514
210 7CCR EM 4.90 2020-10-07 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of the 2:2 cGAS-nucleosome complex Cao, D., Han, X., Fan, X., Xu, R.M., Zhang, X. 10.1038/s41422-020-00422-4 33051594 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 P68431, P04908, P06899, P62805 0.152
211 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 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 Telomere-associated, Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Ubiquitin P0CG48, P38123, P39706, P38827, P43132, Q03323, Q03012 P02281, P84233, P06897, P62799 0.449
212 6UPL EM 7.40 2019-12-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 79 Structure of FACT_subnucleosome complex 2 Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K. 10.1038/s41586-019-1820-0 31775157 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 FACT complex subunit SPT16, FACT complex subunit SSRP1 Histone chaperones, DNA replication, Transcription-associated, DNA repair, FACT Q9Y5B9, Q08945 P62807, P68431, Q93077, P62805 0.173
213 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 Xenopus laevis 2020 Ubiquitin carboxyl-terminal hydrolase 8, Transcription and mRNA export factor SUS1, SAGA-associated factor 11, SAGA-associated factor 73, Polyubiquitin-C Transcription-associated, SAGA, Histone_deubiquitination, Histone PTM erasers, Ubiquitin P50102, Q6WNK7, Q03067, P53165, P0CG48 P02281, P84233, P06897, P62799 0.394
214 6R1U EM 4.36 2019-04-24 octamer 1 canonical_H3,H3.3 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 Xenopus laevis 2019 Lysine-specific histone demethylase 1B, Putative oxidoreductase GLYR1 Histone_methylation_H3K36_reader, Transcription-associated, Euchromatin-associated, Histone PTM readers, Histone PTM erasers, Histone_demethylation_H3K4 Q8NB78, Q49A26 P02281, P84233, P06897, P62799 0.198
215 6QLD EM 4.15 2019-10-02 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 124 Structure of inner kinetochore CCAN-Cenp-A complex Yan, K., Yang, J., Zhang, Z., McLaughlin, S.H., Chang, L., Fasci, D., Ehrenhofer-Murray, A.E., Heck, A.J.R., Barford, D. 10.1038/s41586-019-1609-1 31578520 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2019 Inner kinetochore subunit MIF2, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Inner kinetochore subunit AME1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2 Cell cycle, Centromere-associated, Kinetochore, Nuclear division, CCAN P35201, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P38313, Q12493, Q06162 P02293, P02309, P04911, P02294, P36012 0.328
216 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 Xenopus laevis 2019 Origin recognition complex subunit 1 DNA replication, ORC, Transcription-associated P54784 P02281, P84233, P06897, P62799 -
217 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 Xenopus laevis 2019 P49450, P06899, P04908, P62805 0.482
218 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 Xenopus laevis 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.233
219 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 Xenopus laevis 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 Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P84243, P06899, P04908, P62805 0.149
220 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 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 Euchromatin-associated, RNA polymerases, Transcription-associated P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422 P02281, P84233, P06897, P62799 0.241
221 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 Xenopus laevis 2019 Transcription regulatory protein SNF2 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P02281, P84233, Q6AZJ8, P62799 0.372
222 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 Xenopus laevis 2018 P68431, P04908, P06899, P62805 -
223 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 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 Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Euchromatin-associated, Histone_acetylation_writer Q06337, P80428, P60010, P43572, P53201, P38811, Q08649, P38806, P47128 P02281, P84233, P06897, P62799 0.108
224 7XFH EM 2.90 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 132 Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-3-methyladenine glycosylase DNA repair, DNA modification P29372 P02281, P84233, P06897, P62799 0.515
225 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 Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
226 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 Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.55
227 8VMJ EM 3.10 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K4me3 nucleosome bound to PRC2_AJ119-450 Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 A0A8J1LZU9, Q6AZJ8, Q71DI3, P62805 0.402
228 8T9F EM 2.60 2023-09-06 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 122 Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. 10.1016/j.molcel.2023.07.020 37595555 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P02281, P84233, P0C0S5, P62799 0.516
229 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 Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1 Telomere-associated, Histone PTM writers, Histone_ubiquitination_H2BK123_writer, E3 ubiquitin-protein ligation, Transcription-associated Q07457 P02281, P84233, P06897, P62799 0.535
230 8SNA EM 4.00 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.405
231 8SN6 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.434
232 8SN5 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.41
233 8SN4 EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.439
234 8SMW EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.526
235 8QZ0 EM 3.80 2024-10-02 octamer 1 H3.3 canonical_H4 H2A.X,H2A.Z canonical_H2B 601 113 SWR1-hexasome-dimer complex Jalal, A.S.B., Girvan, P., Chua, E.Y.D., Liu, L., Wang, S., McCormack, E.A., Skehan, M.T., Knight, C.L., Rueda, D.S., Wigley, D.B. 10.1016/j.molcel.2024.08.015 39226902 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Histone H2A.Z-specific chaperone CHZ1, Helicase SWR1, SWR1-complex protein 5, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 INO80, SRCAP (INO80), SWR1 (INO80), Chromatin remodelers, Histone chaperones, Euchromatin-associated, Transcription-associated P40019, Q05471, P38326, Q12509, Q03433, Q03940, Q12464, Q03388 P02293, Q12692, P02309, P04911, P61830 0.293
236 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 Xenopus laevis 2024 Q6ZWY9, P84244, P62806, C0HKE1 0.6
237 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 Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone PTM readers, Transcription factors, Histone_methylation_H3K36_reader, Transcription-associated O75475 P02281, P84233, P06897, P62799 0.548
238 8OF4 EM 2.94 2023-08-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome Bound human SIRT6 (Composite) Smirnova, E., Bignon, E., Schultz, P., Papai, G., Ben Shem, A. 10.7554/eLife.87989 38415718 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P02281, P84233, P06897, P62799 0.446
239 8J90 EM 4.71 2024-07-03 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 111 Cryo-EM structure of DDM1-nucleosome complex Osakabe, A., Takizawa, Y., Horikoshi, N., Hatazawa, S., Negishi, L., Sato, S., Berger, F., Kakutani, T., Kurumizaka, H. 10.1038/s41467-024-49465-w 38992002 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, Q9FJE8, P59259, P59226 0.243
240 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 Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B E3 ubiquitin-protein ligation, Histone PTM writers, Histone_ubiquitination_H2BK120_writer, Transcription-associated Q5VTR2, O75150 P68431, P06899, P0C0S8, P62805 0.532
241 8GPN EM 3.20 2023-02-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 Human menin in complex with H3K79Me2 nucleosome Lin, J., Wu, Y., Tian, G., Yu, D., Yang, E., Lam, W.H., Liu, Z., Jing, Y., Dang, S., Bao, X., Wong, J.W.H., Zhai, Y., Li, X.D. 10.1126/science.adc9318 36795828 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Isoform 2 of Menin Histone_methylation_H3K4_writer, Histone PTM writers, Euchromatin-associated, Transcription-associated O00255 P02281, P84233, P06897, P62799 0.459
242 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., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P06897, P62799 0.575
243 8G57 EM 3.07 2023-04-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Structure of nucleosome-bound Sirtuin 6 deacetylase Chio, U.S., Rechiche, O., Bryll, A.R., Zhu, J., Leith, E.M., Feldman, J.L., Peterson, C.L., Tan, S., Armache, J.P. 10.1126/sciadv.adf7586 37058572 Xenopus laevis Xenopus laevis Homo sapiens Homo sapiens Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P84233, P04908, P06899, P62799 0.493
244 7YI1 EM 2.80 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 Histone PTM writers, NuA4, Transcription-associated, Histone_acetylation_writer, DNA repair Q12432 P02281, P84233, P06897, P62799 0.572
245 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 Xenopus laevis 2022 Myb-like domain-containing protein F1NE16 P68431, P04908, P06899, P62805 0.454
246 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 P68431, P06899, P04908, P07305, P62805 -
247 7XVL X-ray 3.51 2023-05-24 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601_modified 169 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an 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 2023 P68431, P06899, P04908, P07305, P62805 -
248 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 Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
249 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 Xenopus laevis 2017 P68431, P04908, P06899, P62805 -
250 8XBU EM 4.24 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P68431, P04908, P06899, P62805 0.171
251 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 Xenopus laevis 2010 P02281, P84233, P06897, P62799 -
252 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 Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription factors, Transcription-associated P13393, P32773, P32774 P02281, P84233, P06897, P62799 0.49
253 8TXX EM 3.70 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P0CG47 P68431, P04908, P62807, P62805 0.438
254 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 Xenopus laevis 2017 P68431, P04908, P06899, P62805 -
255 9MU5 EM 6.30 2025-02-19 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Structure of a native Drosophila melanogaster hexameric nucleosome Venette-Smith, N.L., Vishwakarma, R.K., Dollinger, R., Schultz, J., Venkatakrishnan, V., Babitzke, P., Anand, G., Gilmour, D.S., Armache, J.-P., Murakami, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2025 P84040, P84051, P02299, P02283 0.206
256 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 Xenopus laevis 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription factors, Transcription-associated P42212, P48431 P68431, P04908, P06899, P62805 0.451
257 7LYB EM 3.28 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Isoform 7 of Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2 D3 Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair, Histone_ubiquitination_H2AK129_writer P38398, Q99728, P61077 P68431, P04908, P06899, P62805 0.458
258 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 Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD3 Histone PTM writers, Histone_methylation_H3K4_writer, Euchromatin-associated, Transcription-associated, Histone_methylation_H3K27_writer Q9BZ95 Q92133, P02281, P06897, P62799 0.542
259 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 Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD2 Histone PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated O96028 Q92133, P02281, P06897, P62799 0.448
260 8OW1 EM 3.70 2023-08-09 hexamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601_modified 153 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Dendooven, T., Zhang, Z., Yang, J., McLaughlin, S.H., Schwab, J., Scheres, S.H.W., Yatskevich, S., Barford, D. 10.1126/sciadv.adg7480 37506202 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2023 Centromere-binding protein 1, Centromere DNA-binding protein complex CBF3 subunit B, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Suppressor of kinetochore protein 1, Inner kinetochore subunit CNN1, Inner kinetochore subunit AME1, Inner kinetochore subunit WIP1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2, Histone H2A.1 CBF3, Cell cycle, Transcription-associated, Centromere-associated, Nuclear division, CCAN, Kinetochore P17106, P40969, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P52286, P43618, P38313, Q2V2P8, Q12493, Q06162, P04911 P02293, P02309, P04911, P36012 0.165
261 8QKV EM 4.70 2024-10-02 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 194 SWR1-nucleosome complex in configuration 2 Girvan, P., Jalal, A.S.B., McCormack, E.A., Skehan, M.T., Knight, C.L., Wigley, D.B., Rueda, D.S. 10.1038/s41586-024-08152-y 39506114 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 INO80, SRCAP (INO80), SWR1 (INO80), Chromatin remodelers, Euchromatin-associated, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02293, P02309, P61830, P04912 0.185
262 8QKU EM 3.80 2024-10-02 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 177 SWR1-nucleosome complex in configuration 1 Girvan, P., Jalal, A.S.B., McCormack, E.A., Skehan, M.T., Knight, C.L., Wigley, D.B., Rueda, D.S. 10.1038/s41586-024-08152-y 39506114 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 INO80, SRCAP (INO80), SWR1 (INO80), Chromatin remodelers, Euchromatin-associated, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02293, P02309, P61830, P04912 0.363
263 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 Xenopus laevis 2013 Regulatory protein SIR3 Transcription-associated P06701 P02281, P84233, P06897, P62799 -
264 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 Xenopus laevis 2022 O60814, P68431, P04908, P62805 0.4
265 5B32 X-ray 2.35 2016-08-03 octamer 1 H3.3 canonical_H4 canonical_H2A,H2A.Z 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 Xenopus laevis 2016 P84243, P06899, P0C0S5, P04908, P62805 -
266 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 Xenopus laevis 2017 Q9D2U9, P68433, P62806, C0HKE1 -
267 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 Xenopus laevis 2022 O60814, P68431, P04908, P62805 0.076
268 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 Xenopus laevis 2010 P02281, P84233, Q6AZJ8, P62799 -
269 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
270 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 Xenopus laevis 2022 P02281, P84233, P06897, P62799 -
271 7C0M EM 3.90 2020-09-16 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Human cGAS-nucleosome complex Kujirai, T., Zierhut, C., Takizawa, Y., Kim, R., Negishi, L., Uruma, N., Hirai, S., Funabiki, H., Kurumizaka, H. 10.1126/science.abd0237 32912999 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 P68431, P04908, P06899, P62805 0.225
272 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 Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Telomere-associated, Histone PTM writers, Histone_methylation_H3K79_writer Q04089, P0CG48 P02281, P84233, P06897, P62799 0.489
273 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 Xenopus laevis 2006 latent nuclear antigen Viral Q9DUM3 P02281, P84233, P06897, P62799 -
274 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 Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.167
275 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 Xenopus laevis 2017 P68431, P04908, P06899, P62805 -
276 8JCC EM 3.42 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.W 601 116 Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Ding, D., Pang, M.Y.H., Deng, M., Nguyen, T.T., Liu, Y., Sun, X., Xu, Z., Zhang, Y., Zhai, Y., Yan, Y., Ishibashi, T. 10.1093/nar/gkae825 39329259 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P68431, P04908, Q7Z2G1, P62805 0.398
277 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 Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
278 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
279 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 Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
280 4KUD X-ray 3.20 2013-08-07 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B alphasat_146 146 Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle Yang, D., Fang, Q., Wang, M., Ren, R., Wang, H., He, M., Sun, Y., Yang, N., Xu, R.M. 10.1038/nsmb.2637 23934152 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2013 Regulatory protein SIR3 Transcription-associated P06701 P02293, P02309, P61830, P04912 -
281 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 Xenopus laevis 2013 P02281, P84233, P06897, P62799 -
