Search results:

Click PDB ID or Title to access structure information.
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 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, Transcription-associated, ORC P54784 P02294, P02309, P04912, P61830 0.311
1 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, Nuclear division, Kinetochore, CCAN P35201 P02309, P02293, P04911, P36012 0.47
2 9R5W EM 3.80 2026-02-04 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 162 Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Hughes, A.L., Sundaramoorthy, R., Owen-Hughes, T. 10.7554/eLife.52513 41439750 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 P06897, P84233, P62799, P02281 0.351
3 9CB7 EM 4.04 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers P53115, P40154 P62799, P02293, P04911, P61830 0.288
4 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
5 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 Transcription-associated, Chromatin remodelers, Histone chaperones, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated P40019, Q05471, P38326, Q12509, Q03433, Q03940, Q12464, Q03388 P61830, Q12692, P02309, P02293, P04911 0.293
6 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 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04911, P61830 0.193
7 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, Transcription-associated, Histone PTM writers, Euchromatin-associated O00255 P06897, P84233, P62799, P02281 0.459
8 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 PTM readers, Histone_methylation_H4K20_reader, Ubiquitin, Histone_ubiquitination_H2AK15_reader, DNA repair, Telomere-associated Q12888, P0CG47 O60814, P16104, P68431, P62805 0.424
9 9QIK EM 3.03 2026-01-21 octamer 1 canonical_H3,H3.3 canonical_H4 H2A.X canonical_H2B 601 132 M2 nucleosome Shukla, S., Ngubo, M., Paul, S., Kunert, F., Persinger, J., Lee, J., Hopfner, K.P., Bartholomew, B. 10.1016/j.molcel.2025.10.010 41290000 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 P06897, A0A8T2P505, A0A8J1LTD2, P02281 -
10 9C9S EM 3.09 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 147 S.c INO80 in complex with S.c 0/40 nucleosome, Class 1 Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62799, P02293, P04911, P61830 0.424
11 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 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04912, P61830 0.185
12 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 P02309, P02293, P04911, P61830 0.3
13 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 -
14 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, P62805, P06899 -
15 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 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, P38326, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04911, P61830 0.324
16 9R5K EM 4.20 2026-01-28 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 162 Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Hughes, A.L., Sundaramoorthy, R., Owen-Hughes, T. 10.7554/eLife.52513 41439750 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 P06897, P84233, P62799, P02281 0.294
17 9MLR EM 3.10 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 126 GammaH2AX containing nucleosome, Half-wrapped (Class 2) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.511
18 9MLN EM 3.30 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 GammaH2AX containing nucleosome, Canonical (Class 1) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.419
19 9C9T EM 3.16 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 147 S.c INO80 in complex with S.c 0/40 nucleosome, Class 2 Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62799, P02293, P04911, P61830 0.399
20 9MMT EM 3.40 2025-10-29 hexamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 89 H2AX containing nucleosome, Unwrapped (Class 2) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.388
21 9MMO EM 3.90 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosomes, Right offset stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.34
22 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 Cell cycle, SWI/SNF, Transcription-associated, Chromatin remodelers P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785 P06897, Q6PI79, P62799, P02281 0.007
23 9MMM EM 4.00 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosomes, Parallel stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.204
24 9MLL EM 3.70 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 137 GammaH2AX containing nucleosomes, Parallel stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.26
25 9QCR EM 4.37 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 129 DNA-PK bound to 153 bp H2AX nucleosome model 2 Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.234
26 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 P02309, P02293, P04911, None 0.556
27 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, A8BI78, A8BUJ9, E2RU29 0.427
28 9QCS EM 4.38 2026-01-14 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 129 Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.185
29 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 Transcription-associated, Cell cycle, Centromere-associated, Nuclear division, E3 ubiquitin-protein ligation, Kinetochore, CCAN, CBF3 P17106, P40969, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P52286, P43618, P38313, Q2V2P8, Q12493, Q06162 P02309, P02293, P04911, P36012 0.165
30 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, P62805, P06899 -
31 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, Transcription-associated, ORC P54784 P02294, P02309, P04912, P61830 0.319
32 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 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464, Q03388 P02309, P02293, P04912, P61830 0.363
