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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 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 Kinetochore, CCAN, CBF3, Nuclear division, Centromere-associated, Transcription-associated, Cell cycle P17106, P40969, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P52286, P43618, P38313, Q2V2P8, Q12493, Q06162, P04911 P04911, P36012, P02293, P02309 0.165
1 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 Kinetochore, CCAN, Nuclear division, Centromere-associated, Cell cycle P35201, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P38313, Q12493, Q06162 P02294, P36012, P04911, P02309, P02293 0.328
2 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 PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, Nuclear division, Transcription-associated, Cell cycle Q9NQR1 P06899, P04908, P68431, P62805 0.514
3 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 PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, Nuclear division, Transcription-associated, Cell cycle Q9NQR1 P06899, P04908, P62805, P49450 0.446
4 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 Kinetochore, Nuclear division, Centromere-associated, CBF3 P40969 P04911, P61830, P02293, P02309 0.3
5 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q96H22 Q93077, P62805, P62807, P49450 0.559
6 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q96H22 Q93077, P62805, P62807, P49450 0.179
7 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q96H22 Q93077, P62805, P62807, P49450 0.114
8 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 Kinetochore, CCAN, Nuclear division, Centromere-associated, Transcription-associated, Cell cycle P17106, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P43618, P38313, Q2V2P8, Q12493, Q06162 P04911, P36012, P02293, P02309 0.2
9 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 Kinetochore, Nuclear division, Centromere-associated O57392, P0AEX9 Q16778, P04908, P84229, P62805 0.387
10 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 Kinetochore, Nuclear division, Centromere-associated Q66LH7 P84040, P02299, P02283, P84051 -
11 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q03188 Q93077, P62805, P62807, P49450 0.573
12 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 Kinetochore, CENP-A NAC/CAD, DNA repair, Fanconi anemia core complex, Nuclear division, Centromere-associated, Transcription-associated, Cell cycle Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q8N2Z9, Q96BT3, Q71F23, Q5EE01, A8MT69, Q03188 Q93077, P62805, P62807, P49450 0.054
13 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 PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, Nuclear division, Transcription-associated, Cell cycle P21827, Q9NQR1 P02281, P06897, P84233, P62799 -
14 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, P06897, P84233, P62799 0.574
15 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 Histone PTM writers, Nuclear division, Cell cycle, Histone_phosphorylation_H3T3_writer Q99986 Q71DI3, P0C0S8, P62807, P62805 0.56
16 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q96H22 Q93077, P62805, P62807, P49450 0.39
17 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q03188, Q96H22 Q93077, Q5QNW6, P62805, P49450 0.401
18 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q03188 Q93077, P62805, P62807, P49450 0.571
19 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q03188 P62807, P62805, Q6FI13, P49450 0.416
20 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 Kinetochore, CENP-A NAC/CAD, Nuclear division, Centromere-associated, Transcription-associated, Cell cycle Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q13352, Q71F23, Q03188 Q93077, P62805, P62807, P49450 0.075
21 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q03188 P62807, P62805, Q6FI13, P49450 0.309
22 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q03188 P62807, P62805, Q6FI13, P49450 0.372
23 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 PTM writers, Heterochromatin-associated, Histone_methylation_H4K20_writer, Nuclear division, Transcription-associated, Cell cycle Q9NQR1 P02281, P06897, P84233, P62799 0.475
24 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 Kinetochore, CCAN, Nuclear division, Centromere-associated, Cell cycle P35201 P04911, P36012, P02293, P02309 0.47
25 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 Kinetochore, Nuclear division, Centromere-associated, CENP-A NAC/CAD Q03188, Q96H22 Q93077, Q5QNW6, P62805, P49450 0.369
26 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 Q6AZJ8, P02281, P84233, P62799 -