282 3WA9 X-ray 3.07 2013-12-18 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The nucleosome containing human H2A.Z.1 Horikoshi, N., Sato, K., Shimada, K., Arimura, Y., Osakabe, A., Tachiwana, H., Hayashi-Takanaka, Y., Iwasaki, W., Kagawa, W., Harata, M., Kimura, H., Kurumizaka, H. 10.1107/S090744491302252X 24311584 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P68431, P06899, P0C0S5, P62805 -
283 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 Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
284 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 Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
285 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
286 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 Xenopus laevis 2011 P04908, P06899, Q71DI3, P62805 -
287 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 Xenopus laevis 2010 P68431, P04908, P06899, P62805 -
288 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 Xenopus laevis 2016 C-terminal domain of Regulatory protein IE1 Viral P03169 P02281, P84233, P06897, P62799 -
289 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 Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.452
290 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 Xenopus laevis 2023 Maltodextrin-binding protein,POU domain, class 5, transcription factor 1, Single-chain variable fragment P0AEX9 Q16777, P68431, Q16778, P62805 0.531
291 6HTS EM 4.80 2018-11-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Cryo-EM structure of the human INO80 complex bound to nucleosome Ayala, R., Willhoft, O., Aramayo, R.J., Wilkinson, M., McCormack, E.A., Ocloo, L., Wigley, D.B., Zhang, X. 10.1038/s41586-018-0021-6 29643506 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit B INO80, Chromatin remodelers, DNA replication, Cell cycle, Transcription-associated, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q9C086 P68431, P04908, P06899, P62805 0.181
292 8SN3 EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P61077, P0CG47 P68431, P04908, P06899, P62805 0.429
293 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 Xenopus laevis 2007 P02281, P84233, P06897, P62799 -
294 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 Xenopus laevis 2018 P68431, P04908, P06899, P62805 -
295 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 Xenopus laevis 2003 P02281, P06897, P02302, P62799 -
296 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 Xenopus laevis 2003 P02281, P06897, P02302, P62799 -
297 8JCD EM 3.14 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.W 601 120 Human H2BFWTH100R nucleosome with 601 DNA Ding, D., Pang, M.Y.H., Deng, M., Nguyen, T.T., Liu, Y., Sun, X., Xu, Z., Zhang, Y., Zhai, Y., Yan, Y., Ishibashi, T. 10.1093/nar/gkae825 39329259 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P68431, P04908, Q7Z2G1, P62805 0.445
298 8XBT EM 4.12 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P68431, P04908, P06899, P62805 0.199
299 8Y3E EM 5.32 2025-01-29 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Cryo-EM structure of the overlapping di-nucleosome (open form) Shimizu, M., Tanaka, H., Nishimura, M., Sato, N., Nozawa, K., Ehara, H., Sekine, S.I., Morishima, K., Inoue, R., Takizawa, Y., Kurumizaka, H., Sugiyama, M. 10.1093/pnasnexus/pgae484 39539301 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P68431, P04908, P06899, P62805 -
300 8Q3M X-ray 2.50 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Batchelor, L.K., De Falco, L., Dyson, P.J., Davey, C.A. 10.1039/d4ra01617c 38495982 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Kaposi sarcoma associated herpesvirus LANA peptide with a methionine to ornithine substitution Viral Q9QR71 O60814, P68431, P04908, P62805 -
301 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 Xenopus laevis 2022 Isoform 2 of Transcription activator BRG1 Chromatin remodelers, SWI/SNF, Transcription-associated P51532 P02281, P84233, P06897, P62799 0.549
302 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 P10412, Q71DI3, P04908, P62805, O60814 0.264
303 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 P10412, Q71DI3, P04908, P62805, O60814 0.268
304 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 Xenopus laevis 2022 O60814, P04908, Q71DI3, P62805 0.221
305 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 P10412, Q71DI3, P04908, P62805, O60814 0.084
306 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 P10412, Q71DI3, P04908, P62805, O60814 0.27
307 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 P10412, Q71DI3, P04908, P62805, O60814 0.351
308 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 P10412, Q71DI3, P04908, P62805, O60814 0.101
309 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 P10412, Q71DI3, P04908, P62805, O60814 0.267
310 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 Xenopus laevis 2021 P02281, P84233, P06897, P62799 0.587
311 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 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 CHD, Chromatin remodelers, RNA polymerases, Transcription factors, Euchromatin-associated, Transcription-associated, Heterochromatin-associated, SPT4-SPT5 complex, Centromere-associated P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P32657, P32914, P27692 P02281, P84233, P06897, P62799 0.444
312 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 Xenopus laevis 2021 P02281, P84233, Q6AZJ8, P62799 0.494
313 7CCQ EM 3.80 2020-10-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of the 1:1 cGAS-nucleosome complex Cao, D., Han, X., Fan, X., Xu, R.M., Zhang, X. 10.1038/s41422-020-00422-4 33051594 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 P68431, P04908, P06899, P62805 0.371
314 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 Xenopus laevis 2020 P02281, P84233, P06897, P62799 0.508
315 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 Xenopus laevis 2020 Transcription factor SOX-2 Transcription factors, Transcription-associated P48431 O60814, P04908, Q71DI3, P62805 0.217
316 6R90 EM 4.50 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, UV-DDB complex, DCX complex Q16531, Q92466 P68431, P04908, P06899, P62805 0.278
317 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 Xenopus laevis Xenopus laevis 2019 Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone-lysine N-methyltransferase Histone PTM writers, Histone_methylation_H3K36_writer, Euchromatin-associated, Transcription-associated, Ubiquitin P0CH09, G0S676 P02281, P0CH09, P02302, P62799 0.261
318 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 Xenopus laevis Xenopus laevis 2019 P02281, P0CH09, P02302, P62799 0.49
319 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 Xenopus laevis 2019 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164 P02281, P84233, P06897, P62799 0.26
320 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 Xenopus laevis 2019 P84040, P84051, P02299, P02283 0.409
321 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 Xenopus laevis 2019 P68431, P04908, P06899, P62805 0.085
322 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 Xenopus laevis 2019 P68431, P04908, P06899, P62805 -
323 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 Xenopus laevis 2022 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 P62807, P49450, Q93077, P62805 0.573
324 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 Xenopus laevis 2023 ISWI one complex protein 3, ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P43596, P38144 P02281, P84233, P06897, P62799 0.192
325 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 Xenopus laevis 2017 P02281, P84233, Q6AZJ8, P62799 0.167
326 7YRG EM 4.20 2023-12-13 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 histone methyltransferase Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. 10.1016/j.molcel.2023.07.001 37536340 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P02281, P84233, P0C0S5, P62799 0.227
327 8Q36 X-ray 2.60 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Batchelor, L.K., De Falco, L., Dyson, P.J., Davey, C.A. 10.1039/d4ra01617c 38495982 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 GAG structural protein Viral, DNA integration P14349 O60814, P68431, P04908, P62805 -
328 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 Xenopus laevis 2024 RING1 and YY1-binding protein, Ubiquitin-40S ribosomal protein S27a (Fragment) Polycomb, Histone_ubiquitination_reader, Transcription-associated, Histone PTM readers, Heterochromatin-associated, Ubiquitin Q8N488, P0CG47 P84040, P84051, P02299, P02283 0.465
329 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 Xenopus laevis 2024 Nuclear receptor subfamily 5 group A member 2 Transcription factors, Transcription-associated O00482 Q6ZWY9, P84244, P62806, C0HKE3 0.572
330 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 Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone PTM readers, Transcription factors, Histone_methylation_H3K36_reader, Transcription-associated O75475 P02281, P84233, P06897, P62799 0.521
331 8OX1 EM 2.70 2023-08-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 Structure of TRF1core in complex with telomeric nucleosome Hu, H., van Roon, A.M., Ghanim, G.E., Ahsan, B., Oluwole, A.O., Peak-Chew, S.Y., Robinson, C.V., Nguyen, T.H.D. 10.1126/sciadv.adi4148 37624885 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Telomeric repeat-binding factor 1 DNA repair, Shelterin, Cell cycle, Telomere-associated P54274 P62807, P68431, Q93077, P62805 0.579
332 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 Xenopus laevis 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 INO80, Chromatin remodelers G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62807, P68431, Q93077, P62805 0.554
333 8KD2 EM 3.02 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 174 Rpd3S in complex with 187bp nucleosome Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.35
334 8KCY EM 2.80 2025-03-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 193 Structure of nucleosome complexed with two DEK molecules Kujirai, T., Echigoya, K., Kishi, Y., Saeki, M., Ito, T., Kato, J., Negishi, L., Kimura, H., Masumoto, H., Takizawa, Y., Gotoh, Y., Kurumizaka, H. 10.1038/s41594-025-01493-w 39984731 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Protein DEK P35659 P68431, P04908, P06899, P62805 0.479
335 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 Xenopus laevis 2023 P84243, P06899, P04908, P62805 0.655
336 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 Xenopus laevis 2023 P68431, P04908, P06899, P62805 0.453
337 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 Xenopus laevis 2023 P68431, P04908, P06899, P62805 0.569
338 8HXZ EM 3.40 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Cryo-EM structure of Eaf3 CHD in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin modification-related protein EAF3 Histone PTM writers, NuA4, Transcription-associated, Histone_acetylation_writer, DNA repair Q12432 P02281, P84233, P06897, P62799 0.326
339 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 Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P16403, P68431, P06899, P04908, P62805 0.16
340 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 Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P16403, P68431, P06899, P04908, P62805 0.228
341 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 Xenopus laevis 2023 P68431, P06899, P0C0S8, P62805 0.588
342 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 Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.356
343 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 Xenopus laevis 2023 P02281, P02302, P62799, Q6AZJ8 0.387
344 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 Xenopus laevis 2023 Q4GYX7, Q57Z31, Q389T1, Q57YA3 0.439
345 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 Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone PTM readers, Transcription factors, Histone_methylation_H3K36_reader, Transcription-associated O75475 P02281, P84233, P06897, P62799 0.304
346 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 Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone PTM readers, Transcription factors, Histone_methylation_H3K36_reader, Transcription-associated O75475 P02281, P84233, P06897, P62799 0.392
347 8AAG EM 10.00 2022-12-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0-B 601L 185 H1-bound palindromic nucleosome, state 1 Louro, J.A., Boopathi, R., Beinsteiner, B., Mohideen Patel, A.K., Cheng, T.C., Angelov, D., Hamiche, A., Bendar, J., Kale, S., Klaholz, B.P., Dimitrov, S. 10.1016/j.str.2022.12.005 36610392 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P22844, P06897, Q71DI3, P62805, P02281 -
348 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 Xenopus laevis 2018 Chromo domain-containing protein 1 CHD, Chromatin remodelers, Transcription-associated P32657 Q92133, A0A1L8G0X3, P06897, P62799 0.095
349 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 Xenopus laevis 2017 P02281, P84233, Q6AZJ8, P62799 0.198
350 9DDE EM 3.20 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 162 ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Homo sapiens 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, RING1 and YY1-binding protein, Ubiquitin Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer, Histone PTM readers, Histone_ubiquitination_reader, Ubiquitin P35226, Q99496, Q8N488, P0CG48 P84233, P06897, P10412, P62799, P02281 0.456
351 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 Xenopus laevis 2022 Ino80 ATPase, PAPA-1 domain-containing protein INO80, Chromatin remodelers G0RY01 P0C0S8, P62807, Q71DI3, P62805 0.474
352 8BYQ EM 4.10 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta RNA polymerases, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated, DNA repair P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P02281, P84233, P06897, P62799 0.187
353 8OW0 EM 3.40 2023-08-09 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601_modified 121 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Dendooven, T., Zhang, Z., Yang, J., McLaughlin, S.H., Schwab, J., Scheres, S.H.W., Yatskevich, S., Barford, D. 10.1126/sciadv.adg7480 37506202 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2023 Centromere-binding protein 1, Inner kinetochore subunit MCM16, Inner kinetochore subunit CTF3, Inner kinetochore subunit MCM22, Inner kinetochore subunit IML3, Inner kinetochore subunit CHL4, Inner kinetochore subunit MCM21, Inner kinetochore subunit CTF19, Inner kinetochore subunit OKP1, Inner kinetochore subunit CNN1, Inner kinetochore subunit AME1, Inner kinetochore subunit WIP1, Inner kinetochore subunit NKP1, Inner kinetochore subunit NKP2 Cell cycle, Transcription-associated, Centromere-associated, Nuclear division, CCAN, Kinetochore P17106, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P43618, P38313, Q2V2P8, Q12493, Q06162 P02293, P02309, P04911, P36012 0.2
354 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 Xenopus laevis 2023 P68431, P04908, P06899, P62805 0.724
355 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 P10412, Q71DI3, P04908, P62805, O60814 0.217
356 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 Xenopus laevis 2020 DNA (cytosine-5)-methyltransferase 3A, DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 P02281, P84233, P06897, P62799 0.403
357 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 Xenopus laevis 2018 P68431, P04908, P06899, P62805 -
358 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 Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD3 Histone PTM writers, Histone_methylation_H3K4_writer, Euchromatin-associated, Transcription-associated, Histone_methylation_H3K27_writer Q9BZ95 Q92133, P02281, P06897, P62799 0.507
359 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 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 PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, O00267 P02281, P84233, Q6AZJ8, P62799 0.344
360 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 Xenopus laevis 2011 P84243, P06899, P04908, P62805 -