33 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
34 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 Transcription-associated, Cell cycle, Centromere-associated, Nuclear division, Kinetochore, CCAN P17106, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P43618, P38313, Q2V2P8, Q12493, Q06162 P02309, P02293, P04911, P36012 0.2
35 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, P62805, P06899 -
36 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 P02309, P02293, P04912, P61830 -
37 9Q8X EM 2.94 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 151 Ku70/80 bound to a 153 bp H2AX nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P16104, P68431, P62805, P06899 0.321
38 9Q80 EM 3.39 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 151 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5 DNA repair P12956, P13010 P16104, P68431, P62805, P06899 0.3
39 9MLS EM 3.60 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 107 GammaH2AX containing nucleosome, Extended (Class 3) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.413
40 9C9G EM 2.91 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 144 S.c INO80 in complex with S.c 0/80 nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62799, P02293, P04911, P61830 0.445
41 9LRV EM 2.99 2026-02-04 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 144 Cryo-EM structure of Fission yeast centromeric nucleosome Class 1 Xiong, Y., Jian, Y., Zhang, Y., Zhang, M., Zhang, X., Zhang, K., Fu, C., Tian, T., Zang, J. 10.1093/jmcb/mjaf056 41453208 Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Xenopus laevis 2026 P04913, Q9Y812, P04909, P09322 0.508
42 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, P04912, P61830 -
43 9Q9F EM 4.54 2026-01-14 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 129 DNA-PK bound to a 153 bp H2AX nucleosome model 1 Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.215
44 9R5S EM 3.80 2026-01-28 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 160 Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Hughes, A.L., Sundaramoorthy, R., Owen-Hughes, T. 10.7554/eLife.52513 41439750 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 Chromo domain-containing protein 1 CHD, Transcription-associated, Chromatin remodelers P32657 P06897, P84233, P62799, P02281 0.256
45 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 Transcription-associated, Chromatin remodelers, SRCAP (INO80), INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q03388, Q12509, Q03433, Q03940, Q12464, P31376 P02293, P04911, A0A0B4KFZ9, P02299 0.191
46 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 Q6CMU6, Q6CK60, Q6CK59, P36012 0.623
47 9OB1 EM 3.20 2026-03-04 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 145 S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2026 Chromatin-remodeling ATPase INO80, Actin-related protein 5, Chromatin-remodeling complex subunit IES6, RuvB-like protein 1, RuvB-like protein 2, Ino eighty subunit 2 INO80, DNA repair, Chromatin remodelers, Transcription-associated P53115, P53946, P32617, Q03940, Q12464, P40154 P62798, P02293, P04911, P61830 0.374
48 9LRW EM 3.04 2026-02-04 octamer 1 cenH3 canonical_H4 H2A.X canonical_H2B 601 140 Cryo-EM structure of Fission yeast centromeric nucleosome Class 2 Xiong, Y., Jian, Y., Zhang, Y., Zhang, M., Zhang, X., Zhang, K., Fu, C., Tian, T., Zang, J. 10.1093/jmcb/mjaf056 41453208 Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Schizosaccharomyces pombe (strain 972 / ATCC 24843) Xenopus laevis 2026 P04913, Q9Y812, P04909, P09322 0.436
49 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 Transcription-associated, Chromatin remodelers, INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P02293, P04911, P61830 0.195
50 9QMS EM 5.00 2026-01-14 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 141 DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Hall, C., Frit, P., Kefala-Stavridi, A., Pelletier, A., Hardwick, S.W., Amin, H., Bilyard, M.K., Maia De Oliviera, T., Tariq, A., Zahid, S., Chirgadze, D.Y., Balasubramanian, S., Meek, K., Ropars, V., Charbonnier, J.B., Modesti, M., Calsou, P., Britton, S., Blundell, T.L., Schalch, T., Chaplin, A.K. 10.1038/s41467-025-67376-2 41444611 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 X-ray repair cross-complementing protein 6, X-ray repair cross-complementing protein 5, DNA-dependent protein kinase catalytic subunit DNA repair P12956, P13010, P78527 P16104, P68431, P62805, P06899 0.168
51 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, Nuclear division, Kinetochore, CCAN P35201, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P38313, Q12493, Q06162 P36012, P02294, P02309, P02293, P04911 0.328
52 9MMK EM 3.20 2025-10-29 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosome, Canonical (Class 1) Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.552
53 9MMN EM 3.60 2025-10-29 octamer, octamer 2 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 143 H2AX containing nucleosomes, Left offset stack Panigrahi, R., Edwards, R., Islam, M.T., Lu, J., Kulepa, A., Kim, T.H., Mark Glover, J.N. 10.1093/nar/gkaf1028 41123210 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P16104, P68431, P62805, P06899 0.189
54 9CAU EM 4.18 2025-07-16 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B 601 146 DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome Kaur, U., Wu, H., Cheng, Y., Narlikar, G.J. 10.1126/science.adr3831 40674492 Saccharomyces cerevisiae Xenopus laevis Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 P62799, P02293, P04911, P61830 0.34
55 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 Transcription-associated, Chromatin remodelers, INO80, SWR1 (INO80), Euchromatin-associated Q05471, Q12509, Q03433, Q03940, Q12464 P02309, P02293, P04911, P61830 0.372