361 8RBX EM 4.10 2024-02-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 161 Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Fianu, I., Ochmann, M., Walshe, J.L., Dybkov, O., Cruz, J.N., Urlaub, H., Cramer, P. 10.1038/s41586-024-07269-4 38570683 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 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 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-a, RNA polymerase II subunit K, Transcription elongation factor SPT5, Integrator complex subunit 1, Integrator complex subunit 2, Integrator complex subunit 4, Integrator complex subunit 5, Integrator complex subunit 6, Integrator complex subunit 7, Integrator complex subunit 8, Integrator complex subunit 9, Integrator complex subunit 10, Integrator complex subunit 11, Integrator complex subunit 13, Integrator complex subunit 14, Integrator complex subunit 15, Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform, Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, DSS1, Negative elongation factor A, NELF-B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B, Negative elongation factor C/D RNA polymerases, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, O00267, Q8N201, Q9H0H0, Q96HW7, Q6P9B9, Q9UL03, Q9NVH2, Q75QN2, Q9NV88, Q9NVR2, Q5TA45, Q9NVM9, Q96SY0, Q96N11, P30153, P67775, Q9H3P2, Q8WX92, Q8IXH7 Q6NXT2, P06899, P0C0S8, P62805 0.037
362 9J0P EM 3.30 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 191 Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, 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, RPB12, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, Transcription factors, RNA polymerases, Transcription-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P84243, P06899, P04908, P62805 0.311
363 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., Sui, F., Gu, F., Li, W., Yu, Z., Wang, Q., He, S., Wang, L., Xu, Y. 10.1038/s41421-023-00640-1 38331872 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 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 INO80, SRCAP (INO80), Chromatin remodelers, Histone_acetylation_reader, Histone chaperones, Cell cycle, Euchromatin-associated, Transcription-associated, Histone PTM readers Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62807, P68431, Q93077, P62805 0.292
364 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 Xenopus laevis 2023 Single-chain variable fragment Q16777, P68431, Q16778, P62805 0.568
365 8HAH EM 3.90 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 164 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.159
366 9MU4 EM 3.29 2025-02-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Structure of a native Drosophila melanogaster octameric nucleosome Venette-Smith, N.L., Vishwakarma, R.K., Dollinger, R., Schultz, J., Venkatakrishnan, V., Babitzke, P., Anand, G., Gilmour, D.S., Armache, J.-P., Murakami, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2025 P84040, P84051, P02299, P02283 0.442
367 9J8M EM 3.82 2025-02-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 184 Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Horikoshi, N., Miyake, R., Sogawa-Fujiwara, C., Ogasawara, M., Takizawa, Y., Kurumizaka, H. 10.1038/s41467-025-56823-9 39929866 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Barrier-to-autointegration factor, Lamin-A/C O75531, H0YAB0 P68431, P04908, P06899, P62805 0.345
368 9IPU EM 4.30 2024-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601L 170 cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Shi, Q., Deng, Z., Zhang, L., Tong, Z., Li, J.B., Chu, G.C., Ai, H., Liu, L. 10.1002/anie.202413651 39363740 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair P61077, Q8IYW5, P62979 Q71DI3, P04908, P07305, P62805, O60814 0.237
369 9GD2 EM 4.20 2024-09-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 237 Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp. Engeholm, M., Roske, J.J., Oberbeckmann, E., Dienemann, C., Lidschreiber, M., Cramer, P., Farnung, L. 10.1016/j.molcel.2024.08.022 39270644 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Chromo domain-containing protein 1 CHD, Chromatin remodelers, Transcription-associated P32657 P02281, P84233, P06897, P62799 0.295
370 9GD1 EM 4.00 2024-09-18 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 259 Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Engeholm, M., Roske, J.J., Oberbeckmann, E., Dienemann, C., Lidschreiber, M., Cramer, P., Farnung, L. 10.1016/j.molcel.2024.08.022 39270644 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Chromo domain-containing protein 1 CHD, Chromatin remodelers, Transcription-associated P32657 P02281, P84233, P06897, P62799 0.332
371 9FBW EM 4.40 2024-10-02 hexamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 112 SWR1 lacking Swc5 subunit in complex with hexasome Jalal, A.S.B., Girvan, P., Chua, E.Y.D., Liu, L., Wang, S., McCormack, E.A., Skehan, M.T., Knight, C.L., Rueda, D.S., Wigley, D.B. 10.1016/j.molcel.2024.08.015 39226902 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, Vacuolar protein sorting-associated protein 72 INO80, SRCAP (INO80), SWR1 (INO80), Chromatin remodelers, Euchromatin-associated, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02293, P02309, P04911, P61830 0.193
372 9EH0 EM 3.60 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 181 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 P02281, P06897, A0A310TTQ1, P62799 0.24
373 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 Xenopus laevis 2021 CENP-C, Maltodextrin-binding protein,Centromere protein N Nuclear division, Centromere-associated, Kinetochore O57392, P0AEX9 P62805, P04908, Q16778, P84229 0.387
374 8TB9 EM 4.00 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.0 601 193 PRC2-J119-450 monomer bound to H1-nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Homo sapiens 2024 Protein Jumonji, Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Histone PTM writers, Histone chaperones, Polycomb, Transcription-associated, Heterochromatin-associated, Histone_methylation_H3K27_writer, Histone PTM erasers Q92833, Q15022, Q15910, O75530, Q09028, Q6ZN18 P84233, P06897, P62799, P07305, P02281 0.261
375 5Z30 X-ray 2.45 2018-07-18 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C 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 Xenopus laevis 2018 P68431, P06899, P0C0S5, P62805 -
376 9GD0 EM 2.80 2024-09-18 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Engeholm, M., Roske, J.J., Oberbeckmann, E., Dienemann, C., Lidschreiber, M., Cramer, P., Farnung, L. 10.1016/j.molcel.2024.08.022 39270644 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 P02281, P84233, P06897, P62799 0.528
377 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 P02299, P02259, P84040, P84051, P02283 -
378 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 Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
379 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 Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
380 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 Xenopus laevis 2017 P04908, A0A1X8XL64, P06899, P62805 -
381 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 Xenopus laevis 2017 LANA peptide Viral Q9QR71 P68431, P04908, P06899, P62805 -
382 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 Xenopus laevis 2017 P20671, P68431, Q96A08, P62805 -
383 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 Xenopus laevis 2016 P04908, P06899, Q71DI3, P62805 -
384 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
385 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 Xenopus laevis 2014 CENP-C Nuclear division, Centromere-associated, Kinetochore Q66LH7 P84040, P84051, P02299, P02283 -
386 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 Xenopus laevis 2015 P68431, P04908, P70696, P62805 -
387 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 tropicalis Xenopus laevis 2008 P84233, P06897, Q28D68, P62799 -
388 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
389 1ID3 X-ray 3.10 2001-09-28 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B alphasat_146 146 CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS White, C.L., Suto, R.K., Luger, K. 10.1093/emboj/20.18.5207 11566884 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2001 P02294, P02309, P04911, P61830 -
390 7XZX EM 4.53 2022-10-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 171 Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Cellular tumor antigen p53 DNA repair, Transcription factors, Cell cycle, Transcription-associated P04637 P68431, P04908, P06899, P62805 0.146
391 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 Xenopus laevis 2017 P68431, P04908, P06899, P62805 -
392 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 Xenopus laevis 2020 Lysine-specific histone demethylase 1A, REST corepressor 1 Histone_demethylation_H3K9, Histone_demethylation_H3K4, Histone PTM erasers, Transcription-associated O60341, Q9UKL0 P02281, P84233, P06897, P62799 -
393 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 Xenopus laevis 2022 WD repeat-containing protein 5, Retinoblastoma-binding protein 5, Polyubiquitin-B Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Transcription-associated, Euchromatin-associated, Ubiquitin P61964, Q15291, P0CG47 P02281, P06897, P02302, P62799 0.237
394 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 Xenopus laevis 2022 SWI/SNF chromatin-remodeling complex subunit SNF5 Chromatin remodelers, SWI/SNF, Transcription-associated P18480 P02281, P84233, P06897, P62799 0.513
395 8A3Y EM 3.30 2024-07-31 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 138 Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Farnung, L., Ochmann, M., Garg, G., Vos, S.M., Cramer, P. 10.1016/j.molcel.2022.06.027 35858621 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, SPT6, RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein LEO1, RNA polymerase-associated protein RTF1 homolog, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q6PD62, Q92541, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A8J1LZU9, P84233, Q6AZJ8, P62799 0.231
396 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 Xenopus laevis 2020 P02281, P49450, P06897, P62799 -
397 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 Xenopus laevis 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription factors, Transcription-associated O08785, Q9WTL8 P68431, P04908, P06899, P62805 0.177
398 8TXW EM 3.60 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P0CG47 P68431, P04908, P62807, P62805 0.455
399 8VO0 EM 3.30 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 P02281, Q6AZJ8, Q71DI3, P62805 0.258
400 8VOB EM 3.10 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis 2025 P0C0S8, P02281, Q71DI3, P62805 0.375
401 8U5H EM 3.23 2024-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome Chen, X., Guo, Y., Zhao, T., Lu, J., Fang, J., Wang, Y., Wang, G.G., Song, J. 10.1038/s41467-024-50526-3 39043678 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA (cytosine-5)-methyltransferase 3A, Ubiquitin Ubiquitin, DNA modification Q9Y6K1, P0CG48 P02281, P06897, P02302, P62799 0.443
402 8SN1 EM 3.30 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.526
403 8SMZ EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.535
404 8SMX EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.549
405 8Q15 EM 3.60 2025-02-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 119 CryoEM structure of canonical rice nucleosome core particle Gandhivel, V.H., Sotelo-Parrilla, P., Raju, S., Jha, S., Gireesh, A., Harshith, C.Y., Gut, F., Vinothkumar, K.R., Berger, F., Jeyaprakash, A.A., Shivaprasad, P.V. 10.1038/s41477-025-01974-2 40200022 Oryza Oryza Oryza Oryza Xenopus laevis 2025 A2WKP5, None, A2YMC6, A2Y533 0.401
406 8KE0 EM 4.00 2025-03-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.2 601L 183 Structure of H1.2 bound to the nucleosome Kujirai, T., Echigoya, K., Kishi, Y., Saeki, M., Ito, T., Kato, J., Negishi, L., Kimura, H., Masumoto, H., Takizawa, Y., Gotoh, Y., Kurumizaka, H. 10.1038/s41594-025-01493-w 39984731 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2025 P16403, P68431, P06899, P04908, P62805 0.352
407 8KD7 EM 3.09 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.324
408 8JNE EM 4.68 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P68431, P04908, P06899, P62805 0.13
409 8JHF EM 3.68 2023-11-15 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 160 Native SUV420H1 bound to 167-bp nucleosome Lin, F., Zhang, R., Shao, W., Lei, C., Ma, M., Zhang, Y., Wen, Z., Li, W. 10.1038/s41421-023-00620-5 38052811 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 O60814, P68431, P0C0S5, P62805 0.433
410 8J92 EM 2.90 2024-07-03 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 149 Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W Osakabe, A., Takizawa, Y., Horikoshi, N., Hatazawa, S., Negishi, L., Sato, S., Berger, F., Kakutani, T., Kurumizaka, H. 10.1038/s41467-024-49465-w 38992002 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2024 O23629, Q9FJE8, P59259, P59226 0.53
411 8J6T EM 6.60 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 92 Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B CAF-1, DNA repair, DNA replication, Histone chaperones Q13111, Q13112 P68431, P62805 0.166
412 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 Xenopus laevis 2023 Protein SSX2, Polyubiquitin-B (Fragment) Histone_ubiquitination_H2AK119_reader, Histone PTM readers, Ubiquitin, Transcription-associated Q16385, P0CG47 O60814, P04908, Q71DI3, P62805 0.47
413 8HE5 EM 6.95 2023-07-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, DNA repair protein RNA polymerases, Transcription factors, Euchromatin-associated, Transcription-associated, DNA repair C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R198 P68431, P04908, P06899, P62805 0.105
414 8GRQ EM 3.87 2023-04-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L. 10.1016/j.chempr.2023.01.012 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Breast cancer type 1 susceptibility protein, BRCA1-associated RING domain protein 1, Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair, Histone_ubiquitination_H2AK129_writer P38398, Q99728, P61077 O60814, P04908, Q71DI3, P62805 0.352
415 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 Xenopus laevis Xenopus laevis Xenopus laevis 2023 P02281, P84233, Q6AZJ8, P62799 0.606
416 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 Xenopus laevis 2023 Single-chain variable fragment, Transcription factor PU.1 Euchromatin-associated, Transcription factors, Transcription-associated P17433 Q16777, P68431, Q16778, P62805 0.509
417 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 Xenopus laevis 2023 Single-chain variable fragment Q16777, P68431, Q16778, P62805 0.531
418 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 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 Euchromatin-associated, Transcription factors, RNA polymerases, Transcription-associated A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, I3LJZ9, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657 P02281, P84233, P06897, P62799 0.244
419 7ZI4 EM 3.20 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Vance, N.R., Ayala, R., Willhoft, O., Tvardovskiy, A., McCormack, E.A., Bartke, T., Zhang, X., Wigley, D.B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 RuvB-like 1, RuvB-like 2, Chromatin-remodeling ATPase INO80, Actin-related protein 5, INO80 complex subunit C, INO80 complex subunit B INO80, Chromatin remodelers, DNA replication, Cell cycle, Transcription-associated, DNA repair Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, Q6PI98, Q9C086 P68431, P04908, P06899, P62805 0.462
420 7XSX EM 3.80 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 108 RNA polymerase II elongation complex transcribing a nucleosome (EC49) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated, DNA repair, FACT C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P84243, P06899, P04908, P62805 0.227
421 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 Xenopus laevis 2022 O60814, P68431, P04908, P62805 0.558
422 7X58 EM 3.93 2022-11-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 121 Cryo-EM structure of human subnucleosome (open form) Nozawa, K., Takizawa, Y., Pierrakeas, L., Sogawa-Fujiwara, C., Saikusa, K., Akashi, S., Luk, E., Kurumizaka, H. 10.1073/pnas.2206542119 36322721 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2022 P68431, P62805 0.35
423 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 Xenopus laevis 2023 Single-chain variable fragment Q16777, P68431, Q16778, P62805 0.559
424 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 Xenopus laevis 2023 GTP-binding nuclear protein Ran, Regulator of chromosome condensation Cell cycle P62826, P18754 P84040, P84051, P02299, P02283 0.609
425 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 Xenopus laevis 2022 O60814, P68431, P04908, P62805 0.093
426 8V25 EM 3.32 2024-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2BK120ub-modified nucleosome ubiquitin position 1 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P06897, P62799 0.519
427 9JNZ EM 3.00 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in Apo state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.493
428 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 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 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated, Ubiquitin Q03164, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.461
429 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 Xenopus laevis 2023 ScFv, Transcription factor PU.1 Euchromatin-associated, Transcription factors, Transcription-associated P17433 Q16777, P68431, Q16778, P62805 0.31
430 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 Xenopus laevis 2010 P02281, P84233, Q6AZJ8, P62799 -
431 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 Xenopus laevis 2005 P02281, P84233, P06897, P62799 -
432 7W9V EM 3.95 2022-07-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L., Kutateladze, T.G., Kurumizaka, H. 10.1016/j.isci.2022.104563 35754730 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.307
433 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 Xenopus laevis 2023 E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B E3 ubiquitin-protein ligation, Histone PTM writers, Histone_ubiquitination_H2BK120_writer, Transcription-associated Q5VTR2, O75150 P68431, P06899, P0C0S8, P62805 0.532
434 9DWK EM 4.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 105 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5 Weaver, T.M., Ryan, B.J., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta P06746 P0C0S8, P62807, Q71DI3, P62805 0.297
435 9DWJ EM 3.40 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 106 Nucleosome containing a 1-nt gap at SHL-3.5 Weaver, T.M., Ryan, B.J., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P0C0S8, P62807, Q71DI3, P62805 0.453
436 9DWG EM 3.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite) Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta P06746 P0C0S8, P62807, Q71DI3, P62805 0.364
437 9B3P EM 3.00 2024-06-12 octamer 1 H3.3 canonical_H4 H2A.Z canonical_H2B 601 128 The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome Jung, H., Sokolova, V., Lee, G., Stevens, V.R., Tan, D. 10.3390/epigenomes8020021 38920622 Homo sapiens Xenopus laevis Mus musculus Xenopus laevis Xenopus laevis 2024 P02281, P84243, P0C0S6, P62799 0.455
438 8YNY EM 4.52 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 137 Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Nagamura, R., Kujirai, T., Kato, J., Shuto, Y., Kusakizako, T., Hirano, H., Endo, M., Toki, S., Saika, H., Kurumizaka, H., Nureki, O. 10.1038/s41467-024-54768-z 39737984 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 CRISPR-associated endonuclease Cas9/Csn1 Q99ZW2 P68431, P04908, P06899, P62805 0.218
439 8YBK EM 2.69 2024-07-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 114 Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Kimura, T., Hirai, S., Kujirai, T., Fujita, R., Ogasawara, M., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1111/gtc.13143 38972377 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P68431, P04908, P06899, P62805 0.598
440 8X7I EM 3.27 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Ai, H., Tong, Z., Deng, Z., Shi, Q., Tao, S., Liang, J., Sun, M., Wu, X., Zheng, Q., Liang, L., Li, J.B., Gao, S., Tian, C., Liu, L., Pan, M. 10.1101/2024.01.02.573964 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Ubiquitin-conjugating enzyme E2 D3, E3 ubiquitin-protein ligase RNF168, Ubiquitin Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, Transcription-associated, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair P61077, Q8IYW5, P62979 O60814, P04908, Q71DI3, P62805 0.443
441 8X32 EM 4.40 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ Complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.114
442 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 Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59259, P59226, Q9LD28 0.394
443 8W9E EM 3.60 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Wang, C., Chu, C., Guo, Z., Zhan, X. 10.1126/sciadv.adk7678 38598631 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 O60814, P68431, P04908, P62805 0.188
444 8VX6 EM 3.20 2024-10-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Human OGG1 bound at the nucleosomal DNA entry site You, Q., Feng, X., Cai, Y., Baylin, S.B., Li, H. 10.1038/s42003-024-06919-7 39341999 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 N-glycosylase/DNA lyase DNA repair, DNA modification O15527 P02281, P84233, P06897, P62799 0.424
445 8VX5 EM 3.30 2024-10-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Nucleosome core particle containing an 8-oxoG damage site You, Q., Feng, X., Cai, Y., Baylin, S.B., Li, H. 10.1038/s42003-024-06919-7 39341999 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 P02281, P84233, P06897, P62799 0.493
446 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 Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.53
447 8V26 EM 3.33 2024-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 H2BK120ub-modified nucleosome ubiquitin position 2 Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P06897, P62799 0.515
448 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 Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.137
449 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 Xenopus laevis 2022 O60814, P68431, P04908, P62805 0.459
450 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 Xenopus laevis 2023 Myc proto-oncogene protein, Protein max Transcription factors, Transcription-associated P01106, P61244 P68431, P04908, P06899, P62805 0.411
451 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 Xenopus laevis 2010 P04908, Q16695, P06899, P62805 -
452 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 Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
453 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 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 Chromatin remodelers, PBAF (SWI/SNF), Cell cycle, SWI/SNF, Transcription-associated P51532, O96019, P60709, Q68CP9, Q8WUB8, Q9NPI1, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q86U86 P02281, P84233, P06897, P62799 0.315
454 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 Xenopus laevis 2000 P0C1H5, P02263, P62801, P84229 -
455 6Y5E EM 3.15 2020-09-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Pathare, G.R., Decout, A., Gluck, S., Cavadini, S., Makasheva, K., Hovius, R., Kempf, G., Weiss, J., Kozicka, Z., Guey, B., Melenec, P., Fierz, B., Thoma, N.H., Ablasser, A. 10.1038/s41586-020-2750-6 32911482 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 Q16777, O60814, Q71DI3, P62805 0.43
456 8QZM EM 3.10 2024-10-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome Wapenaar, H., Clifford, G., Rolls, W., Pasquier, M., Burdett, H., Zhang, Y., Deak, G., Zou, J., Spanos, C., Taylor, M.R.D., Mills, J., Watson, J.A., Kumar, D., Clark, R., Das, A., Valsakumar, D., Bramham, J., Voigt, P., Sproul, D., Wilson, M.D. 10.1038/s44319-024-00306-3 39528729 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA (cytosine-5)-methyltransferase 3A DNA modification Q9Y6K1 A0A7K7T3V7, P62807, P0C0S8, P62805 0.506
457 7XZZ EM 4.07 2022-10-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Cryo-EM structure of the nucleosome in complex with p53 Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Cellular tumor antigen p53 DNA repair, Transcription factors, Cell cycle, Transcription-associated P04637 P68431, P04908, P06899, P62805 0.192
458 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
459 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 Xenopus laevis 2023 Green fluorescent protein,POU domain, class 5, transcription factor 1, Myc proto-oncogene protein, Protein max Transcription factors, Transcription-associated P42212, P01106, P61244 P68431, P04908, P06899, P62805 0.404
460 1F66 X-ray 2.60 2000-11-27 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z Suto, R.K., Clarkson, M.J., Tremethick, D.J., Luger, K. 10.1038/81971 11101893 Xenopus laevis Mus musculus Homo sapiens Xenopus laevis Xenopus laevis 2000 P02281, P84233, P62806, P0C0S5 -
461 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 Xenopus laevis 2023 P62807, P68431, Q93077, P62805 0.525
462 9JNU EM 2.50 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.566
463 7MBM EM 4.76 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 Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.198
464 6L49 EM 18.90 2019-12-04 octamer, octamer, octamer 3 canonical_H3,cenH3 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 Xenopus laevis 2019 P68431, P06899, P49450, P04908, P62805 0.071
465 9E1N EM 3.40 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Snf2h bound nucleosome complex-ClassA3 Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.512
466 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 Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
467 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 Xenopus laevis 2020 O60814, P68431, P04908, P62805 -
468 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 Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
469 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
470 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 Xenopus laevis 2007 P84040, P84051, P02299, P02283 -
471 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 Xenopus laevis 2002 P02281, P84233, P06897, P62799 -
472 8F86 EM 3.10 2023-04-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 SIRT6 bound to an H3K9Ac nucleosome Wang, Z.A., Markert, J.W., Whedon, S.D., Yapa Abeywardana, M., Lee, K., Jiang, H., Suarez, C., Lin, H., Farnung, L., Cole, P.A. 10.1021/jacs.2c13512 36930461 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 NAD-dependent protein deacylase sirtuin-6 Transcription-associated, Histone_deacetylation_H3K9, Histone PTM erasers, Histone_deacetylation, DNA repair Q8N6T7 P02281, P84233, P06897, P62799 0.434
473 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
474 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 Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
475 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 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 PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P02281, P84233, Q6AZJ8, P62799 0.216
476 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 Xenopus laevis 2013 P68431, P04908, P06899, P62805 -
477 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 P10412, Q71DI3, P04908, P62805, O60814 0.269
478 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 Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Telomere-associated, Histone PTM writers, Histone_methylation_H3K79_writer Q04089, P0CG48 P02281, P84233, P06897, P62799 0.473
479 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 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 RSC (SWI/SNF), Chromatin remodelers, SWI/SNF, Transcription-associated P22082, P09547, P18480, P32591, P53628, P18888, P43554, P53330, Q12406, Q05123 P02281, P84233, Q6AZJ8, P62799 0.105
480 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 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 PTM writers, Polycomb, Transcription-associated, Heterochromatin-associated, Histone_methylation_H3K27_writer Q15910, Q15022 P02281, P84233, P06897, P62799 0.29
481 6Y5D EM 4.10 2020-09-23 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Structure of human cGAS (K394E) bound to the nucleosome Pathare, G.R., Decout, A., Gluck, S., Cavadini, S., Makasheva, K., Hovius, R., Kempf, G., Weiss, J., Kozicka, Z., Guey, B., Melenec, P., Fierz, B., Thoma, N.H., Ablasser, A. 10.1038/s41586-020-2750-6 32911482 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8N884 Q6FI13, O60814, Q71DI3, P62805 0.195
482 6X0N EM 10.00 2020-09-16 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Bilokapic, S., Suskiewicz, M.J., Ahel, I., Halic, M. 10.1038/s41586-020-2725-7 32939087 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2 DNA repair, Histone PTM writers, Histone_PARylation_writer Q9NWY4, Q9UGN5 P02281, P84233, P06897, P62799 0.113
483 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 Xenopus laevis 2020 P68431, P04908, P06899, P62805 0.419
484 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 Xenopus laevis 2019 PC4 and SFRS1-interacting protein Histone PTM readers, Transcription factors, Histone_methylation_H3K36_reader, Transcription-associated O75475 P02281, P84233, P06897, P62799 0.529
485 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 Xenopus laevis 2019 P02281, P84233, P06897, P62799 0.339
486 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 Xenopus laevis 2019 Retinoblastoma-binding protein 5 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291 P02281, P84233, P06897, P62799 0.332
487 6PWV EM 6.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of MLL1 core complex 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 Xenopus laevis 2019 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2, Protein dpy-30 homolog Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3, Q9C005 P02281, P84233, P06897, P62799 0.188
488 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 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 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated, Ubiquitin Q03164, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.343
489 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 Xenopus laevis 2020 O60814, P68431, P04908, P62805 -
490 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 Xenopus laevis 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.23
491 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 Xenopus laevis 2019 Transcription regulatory protein SNF2 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P02281, P84233, P06897, P62799 0.399
492 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 Xenopus laevis 2019 P68431, P04908, P06899, P62805 -
493 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 Xenopus laevis 2017 P84243, P06899, P04908, P62805 -
494 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
495 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
496 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 Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
497 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 Xenopus laevis 2014 Q96A08, P68431, P04908, P62805 -
498 6X59 EM 2.98 2020-09-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 The mouse cGAS catalytic domain binding to human assembled nucleosome Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P. 10.1038/s41586-020-2749-z 32911481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P0C0S8, P62807, Q71DI3, P62805 0.54
499 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 Xenopus laevis 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 Chromatin remodelers, PBAF (SWI/SNF), Cell cycle, SWI/SNF, Transcription-associated P51532, P60709, O96019, Q68CP9, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q8WUB8, Q9NPI1, Q86U86 P62807, P68431, Q93077, P62805 0.172
500 8VWS EM 3.10 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Nucleosome containing 8oxoG at SHL-6 Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P0C0S8, P62807, Q71DI3, P62805 0.534
501 8HY0 EM 3.10 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.463
502 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 Xenopus laevis 2019 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.42
503 9JNV EM 3.00 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP(S) state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.49
504 9GMR EM 2.80 2025-01-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 SIRT7-H3K36MTUnucleosome complex Moreno-Yruela, C., Ekundayo, B.E., Foteva, P.N., Ni, D., Calvino-Sanles, E., Stahlberg, H., Fierz, B. 10.1038/s41467-025-56529-y 39900593 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 NAD-dependent protein deacetylase sirtuin-7 Q9NRC8 Q6FI13, P06899, Q71DI3, P62805 -
505 9GMK EM 3.50 2025-01-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 SIRT7:H3K18DTU nucleosome complex Moreno-Yruela, C., Ekundayo, B.E., Foteva, P.N., Ni, D., Calvino-Sanles, E., Stahlberg, H., Fierz, B. 10.1038/s41467-025-56529-y 39900593 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 NAD-dependent protein deacetylase sirtuin-7 Q9NRC8 Q6FI13, P06899, Q71DI3, P62805 -
506 9EGY EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 160 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P02281, P06897, A0A310TTQ1, P62799 0.256
507 9E1Y EM 2.60 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 153 Empty Nucleosome with 601 widom sequence Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1101/2024.12.31.630910 39803580 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 P02281, P84233, P06897, P62799 0.685
508 9E1X EM 3.40 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Snf2h bound nucleosome complex - ClassD1 Malik, D., Deshmukh, A., Bilokapic, S., Halic, M. 10.1101/2024.12.31.630910 39803580 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, Q6AZJ8, P62799 0.499
509 9E1M EM 3.25 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Snf2h bound nucleosome complex - ClassA2 Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.535
510 9E1L EM 3.15 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Snf2h bound nucleosome complex - ClassA1 Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.559
511 8YBJ EM 2.38 2024-07-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Kimura, T., Hirai, S., Kujirai, T., Fujita, R., Ogasawara, M., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1111/gtc.13143 38972377 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P68431, P04908, P06899, P62805 0.631
512 8X31 EM 6.20 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.123
513 8X30 EM 4.30 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 Structure of piccolo NuA4 and H2A.Z nucleosome 2:1 complex Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, Q540A3, P38806, P47128 Q12692, P02309, P02293, P61830 0.165
514 8X2X EM 3.80 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P0AEX9, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.261
515 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., He, Z., Deng, Z., Chu, G.C., Shi, Q., Tong, Z., Li, J.B., Pan, M., Liu, L. 10.1038/s41594-024-01342-2 38918638 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Ubiquitin carboxyl-terminal hydrolase 16, Ubiquitin B Histone_deubiquitination_H2AK119, Cell cycle, Transcription-associated, Histone PTM erasers, Ubiquitin Q9Y5T5, P0CG47 O60814, P68431, P04908, P62805 0.306
516 8W9D EM 3.90 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Wang, C., Chu, C., Guo, Z., Zhan, X. 10.1126/sciadv.adk7678 38598631 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, Unclear peptide Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 O60814, P68431, P04908, P62805 0.263
517 8VWT EM 3.30 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 N-glycosylase/DNA lyase DNA repair, DNA modification O15527 P0C0S8, P62807, Q71DI3, P62805 0.41
518 8VG0 EM 3.07 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 159 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4 P0AEX9 P68431, P04908, P06899, P62805 0.482
519 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 Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.477
520 8UXQ EM 6.30 2024-09-25 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 97 Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Sokolova, V., Miratsky, J., Svetlov, V., Brenowitz, M., Vant, J., Lewis, T.S., Dryden, K., Lee, G., Sarkar, S., Nudler, E., Singharoy, A., Tan, D. 10.1016/j.str.2024.09.013 39383876 Xenopus laevis Xenopus laevis Mus musculus Xenopus laevis Xenopus laevis 2024 Chromobox protein homolog 5 Histone_methylation_H3K9_reader, Histone PTM readers, Heterochromatin-associated, Transcription-associated P45973 P02281, P84233, P0C0S6, P62799 0.143
521 8THU EM 3.10 2023-09-06 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 145 Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. 10.1016/j.molcel.2023.07.020 37595555 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 P02281, P84233, P0C0S5, P62799 0.508
522 8SN2 EM 3.60 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.452
523 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 Xenopus laevis 2022 Histone acetyltransferase ESA1, Enhancer of polycomb-like protein 1, Chromatin modification-related protein YNG2, Chromatin modification-related protein EAF6 Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Euchromatin-associated, Histone_acetylation_writer Q08649, P43572, P38806, P47128 P02281, P84233, P06897, P62799 0.314
524 9JNP EM 2.30 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ATP state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.587
525 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 Xenopus laevis 2023 Chromatin-remodeling ATPase Ino80 P62807, P68431, Q93077, P62805 0.494
526 8SN0 EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.547
527 8Y3D EM 5.10 2025-01-29 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Shimizu, M., Tanaka, H., Nishimura, M., Sato, N., Nozawa, K., Ehara, H., Sekine, S.I., Morishima, K., Inoue, R., Takizawa, Y., Kurumizaka, H., Sugiyama, M. 10.1093/pnasnexus/pgae484 39539301 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P68431, P04908, P06899, P62805 -
528 8VG2 EM 3.04 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 196 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Hepatocyte nuclear factor 3-alpha Transcription factors, Transcription-associated P55317 P68431, P06899, P10412, P04908, P62805 0.493
529 8T9H EM 3.37 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 99 Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Abini-Agbomson, S., Gretarsson, K., Shih, R.M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M.D., Armache, J.P., Nudler, E., Narlikar, G., Liu, S., Lu, C., Armache, K.J. 10.1016/j.molcel.2023.07.020 37595555 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P02281, P84233, P06897, P62799 0.393
530 8RGM EM 4.00 2025-01-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 603 145 Cryo-EM structure of nucleosome containing Widom603 DNA Armeev, G.A., Moiseenko, A.V., Motorin, N.A., Afonin, D.A., Zhao, L., Vasilev, V.A., Oleinikov, P.D., Glukhov, G.S., Peters, G.S., Studitsky, V.M., Feofanov, A.V., Shaytan, A.K., Shi, X., Sokolova, O.S. 10.1016/j.str.2025.02.007 40101710 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P68431, P04908, P06899, P62805 0.352
531 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 Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone PTM readers, Transcription factors, Histone_methylation_H3K36_reader, Transcription-associated O75475 P02281, P84233, P06897, P62799 0.399
532 8KD1 EM 3.20 2025-03-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601L 173 Structure of nucleosome complexed with one DEK molecule Kujirai, T., Echigoya, K., Kishi, Y., Saeki, M., Ito, T., Kato, J., Negishi, L., Kimura, H., Masumoto, H., Takizawa, Y., Gotoh, Y., Kurumizaka, H. 10.1038/s41594-025-01493-w 39984731 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Protein DEK P35659 P68431, P04908, P06899, P62805 0.404
533 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 Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.145
534 8HXY EM 3.10 2023-09-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.44
535 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 Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.598
536 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 Xenopus laevis 2022 P68431, P04908, P06899, P62805 0.32
537 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 Xenopus laevis 2022 P68431, P04908, P06899, P62805 0.256
538 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 Xenopus laevis 2020 Transcription factor SOX-11 Transcription factors, Transcription-associated P35716 O60814, P04908, Q71DI3, P62805 0.323
539 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 Xenopus laevis 2019 P68431, P04908, P06899, P62805 0.363
540 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 Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.42
541 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 Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
542 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 Xenopus laevis 2010 Regulator of chromosome condensation Nuclear division, Cell cycle P25171 P02281, P84233, Q6AZJ8, P62799 -
543 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 Xenopus laevis 2010 P02281, P84233, P06897, P62799 -
544 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 Xenopus laevis 2019 Centromere protein C, Centromere protein N Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188, Q96H22 P49450, Q93077, Q5QNW6, P62805 0.369
545 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 P68431, P06899, P04908, P07305, P62805 0.489
546 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 Xenopus laevis 2023 Single-chain variable fragment, Transcription factor PU.1 Euchromatin-associated, Transcription factors, Transcription-associated P17433 Q16777, P68431, Q16778, P62805 0.559
547 6R8Y EM 4.30 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, UV-DDB complex, DCX complex Q16531, Q92466 P68431, P04908, P06899, P62805 0.313
548 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 Xenopus laevis 2023 P62807, P68431, Q93077, P62805 0.607
549 8KD5 EM 2.90 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.378
550 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Polyubiquitin-B Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P02281, P84233, P06897, P62799 0.38
551 6R91 EM 4.10 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, UV-DDB complex, DCX complex Q16531, Q92466 P68431, P04908, P06899, P62805 0.212
552 6R25 EM 4.61 2019-04-24 octamer 1 canonical_H3,H3.3 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 Xenopus laevis 2019 Lysine-specific histone demethylase 1B, NPAC Histone_methylation_H3K36_reader, Transcription-associated, Euchromatin-associated, Histone PTM readers, Histone PTM erasers, Histone_demethylation_H3K4 Q8NB78, Q49A26 P02281, P84233, P06897, P62799 0.186
553 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG48 P02281, P84233, P06897, P62799 0.436
554 6KVD X-ray 2.21 2019-12-18 octamer 1 canonical_H3 canonical_H4 H2A.J canonical_H2B alphasat_146 146 Crystal structure of human nucleosome containing H2A.J Tanaka, H., Sato, S., Koyama, M., Kujirai, T., Kurumizaka, H. 10.1093/jb/mvz109 31793981 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P68431, P06899, Q9BTM1, P62805 -
555 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase 2A, Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q03164, Q15291, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.338
556 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 Xenopus laevis 2019 Transcription regulatory protein SNF2 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P02281, P84233, P06897, P62799 0.427
557 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 Xenopus laevis 2020 P68431, P04908, P06899, P62805 -
558 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 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2018 Polyubiquitin-B, Chromatin-remodeling ATPase Ubiquitin, Chromatin remodelers, CHD, Transcription-associated P0CG47, P32657 Q28D68, S4RAZ3, P06897, P62799, P02302 0.23
559 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 Xenopus laevis 2017 P02281, P84233, Q6AZJ8, P62799 0.378
560 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 Xenopus laevis 2019 scFv P49450, P06899, P04908, P62805 0.57
561 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 Xenopus laevis 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 Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P84243, P06899, P04908, P62805 0.138
562 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 Xenopus laevis 2017 P02281, P84233, P06897, P62799 -
563 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 Xenopus laevis 2017 Chromo domain-containing protein 1 CHD, Chromatin remodelers, Transcription-associated P32657 P02281, P84233, P06897, P62799 0.018
564 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 Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
565 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 Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
566 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 Xenopus laevis 2010 P02281, P84233, Q6AZJ8, P62799 -
567 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 Xenopus laevis 2006 P02281, P84233, P06897, P62799 -
568 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
569 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 Xenopus laevis 2003 P02281, P06897, P02302, P62799 -
570 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 tropicalis Xenopus laevis 2008 P84233, P06897, Q28D68, P62799 -
571 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 Xenopus laevis 2022 P0C0S8, P62807, Q71DI3, P62805 0.537
572 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 Xenopus laevis 2011 P02281, P84233, P06897, P62799 -
573 6R8Z EM 3.90 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP_THF2(-1)-UV-DDB Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, UV-DDB complex, DCX complex Q16531, Q92466 P68431, P04908, P06899, P62805 0.307
574 6R92 EM 4.80 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 2 DNA repair, UV-DDB complex, DCX complex Q16531, Q92466 P68431, P04908, P06899, P62805 0.22
575 8JNF EM 6.91 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 The cryo-EM structure of the RAD51 filament bound to the nucleosome Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P68431, P04908, P06899, P62805 0.143
576 6R93 EM 4.00 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 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 Xenopus laevis 2019 P68431, P04908, P06899, P62805 0.352
577 8JND EM 3.66 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 156 The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H. 10.1038/s41586-024-07196-4 38509361 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA repair protein RAD51 homolog 1 DNA repair Q06609 P68431, P04908, P06899, P62805 0.19
578 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 Xenopus laevis 2023 P04908, P06899, Q71DI3, P62805 0.579
579 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 Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P84243, P06899, P04908, P62805 0.255
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 Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.2
581 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 Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Euchromatin-associated, Transcription factors, Transcription-associated Q01860 P02281, P84233, Q6AZJ8, P62799 0.218
582 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 Xenopus laevis 2023 P62798, A0A1B8Y854, A0A310TTQ1, Q6AZJ8 0.322
583 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 Xenopus laevis 2023 Single-chain variable fragment Q16777, P68431, Q16778, P62805 0.535
584 7XYF EM 3.80 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 Xenopus laevis 2023 ATP-dependent helicase fft3 Heterochromatin-associated, Chromatin remodelers O42861 P84040, P84051, P02299, P02283 0.272
585 7UX9 EM 3.20 2023-08-09 octamer 1 canonical_H3 canonical_H4 H2A.W canonical_H2B 601 141 Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA) Lee, S.C., Adams, D.W., Ipsaro, J.J., Cahn, J., Lynn, J., Kim, H.S., Berube, B., Major, V., Calarco, J.P., LeBlanc, C., Bhattacharjee, S., Ramu, U., Grimanelli, D., Jacob, Y., Voigt, P., Joshua-Tor, L., Martienssen, R.A. 10.1016/j.cell.2023.08.001 37643610 Arabidopsis thaliana Xenopus laevis Arabidopsis thaliana Arabidopsis thaliana Xenopus laevis 2023 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 Q9FJE8, O23629, P59169, P62799 0.445
586 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 P10412, Q71DI3, P04908, P62805, O60814 0.236
587 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 P10412, Q71DI3, P04908, P62805, O60814 0.109
588 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 P10412, Q71DI3, P04908, P62805, O60814 0.302
589 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 Xenopus laevis 2022 O60814, P04908, Q71DI3, P62805 0.274
590 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 Xenopus laevis 2022 O60814, P04908, Q71DI3, P62805 0.281
591 7ON1 EM 3.35 2021-07-07 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 123 Cenp-A nucleosome in complex with Cenp-C Yan, K., Yang, J., Zhang, Z., Barford, D. 0 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2021 BJ4_G0006610.mRNA.1.CDS.1 Cell cycle, Centromere-associated, Kinetochore, Nuclear division, CCAN P35201 P02293, P02309, P04911, P36012 0.47
592 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 P84233, P15308, P62799, Q6DKE3, P02281 0.29
593 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 P68431, P06899, P10412, P04908, P62805 0.527
594 7E9F EM 4.00 2022-09-07 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 123 Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M. 0 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2022 Origin recognition complex subunit 1 DNA replication, ORC, Transcription-associated P54784 P02294, P02309, P61830, P04912 0.319
595 7E9C EM 3.50 2022-09-07 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 130 Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M. 0 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2022 Origin recognition complex subunit 1 DNA replication, ORC, Transcription-associated P54784 P02294, P02309, P61830, P04912 0.311
596 7D69 EM 3.57 2021-09-08 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601L 125 Cryo-EM structure of the nucleosome containing Giardia histones Sato, S., Takizawa, Y., Hoshikawa, F., Dacher, M., Tanaka, H., Tachiwana, H., Kujirai, T., Iikura, Y., Ho, C.H., Adachi, N., Patwal, I., Flaus, A., Kurumizaka, H. 10.1093/nar/gkab644 34352093 Giardia intestinalis Giardia intestinalis Giardia intestinalis Giardia intestinalis Xenopus laevis 2021 A8BHS7, A8BUJ9, A8BI78, E2RU29 0.427
597 7A08 EM 3.11 2020-09-23 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 132 CryoEM Structure of cGAS Nucleosome complex Michalski, S., de Oliveira Mann, C.C., Stafford, C.A., Witte, G., Bartho, J., Lammens, K., Hornung, V., Hopfner, K.P. 10.1038/s41586-020-2748-0 32911480 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Cyclic GMP-AMP synthase DNA repair, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense Q8C6L5 P62807, P84243, Q93077, P62805 0.533
598 8VG1 EM 2.48 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 171 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Hepatocyte nuclear factor 3-alpha, Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4 Transcription factors, Transcription-associated P55317, P0AEX9 P68431, P04908, P06899, P62805 0.541
599 9JNW EM 2.90 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Structure of isw1-nucleosome complex in ADP+ state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.496
600 9JNT EM 2.70 2025-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Structure of isw1-nucleosome complex in ADP* state Sia, Y., Pan, H., Chen, K., Chen, Z. 10.1126/science.adu5654 40179160 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 A0A8J0U496, A0A310TTQ1, Q6AZJ8, A0A8J1LTD2 0.532
601 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 Xenopus laevis 2020 Transcription factor SOX-11 Transcription factors, Transcription-associated P35716 O60814, P04908, Q71DI3, P62805 0.37
602 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 Xenopus laevis 2019 chromatin remodeling factor ISWI Chromatin remodelers, ISWI G0S9L5 P84040, P84051, P02299, P02283 0.39
603 6M4H EM 3.90 2020-09-23 octamer 1 canonical_H3 canonical_H4 H2A.B canonical_H2B 601 103 Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Zhou, M., Dai, L., Li, C., Shi, L., Huang, Y., Guo, Z., Wu, F., Zhu, P., Zhou, Z. 10.15252/embj.2020105907 33073403 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P68431, P0C5Z0, Q16778, P62805 0.365
604 6M4D EM 4.40 2020-09-23 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 125 Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Zhou, M., Dai, L., Li, C., Shi, L., Huang, Y., Guo, Z., Wu, F., Zhu, P., Zhou, Z. 10.15252/embj.2020105907 33073403 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P68431, Q16778, Q71UI9, P62805 0.311
605 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 Xenopus laevis 2020 O60814, P68431, P04908, P62805 -
606 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 Xenopus laevis 2020 P62805, P04908, P06899, Q4QHB5 -
607 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 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 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated, Ubiquitin Q8NEZ4, Q15291, P62979, P61964, Q9UBL3 P02281, P84233, P06897, P62799 0.33
608 6K1K X-ray 2.20 2020-01-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601L 145 Human nucleosome core particle with H2A.X S139E variant 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 Xenopus laevis 2020 P16104, P68431, P06899, P62805 -
609 6K1I X-ray 2.75 2020-01-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601_modified 147 Human nucleosome core particle with gammaH2A.X variant 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 Xenopus laevis 2020 P16104, P68431, P06899, P62805 -
610 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P0CG47 P02281, P84233, Q6AZJ8, P62799 0.144
611 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 Xenopus laevis 2019 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 P02281, P84233, P06897, P62799 0.435
612 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 Xenopus laevis 2018 P02281, P84233, P06897, P62799 0.301
613 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 Xenopus laevis 2018 RuvB-like helicase, Ino80, les2, Ies6, Actin related protein 5 INO80, Chromatin remodelers G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P0C0S8, P62807, Q71DI3, P62805 0.33
614 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 Xenopus laevis 2019 scFv P84040, P84051, P02299, P02283 0.589
615 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 Xenopus laevis 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 Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P84243, P06899, P04908, P62805 0.14
616 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 Xenopus laevis 2017 Transcription regulatory protein SNF2 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P02281, P84233, P06897, P62799 0.315
617 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 Xenopus laevis 2017 Transcription regulatory protein SNF2 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P02281, P84233, P06897, P62799 0.372
618 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 Xenopus laevis 2016 P68431, P04908, P06899, P62805 -
619 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 Xenopus laevis 2016 P68431, P04908, P06899, P62805 -
620 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 Xenopus laevis 2014 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer P35226, Q99496 P02281, P84233, P06897, P62799 -
621 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 Xenopus laevis 2013 P02281, P84233, P06897, P62799 -
622 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 Xenopus laevis 2013 P68431, P04908, P06899, P62805 -
623 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 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
624 6USJ EM 10.50 2020-10-14 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Structure of two nucleosomes bridged by human PARP2 Gaullier, G., Roberts, G., Muthurajan, U.M., Bowerman, S., Rudolph, J., Mahadevan, J., Jha, A., Rae, P.S., Luger, K. 10.1371/journal.pone.0240932 33141820 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Poly [ADP-ribose] polymerase 2 DNA repair, Histone PTM writers, Histone_PARylation_writer Q9UGN5 P68431, P04908, P06899, P62805 0.092
625 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 Xenopus laevis 2011 P02281, P84233, P06897, P62799 -
626 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 Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.135
627 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 Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone PTM readers, Transcription factors, Histone_methylation_H3K36_reader, Transcription-associated O75475 P02281, P84233, P06897, P62799 0.484
628 8OL1 EM 3.50 2024-02-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Xu, P., Liu, Y., Liu, C., Guey, B., Li, L., Melenec, P., Ricci, J., Ablasser, A. 10.1038/s41586-024-07112-w 38418882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Cyclic GMP-AMP synthase, SPRY domain-containing SOCS box protein 3, Elongin-C, Elongin-B Synthesis of second messengers, Transcription factors, E3 ubiquitin-protein ligation, Transcription-associated, 2'3'-cGAMP, DNA repair, Antiviral defense Q8N884, Q6PJ21, Q15369, Q15370 Q96KK5, Q71DI3, Q99878, Q93079, P62805, Q99877 0.4
629 8KD4 EM 2.93 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, P84233, P06897, P62799 0.373
630 8JBX EM 3.35 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Human canonical 601 DNA nucleosome Ding, D., Pang, M.Y.H., Deng, M., Nguyen, T.T., Liu, Y., Sun, X., Xu, Z., Zhang, Y., Zhai, Y., Yan, Y., Ishibashi, T. 10.1093/nar/gkae825 39329259 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P68431, P04908, P62807, P62805 0.43
631 8J6S EM 3.80 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 99 Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B CAF-1, DNA repair, DNA replication, Histone chaperones Q13111, Q13112 P68431, P62805 0.301
632 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 Xenopus laevis 2022 Centromere protein H, Centromere protein I, Centromere protein K, Centromere protein L, Centromere protein M, Centromere protein N, Centromere protein O, Centromere protein P, Centromere protein Q, Centromere protein R, Centromere protein U, Centromere protein C CENP-A NAC/CAD, Cell cycle, Transcription-associated, Centromere-associated, Nuclear division, Kinetochore Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q71F23, Q03188 P62807, P49450, Q93077, P62805 0.075
633 7Y61 EM 5.60 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 92 Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B CAF-1, DNA repair, DNA replication, Histone chaperones Q13111, Q13112 P68431, P62805 0.189
634 7Y60 EM 3.80 2023-08-16 H3_H4_tetramer, H3_H4_tetramer 2 canonical_H3 canonical_H4 601 108 Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome Liu, C.P., Yu, Z., Xiong, J., Hu, J., Song, A., Ding, D., Yu, C., Yang, N., Wang, M., Yu, J., Hou, P., Zeng, K., Li, Z., Zhang, Z., Zhang, X., Li, W., Zhang, Z., Zhu, B., Li, G., Xu, R.M. 10.1126/science.add8673 37616371 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2023 Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B CAF-1, DNA repair, DNA replication, Histone chaperones Q13111, Q13112 P68431, P62805 0.304
635 7XYG EM 4.20 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 Xenopus laevis 2023 ATP-dependent helicase fft3 Heterochromatin-associated, Chromatin remodelers O42861 P84040, P84051, P02299, P02283 0.219
636 7XX5 X-ray 3.19 2023-05-31 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.3 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 P68431, P06899, P04908, P16402, P62805 -
637 7WLR EM 3.54 2022-07-13 octamer 1 H3.3 canonical_H4 H2A.X canonical_H2B 601 145 Cryo-EM structure of the nucleosome containing Komagataella pastoris histones Fukushima, Y., Hatazawa, S., Hirai, S., Kujirai, T., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1093/jb/mvac043 35485963 Komagataella pastoris Komagataella pastoris Komagataella pastoris Komagataella pastoris Xenopus laevis 2022 A0A1B2JA70, A0A1B2JB78, A0A1B2JBS1, A0A1B2JD99 0.45
638 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 Xenopus laevis 2022 O60814, P68431, P04908, P62805 0.043
639 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 Xenopus laevis 2022 P0C0S8, P62807, Q71DI3, P62805 0.385
640 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 Xenopus laevis 2023 Single-chain variable fragment, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 P0AEX9 Q16777, P68431, Q16778, P62805 0.548
641 7OTQ EM 4.80 2021-09-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 149 Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome Bacic, L., Gaullier, G., Sabantsev, A., Lehmann, L.C., Brackmann, K., Dimakou, D., Halic, M., Hewitt, G., Boulton, S., Deindl, S., Workman, J.L. 10.7554/eLife.71420 34486521 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.282
642 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 Xenopus laevis 2021 P68431, P04908, P06899, P62805 0.519
643 7MBN EM 4.02 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 Xenopus laevis 2021 Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2 Histone PTM writers, Histone_methylation_H3K4_writer, COMPASS, Euchromatin-associated, Transcription-associated Q15291, P61964, Q03164, Q9UBL3 P02281, P84233, P06897, P62799 0.217
644 7JZV EM 3.90 2021-02-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Witus, S.R., Burrell, A.L., Farrell, D.P., Kang, J., Wang, M., Hansen, J.M., Pravat, A., Tuttle, L.M., Stewart, M.D., Brzovic, P.S., Chatterjee, C., Zhao, W., DiMaio, F., Kollman, J.M., Klevit, R.E. 10.1038/s41594-020-00556-4 33589814 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 BRCA1,Ubiquitin-conjugating enzyme E2 D3, BRCA1-associated RING domain protein 1 Histone PTM writers, Histone_ubiquitination_H2AK127_writer, Histone_ubiquitination_H2AK125_writer, E3 ubiquitin-protein ligation, Transcription-associated, DNA repair, Histone_ubiquitination_H2AK129_writer P38398, Q99728 Q6FI13, O60814, Q71DI3, P62805 0.313
645 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 P68431, P06899, P04908, P07305, P62805 -
646 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 Xenopus laevis 2021 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P62979 O60814, P68431, P04908, P62805 0.332
647 6ZHY EM 3.00 2020-12-23 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 110 Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class. Lehmann, L.C., Bacic, L., Hewitt, G., Brackmann, K., Sabantsev, A., Gaullier, G., Pytharopoulou, S., Degliesposti, G., Okkenhaug, H., Tan, S., Costa, A., Skehel, J.M., Boulton, S.J., Deindl, S. 10.1016/j.celrep.2020.108529 33357431 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.516
648 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 Xenopus laevis 2013 P68431, P04908, P06899, P62805 -
649 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 Xenopus laevis 2010 P02281, P84233, Q6AZJ8, P62799 -
650 9J0O EM 3.30 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 191 Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, 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, RPB12, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, Transcription factors, RNA polymerases, Transcription-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P84243, P06899, P04908, P62805 0.313
651 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 Xenopus laevis 2011 Regulatory protein SIR3 Transcription-associated P06701 P02281, P84233, P06897, P62799 -
652 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 Xenopus laevis 2016 Ubiquitin carboxyl-terminal hydrolase 8, Transcription and mRNA export factor SUS1, SAGA-associated factor 11, Polyubiquitin-B, SAGA-associated factor 73 Transcription-associated, SAGA, Histone_deubiquitination, Histone PTM erasers, Ubiquitin P50102, Q6WNK7, Q03067, P0CG47, P53165 P02281, P84233, P06897, P62799 -
653 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 Xenopus laevis 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 Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P84243, P06899, P04908, P62805 0.151
654 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 P68431, P06899, P10412, P04908, P62805 0.492
655 7YQK EM 3.38 2022-08-17 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 145 cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 Ai, H., Chu, G.C., Gong, Q., Tong, Z.B., Deng, Z., Liu, X., Yang, F., Xu, Z., Li, J.B., Tian, C., Liu, L. 10.1021/jacs.2c06156 36166692 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 UDR motif of 53BP1, TP53-binding protein 1, Polyubiquitin-B Histone_ubiquitination_H2AK15_reader, Telomere-associated, Histone PTM readers, Ubiquitin, DNA repair, Histone_methylation_H4K20_reader Q12888, P0CG47 P16104, O60814, P68431, P62805 0.424
656 6GEJ EM 3.60 2018-10-17 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 154 Chromatin remodeller-nucleosome complex at 3.6 A resolution. Willhoft, O., Ghoneim, M., Lin, C.L., Chua, E.Y.D., Wilkinson, M., Chaban, Y., Ayala, R., McCormack, E.A., Ocloo, L., Rueda, D.S., Wigley, D.B. 10.1126/science.aat7716 30309918 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2018 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2 INO80, SWR1 (INO80), Chromatin remodelers, Euchromatin-associated, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02293, P02309, P04911, P61830 0.372
657 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 Xenopus laevis 2024 P68431, P04908, P06899, P62805 0.109
658 9J8O EM 4.05 2025-02-26 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B generic_H1 601 176 Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Horikoshi, N., Miyake, R., Sogawa-Fujiwara, C., Ogasawara, M., Takizawa, Y., Kurumizaka, H. 10.1038/s41467-025-56823-9 39929866 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2025 Barrier-to-autointegration factor, Lamin-A/C O75531, P02545 Q02539, P68431, P06899, P04908, P62805 0.292
659 9FH9 EM 2.50 2024-07-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Structure of CyclinB1 N-terminus bound to the NCP Cirillo, L., Young, R., Veerapathiran, S., Roberti, A., Martin, M., Abubacar, A., Perosa, C., Coates, C., Muhammad, R., Roumeliotis, T.I., Choudhary, J.S., Alfieri, C., Pines, J. 10.1038/s44318-024-00194-2 39143240 Homo sapiens Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis 2024 G2/mitotic-specific cyclin-B1 APC/C, Cell cycle P14635 Q7L7L0, P02281, P68431, P62805 0.534
660 9FGQ EM 2.50 2024-07-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 132 Structure of human APC3loop 375-381 bound to the NCP Cirillo, L., Young, R., Veerapathiran, S., Roberti, A., Martin, M., Abubacar, A., Perosa, C., Coates, C., Muhammad, R., Roumeliotis, T.I., Choudhary, J.S., Alfieri, C., Pines, J. 10.1038/s44318-024-00194-2 39143240 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Cell division cycle protein 27 homolog Histone PTM writers, APC/C, Cell cycle P30260 Q6FI13, P33778, P68431, P62805 0.651
661 9EH2 EM 3.10 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 65 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16, FACT complex subunit SSRP1 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, DNA replication, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated, DNA repair, FACT A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2, Q9Y5B9, Q08945 P02281, P06897, A0A310TTQ1, P62799 0.252
662 9E1R EM 3.10 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassB4 Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.616
663 9E1Q EM 3.10 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassB3 Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.614
664 9E1P EM 3.25 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 152 Snf2h bound nucleosome complex - ClassB2 Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.576
665 9E1O EM 3.30 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Snf2h bound nucleosome complex - ClassB1 Malik, D., Deshmukh, A.A., Bilokapic, S., Halic, M. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.538
666 9DWI EM 3.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite) Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta P06746 P0C0S8, P62807, Q71DI3, P62805 0.405
667 9DG3 EM 3.46 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 RING1 and YY1-binding protein, Ubiquitin Polycomb, Histone_ubiquitination_reader, Transcription-associated, Histone PTM readers, Heterochromatin-associated, Ubiquitin Q8N488, P0CG48 P02281, P84233, P06897, P62799 0.382
668 9DBY EM 2.80 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 148 ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S., Thomas, J.F., Lee, R., De Ioannes, P., Sosa, B.A., Armache, J.P., Armache, K.J. 10.1038/s41586-024-08183-5 39537923 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb complex protein BMI-1, E3 ubiquitin-protein ligase RING2, RING1 and YY1-binding protein, Ubiquitin Histone PTM writers, Histone_ubiquitination_H2AK119_writer, Polycomb, Transcription-associated, E3 ubiquitin-protein ligation, Heterochromatin-associated, Histone_methylation_H3K27_writer, Histone PTM readers, Histone_ubiquitination_reader, Ubiquitin P35226, Q99496, Q8N488, P0CG48 P02281, P84233, P06897, P62799 0.39
669 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., Sui, F., Gu, F., Li, W., Yu, Z., Wang, Q., He, S., Wang, L., Xu, Y. 10.1038/s41421-023-00640-1 38331872 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 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 INO80, SRCAP (INO80), Chromatin remodelers, Histone_acetylation_reader, Histone chaperones, Cell cycle, Euchromatin-associated, Transcription-associated, Histone PTM readers Q6ZRS2, Q15906, Q9GZN1, O43257, Q9Y265, Q9Y230, P60709, O96019, Q9NPF5, O95619 P62807, P68431, Q93077, P62805 0.297
670 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 Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59259, P59226, Q9LD28 0.306
671 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 Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59259, P59226, Q9LD28 0.336
672 8VWU EM 3.00 2024-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Nucleosome containing 8oxoG at SHL4 Cordero, C., Mehta, K.P.M., Weaver, T.M., Ling, J.A., Freudenthal, B.D., Cortez, D., Roberts, S.A. 10.1038/s41467-024-55497-z 39715760 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 P0C0S8, P62807, Q71DI3, P62805 0.559
673 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 Xenopus laevis 2022 Chromo domain-containing protein 1 CHD, Chromatin remodelers, Transcription-associated P32657 P02281, P84233, P06897, P62799 -
674 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 Xenopus laevis 2017 P02281, P84233, Q6AZJ8, P62799 0.209
675 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
676 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 Xenopus laevis 2010 P02281, P84233, Q6AZJ8, P62799 -
677 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
678 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
679 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
680 8CEO EM 3.60 2023-03-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Schilbach, S., Wang, H., Dienemann, C., Cramer, P. 10.1073/pnas.2220542120 37014863 Xenopus laevis Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPD, TFB1 isoform 1, RNA polymerase II transcription factor B subunit 2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, TOA1 isoform 1, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta, Mediator of RNA polymerase II transcription subunit 6, Mediator of RNA polymerase II transcription subunit 8, Mediator of RNA polymerase II transcription subunit 11, Mediator of RNA polymerase II transcription subunit 17, Mediator of RNA polymerase II transcription subunit 18, Mediator of RNA polymerase II transcription subunit 20, Mediator of RNA polymerase II transcription subunit 22, Mediator of RNA polymerase II transcription subunit 4, Mediator of RNA polymerase II transcription subunit 7, Mediator of RNA polymerase II transcription subunit 9, Mediator of RNA polymerase II transcription subunit 10, Mediator of RNA polymerase II transcription subunit 14, Mediator of RNA polymerase II transcription subunit 19, Mediator of RNA polymerase II transcription subunit 21, Mediator of RNA polymerase II transcription subunit 31, Mediator of RNA polymerase II transcription subunit 1 RNA polymerases, Transcription factors, Mediator, Euchromatin-associated, Transcription-associated, DNA repair P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145, P38782, P38304, Q99278, P32569, P32585, P34162, P32570, Q12343, Q08278, P33308, Q06213, P19263, P25046, P47822, P38633, Q12321 P02281, P84233, P06897, P62799 0.222
681 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 Xenopus laevis 2021 Histone-lysine N-methyltransferase NSD2 Histone PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated O96028 P68431, P06899, P0C0S8, P62805 0.556
682 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, J3QS39 P02281, P84233, P06897, P62799 0.356
683 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 Xenopus laevis 2019 Transcription regulatory protein SNF2 Chromatin remodelers, SWI/SNF, Transcription-associated P22082 P02281, P84233, Q6AZJ8, P62799 0.356
684 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 Xenopus laevis 2019 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 Q6FI13, P49450, P62807, P62805 0.416
685 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
686 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
687 9EGX EM 2.90 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 P02281, P06897, A0A310TTQ1, P62799 0.25
688 7NKY EM 3.20 2021-07-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 148 RNA Polymerase II-Spt4/5-nucleosome-FACT structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, FACT complex subunit POB3, FACT complex subunit SPT16, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, Transcription-associated, Heterochromatin-associated, SPT4-SPT5 complex, Centromere-associated, DNA repair, FACT P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, Q04636, P32558, P32914, P27692 P02281, P84233, P06897, P62799 0.358
689 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 Xenopus laevis 2019 Q6FI13, P49450, P62807, P62805 0.328
690 8X2Y EM 4.10 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class1 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P0AEX9, P08515, P38806 Q12692, P02309, P02293, P61830 0.229
691 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., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P06897, P62799 0.434
692 9J0N EM 3.40 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 167 Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, 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, RPB12, Transcription elongation factor A protein 1, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Euchromatin-associated, Transcription factors, RNA polymerases, Transcription-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, P23193, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P84243, P06899, P04908, P62805 0.316
693 6K1J X-ray 2.85 2020-01-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B alphasat_147 145 Human nucleosome core particle with H2A.X variant 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 Xenopus laevis 2020 P16104, P68431, P06899, P62805 -
694 9EGZ EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Histone PTM writers, Histone chaperones, RNA polymerases, Histone_ubiquitination_H2BK120_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, Transcription factors, Cell cycle, Euchromatin-associated, Transcription-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 P02281, P06897, A0A310TTQ1, P62799 0.261
695 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 Xenopus laevis 2020 Histone-lysine N-methyltransferase NSD3 Histone PTM writers, Histone_methylation_H3K4_writer, Euchromatin-associated, Transcription-associated, Histone_methylation_H3K27_writer Q9BZ95 Q92133, P02281, P06897, P62799 0.464
696 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 Xenopus laevis 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription factors, Transcription-associated O08785, Q9WTL8 P68431, P04908, P06899, P62805 0.219
697 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 Xenopus laevis 2021 Maltose Binding Protein tag, linker,CENP-C P0AEX9 P62805, P04908, P06899, P84229 0.297
698 8Q3E X-ray 2.17 2024-03-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Batchelor, L.K., De Falco, L., Dyson, P.J., Davey, C.A. 10.1039/d4ra01617c 38495982 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 GLY-GLY-TYR-ASN-LEU-ARG-PRO-ARG-THR-TYR-GLN-PRO-GLN-ARG-TYR-GLY-GLY-GLY Viral, DNA integration P14349 O60814, P68431, P04908, P62805 -
699 8RUP EM 2.42 2025-02-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Ruza, R.R., Chung, C.W., Gold, D.B., Serena, M., Roberts, E., Gruneberg, U., Barr, F.A. 10.1101/2025.01.22.634029 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Baculoviral IAP repeat-containing protein 5, Borealin, Inner centromere protein O15392, Q53HL2, Q9NQS7 P84233, P06897, P62799, P02281, A0A310TTQ1 0.551
700 8T9G EM 6.20 2024-09-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 215 Automethylated PRC2 dimer bound to nucleosome Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S. 10.1016/j.molcel.2024.08.025 39303719 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Polycomb protein SUZ12, Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Histone-binding protein RBBP4, Zinc finger protein AEBP2 Histone PTM writers, Histone chaperones, Polycomb, Transcription-associated, Heterochromatin-associated, Histone_methylation_H3K27_writer Q15022, Q15910, O75530, Q09028, Q6ZN18 P02281, P84233, P06897, P62799 0.163
701 8HAG EM 3.20 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.29
702 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., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P06897, P62799 0.552
703 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 Xenopus laevis 2022 RuvB-like helicase, Ino80, PAPA-1 domain-containing protein, YL1_C domain-containing protein, DASH complex subunit DAD4 INO80, Chromatin remodelers G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P0C0S8, P62807, Q71DI3, P62805 -
704 7YI4 EM 3.96 2023-06-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 151 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Guan, H., Wang, P., Zhang, P., Ruan, C., Ou, Y., Peng, B., Zheng, X., Lei, J., Li, B., Yan, C., Li, H. 10.1038/s41586-023-06349-1 37468628 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.23
705 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 Xenopus laevis 2022 N-lysine methyltransferase KMT5A Histone_methylation_H4K20_writer, Histone PTM writers, Cell cycle, Transcription-associated, Heterochromatin-associated, Nuclear division Q9NQR1 P02281, P84233, P06897, P62799 0.475
706 7XFM EM 3.10 2023-04-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 133 Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Zheng, L., Tsai, B., Gao, N. 10.1038/s41421-023-00560-0 37339965 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-3-methyladenine glycosylase DNA repair, DNA modification P29372 P02281, P84233, P06897, P62799 0.466
707 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 Xenopus laevis 2023 P02281, P84233, P06897, P62799 0.525
708 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 Xenopus laevis 2022 Ubiquitin-60S ribosomal protein L40 Ubiquitin P62987 Q2M2T1, P04908, Q71DI3, P62805 0.457
709 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 Xenopus laevis 2023 ISWI chromatin-remodeling complex ATPase ISW1 Chromatin remodelers, ISWI, Transcription-associated P38144 P02281, P84233, P06897, P62799 0.44
710 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 Xenopus laevis 2022 O60814, P68431, P04908, P62805 0.109
711 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 P10412, Q71DI3, P04908, P62805, O60814 0.329
712 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 P10412, Q71DI3, P04908, P62805, O60814 0.203
713 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 Xenopus laevis 2022 O60814, P04908, Q71DI3, P62805 0.29
714 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 Xenopus laevis 2022 O60814, P04908, Q71DI3, P62805 0.224
715 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 P10412, Q71DI3, P04908, P62805, O60814 0.138
716 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 Xenopus laevis 2021 TATA-binding protein Transcription factors, Transcription-associated P13393 P02281, P84233, P06897, P62799 0.435
717 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 Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription factors, Transcription-associated P13393, P32773, P32774 P02281, P84233, P06897, P62799 0.516
718 7M1X EM 3.70 2021-09-29 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B 601 136 Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z Lewis, T.S., Sokolova, V., Jung, H., Ng, H., Tan, D. 10.1093/nar/gkab907 34643712 Xenopus laevis Xenopus laevis Mus musculus Xenopus laevis Xenopus laevis 2021 P02281, P0C0S6, P02302, P62799 0.391
719 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 Xenopus laevis 2021 Q6DKE3, P02281, P84233, P62799 0.445
720 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 P68431, P04908, P07305, P62805, O60814 0.246
721 6ZHX EM 2.50 2020-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class. Lehmann, L.C., Bacic, L., Hewitt, G., Brackmann, K., Sabantsev, A., Gaullier, G., Pytharopoulou, S., Degliesposti, G., Okkenhaug, H., Tan, S., Costa, A., Skehel, J.M., Boulton, S.J., Deindl, S. 10.1016/j.celrep.2020.108529 33357431 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2020 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.625
722 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 Xenopus laevis 2021 Histone deacetylase HDA1, HDA1 complex subunit 3,HDA1 complex subunit 3, HDA1 complex subunit 2 Histone_deacetylation, HDA1, Histone PTM erasers, Transcription-associated P53973, Q06623, Q06629 P84233, P06897, P62799, P02281, Q6AZJ8 0.189
723 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., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C. 10.1093/nar/gkae698 39149911 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Ubiquitin Ubiquitin P0CG47 P02281, P84233, P06897, P62799 0.445
724 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 Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer, Transcription-associated Q92793 P68431, P04908, P06899, P62805 0.195
725 8UW1 EM 2.88 2024-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome Gretarsson, K.H., Abini-Agbomson, S., Gloor, S.L., Weinberg, D.N., McCuiston, J.L., Kumary, V.U.S., Hickman, A.R., Sahu, V., Lee, R., Xu, X., Lipieta, N., Flashner, S., Adeleke, O.A., Popova, I.K., Taylor, H.F., Noll, K., Windham, C.L., Maryanski, D.N., Venters, B.J., Nakagawa, H., Keogh, M.C., Armache, K.J., Lu, C. 10.1126/sciadv.adp0975 39196936 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA (cytosine-5)-methyltransferase 3A DNA modification Q9Y6K1 P02281, P84233, P06897, A0A8J1LTD2 -
726 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 Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer, Transcription-associated Q92793 P68431, P04908, P06899, P62805 0.242
727 9DWH EM 3.30 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 117 DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite) Ryan, B.J., Weaver, T.M., Freudenthal, B.D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA polymerase beta P06746 P0C0S8, P62807, Q71DI3, P62805 0.384
728 9B2S EM 3.01 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 Haspin bound to nucleosome in position 1 Hicks, C.W., Gliech, C.R., Zhang, X., Rahman, S., Vasquez, S., Holland, A.J., Wolberger, C. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 Serine/threonine-protein kinase haspin Q8TF76 P02281, P84233, Q6AZJ8, P62799 0.536
729 9B1E EM 4.40 2024-10-09 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 181 Cryo-EM structure of native SWR1 bound to nucleosome (composite structure) Louder, R.K., Park, G., Ye, Z., Cha, J.S., Gardner, A.M., Lei, Q., Ranjan, A., Hollmuller, E., Stengel, F., Pugh, B.F., Wu, C. 10.1016/j.cell.2024.09.007 39357520 Drosophila melanogaster Drosophila melanogaster Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2024 Helicase SWR1, Vacuolar protein sorting-associated protein 72, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2, SWR1-complex protein 3 INO80, SRCAP (INO80), SWR1 (INO80), Chromatin remodelers, Euchromatin-associated, Transcription-associated Q05471, Q03388, Q12509, Q03433, Q03940, Q12464, P31376 P02293, P04911, P02299, A0A0B4KFZ9 0.191
730 8Y3F EM 4.54 2025-01-29 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Shimizu, M., Tanaka, H., Nishimura, M., Sato, N., Nozawa, K., Ehara, H., Sekine, S.I., Morishima, K., Inoue, R., Takizawa, Y., Kurumizaka, H., Sugiyama, M. 10.1093/pnasnexus/pgae484 39539301 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P68431, P04908, P06899, P62805 -
731 8Y3C EM 5.21 2025-01-29 octamer, hexamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 250 Cryo-EM structure of the overlapping di-nucleosome (closed form) Shimizu, M., Tanaka, H., Nishimura, M., Sato, N., Nozawa, K., Ehara, H., Sekine, S.I., Morishima, K., Inoue, R., Takizawa, Y., Kurumizaka, H., Sugiyama, M. 10.1093/pnasnexus/pgae484 39539301 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P68431, P04908, P06899, P62805 -
732 8X2Z EM 3.90 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.237
733 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 Xenopus laevis 2024 ATP-dependent DNA helicase DDM1 Heterochromatin-associated, Chromatin remodelers Q9XFH4 O23629, P59259, P59226, Q9LD28 0.403
734 8W9F EM 4.40 2024-05-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Wang, C., Chu, C., Guo, Z., Zhan, X. 10.1126/sciadv.adk7678 38598631 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 O60814, P68431, P04908, P62805 0.156
735 8U14 EM 3.90 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.352
736 8TXV EM 3.80 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Polyubiquitin-B Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, Ubiquitin, DNA repair Q8IYW5, P0CG47 P68431, P04908, P62807, P62805 0.432
737 8SMY EM 3.20 2024-01-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Hu, Q., Zhao, D., Cui, G., Bhandari, J., Thompson, J.R., Botuyan, M.V., Mer, G. 10.1016/j.molcel.2023.12.036 38242129 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 E3 ubiquitin-protein ligase RNF168, Ubiquitin-conjugating enzyme E2 D3 Histone_ubiquitination_H2AK15_writer, Histone_ubiquitination_H2AK13_reader, Histone PTM writers, Histone_ubiquitination_H2AK15_reader, E3 ubiquitin-protein ligation, Transcription-associated, Histone PTM readers, Histone_ubiquitination_H2AK13_writer, DNA repair Q8IYW5, P61077 P68431, P04908, P06899, P62805 0.544
738 8SKZ EM 3.50 2024-11-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome Nartey, W., Williams, G.J. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera Heterochromatin-associated, Chromatin remodelers Q9XFH4 P02281, P84233, P06897, A0A8J1LTD2 0.458
739 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 Xenopus laevis 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription factors, Transcription-associated O08785, Q9WTL8 P68431, P04908, P06899, P62805 0.267
740 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 Xenopus laevis 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 INO80, Chromatin remodelers G0RYI5, G0RYC2, G0RY01, G0S590, G0S589 P62807, P68431, Q93077, P62805 0.556
741 8KD3 EM 2.90 2023-09-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 164 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Dong, S., Li, H., Wang, M., Rasheed, N., Zou, B., Gao, X., Guan, J., Li, W., Zhang, J., Wang, C., Zhou, N., Shi, X., Li, M., Zhou, M., Huang, J., Li, H., Zhang, Y., Wong, K.H., Zhang, X., Chao, W.C.H., He, J. 10.1038/s41422-023-00869-1 37666978 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Histone deacetylase RPD3, Transcriptional regulatory protein SIN3, Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P32561, P22579, Q12432, Q04779 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.376
742 8JHO EM 7.60 2023-09-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 340 Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Li, W., Cui, H., Lu, Z., Wang, H. 10.1038/s41594-023-01121-5 37798513 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, RCO1 isoform 1 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q12432, Q04779 P02281, P84233, P06897, P62799 0.067
743 8JHG EM 3.58 2023-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 160 Native SUV420H1 bound to 167-bp nucleosome Lin, F., Zhang, R., Shao, W., Lei, C., Ma, M., Zhang, Y., Wen, Z., Li, W. 10.1038/s41421-023-00620-5 38052811 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone-lysine N-methyltransferase KMT5B Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 O60814, P68431, P04908, P62805 0.456
744 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 Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P84243, P06899, P04908, P62805 0.313
745 8IHT EM 3.72 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Rpd3S bound to the nucleosome Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. 10.1038/s41422-023-00884-2 37845487 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, RCO1 isoform 1, Chromatin modification-related protein EAF3 Telomere-associated, Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair P22579, P32561, Q04779, Q12432 P02281, P84233, P06897, P62799 0.345
746 8IHM EM 3.58 2024-03-20 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 158 Eaf3 CHD domain bound to the nucleosome Zhang, Y., Xu, M., Wang, P., Zhou, J., Wang, G., Han, S., Cai, G., Wang, X. 10.1038/s41422-023-00884-2 37845487 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 Rco1-ABR, Chromatin modification-related protein EAF3 Histone PTM writers, NuA4, Transcription-associated, Rpd3, Histone PTM erasers, Histone_acetylation_writer, Histone_deacetylation, DNA repair Q04779, Q12432 P02281, P84233, P06897, P62799 0.434
747 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 Xenopus laevis 2023 CREB-binding protein Histone_acetylation_H3K18_writer, Histone PTM writers, Histone_acetylation_H3K27_writer, Transcription-associated Q92793 P68431, P04908, P06899, P62805 0.209
748 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 Xenopus laevis 2020 Transcription factor SOX-11 Transcription factors, Transcription-associated P35716 O60814, P04908, Q71DI3, P62805 0.355
749 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 Xenopus laevis 2020 O60814, P04908, Q71DI3, P62805 0.47
750 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 Xenopus laevis 2019 Q6FI13, P49450, P62807, P62805 0.512
751 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 Xenopus laevis 2019 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 Q6FI13, P49450, P62807, P62805 0.372
752 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
753 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
754 7YRD EM 3.20 2023-08-16 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 histone methyltransferase Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. 10.1016/j.molcel.2023.07.001 37536340 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P06899, P0C0S5, Q71DI3, P62805 0.484
755 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_deubiquitination_H2AK119, Polycomb, Transcription-associated, Heterochromatin-associated, Histone PTM erasers, Ubiquitin Q92560, P0CG47, Q8IXJ9 P20671, P68431, P10412, Q16778, P62805 0.435
756 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 Xenopus laevis 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.264
757 7LYC EM 2.94 2021-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G. 10.1038/s41586-021-03716-8 34321665 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 Ubiquitin, BRCA1-associated RING domain protein 1 Histone PTM writers, Histone_ubiquitination_H2AK127_writer, E3 ubiquitin-protein ligation, Transcription-associated, Histone_ubiquitination_H2AK125_writer, Ubiquitin, DNA repair, Histone_ubiquitination_H2AK129_writer P0CG47, Q99728 P68431, P04908, P06899, P62805 0.566
758 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 Xenopus laevis 2021 P68431, P04908, P06899, P62805 0.59
759 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 Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P84243, P06899, P04908, P62805 0.238
760 7XTI EM 3.90 2022-10-12 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 85 RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Histone chaperones, RNA polymerases, DNA replication, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated, DNA repair, FACT C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P84243, P06899, P04908, P62805 0.223
761 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 Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P84243, P06899, P04908, P62805 0.248
762 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 Xenopus laevis 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, F2QTN1, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.123
763 7ENN EM 2.80 2021-07-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 146 The structure of ALC1 bound to the nucleosome Wang, L., Chen, K., Chen, Z. 10.1038/s41467-021-24320-4 34210977 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 Chromodomain-helicase-DNA-binding protein 1-like CHD, DNA repair, Chromatin remodelers Q86WJ1 P02281, P84233, P06897, P62799 0.567
764 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 Xenopus laevis 2017 P68431, P04908, P06899, P62805 -
765 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 Xenopus laevis 2010 P02281, P84233, P06897, P62799 -
766 8HAI EM 4.70 2023-05-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 147 Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Kikuchi, M., Morita, S., Wakamori, M., Sato, S., Uchikubo-Kamo, T., Suzuki, T., Dohmae, N., Shirouzu, M., Umehara, T. 10.1038/s41467-023-39735-4 37460559 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Histone acetyltransferase p300 Histone PTM writers, p300, Cell cycle, Transcription-associated, Histone_acetylation_writer, DNA repair Q09472 P68431, P04908, P06899, P62805 0.212
767 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 Xenopus laevis 2019 scFv P49450, P06899, P04908, P62805 0.59
768 9MU9 EM 7.80 2025-02-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 174 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Venette-Smith, N.L., Vishwakarma, R.K., Dollinger, R., Schultz, J., Venkatakrishnan, V., Babitzke, P., Anand, G., Gilmour, D.S., Armache, J.-P., Murakami, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2025 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 RPB5, DNA-directed RNA polymerases I, II, and III subunit RPABC2, 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 polymerase II subunit RPB12 P04052, P08266, O97183, Q7JZF5, Q24320, Q9VNZ3, P36958, Q9VC49, Q9VJE4, Q6IGE3 P84040, P84051, P02299, P02283 0.202
769 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 Q92522, P68431, P06899, P04908, P62805 -
770 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 Xenopus laevis 2024 O23629, P59259, P59226, Q9LD28 0.5
771 8VMN EM 3.50 2025-01-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 157 H3K4me3 nucleosome bound to PRC2_AJ1-450 Cookis, T., Lydecker, A., Sauer, P., Kasinath, V., Nogales, E. 10.1038/s41594-024-01452-x 39774834 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 A0A8J1LZU9, Q6AZJ8, Q71DI3, P62805 0.39
772 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 Xenopus laevis 2024 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 Chromatin remodelers, SWI/SNF, Transcription-associated O60264 P02281, P84233, P06897, P62799 0.456
773 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 Xenopus laevis 2004 P02281, P84233, P06897, P62799 -
774 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 Xenopus laevis 2007 P84040, P84051, P02299, P02283 -
775 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 Xenopus laevis 2011 P68431, P04908, P06899, P62805 -
776 6GEN EM 3.60 2018-10-17 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 173 Chromatin remodeller-nucleosome complex at 4.5 A resolution. Willhoft, O., Ghoneim, M., Lin, C.L., Chua, E.Y.D., Wilkinson, M., Chaban, Y., Ayala, R., McCormack, E.A., Ocloo, L., Rueda, D.S., Wigley, D.B. 10.1126/science.aat7716 30309918 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2018 Helicase SWR1, Actin-like protein ARP6, Vacuolar protein sorting-associated protein 71, RuvB-like protein 1, RuvB-like protein 2 INO80, SWR1 (INO80), Chromatin remodelers, Euchromatin-associated, Transcription-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02293, P02309, P04911, P61830 0.195
777 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 Xenopus laevis 2019 Centromere protein C Nuclear division, CENP-A NAC/CAD, Centromere-associated, Kinetochore Q03188 Q6FI13, P49450, P62807, P62805 0.309
778 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 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
779 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 Xenopus laevis 2019 P84243, P62807, P0C0S8, P62805 0.373
780 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 Xenopus laevis Xenopus laevis 2019 Histone-lysine N-methyltransferase Histone PTM writers, Euchromatin-associated, Histone_methylation_H3K36_writer, Transcription-associated G0S676 P02281, P0CH09, P02302, P62799 0.364
781 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 Xenopus laevis 2020 P68431, P04908, P06899, P62805 -
782 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3 P02281, P84233, Q6AZJ8, P62799 0.132
783 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 Xenopus laevis 2019 Histone-lysine N-methyltransferase, H3 lysine-79 specific, Ubiquitin Ubiquitin, Histone PTM writers, Histone_methylation_H3K79_writer, Histone_ubiquitination_H2BK120_reader Q8TEK3, P62979 P02281, A0A310TTQ1, P62799, Q6AZJ8 0.132
784 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 Xenopus laevis 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 RNA polymerases, Transcription factors, Euchromatin-associated, SPT4-SPT5 complex, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P84243, P06899, P04908, P62805 0.244
785 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 Xenopus laevis 2019 P68431, P04908, P06899, P62805 -
786 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 Xenopus laevis 2017 Maltose-binding periplasmic protein, Centromere protein N chimera P0AEX9 P49450, P06899, P04908, P62805 0.372
787 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 Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
788 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 Xenopus laevis 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 Euchromatin-associated, RNA polymerases, Transcription-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1 P84243, P06899, P04908, P62805 0.11
789 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 Xenopus laevis 2016 P04908, P06899, Q71DI3, P62805 -
790 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 Xenopus laevis 2016 P04908, P0DPK2, P06899, P62805 -
791 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 Xenopus laevis 2015 P02281, P84233, P06897, P62799 -
792 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 Xenopus laevis 2016 Q6NXT2, P04908, P06899, P62805 -
793 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 Xenopus laevis 2015 P68431, P04908, P06899, P62805 -
794 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 Xenopus laevis 2016 P02281, P84233, P06897, P62799 -
795 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 Xenopus laevis 2014 P02281, P84233, Q6AZJ8, P62799 -
796 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 Xenopus laevis 2012 P02281, P84233, P06897, P62799 -
797 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 Xenopus laevis 1998 P02281, P06897, P02302, P62799 -