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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	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
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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	-
22	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
23	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	-
24	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	-
25	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	-
26	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
27	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
28	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
29	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
30	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
31	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
32	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
33	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
34	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
35	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
36	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
37	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	-
38	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
39	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
40	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
41	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	-
42	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
43	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
44	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
45	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
46	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
47	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
48	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
49	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
50	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
51	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
52	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	-
53	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	-
54	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
55	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
56	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
57	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
58	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
59	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
60	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
61	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	-
62	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
63	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
64	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
65	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
66	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
67	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
68	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
69	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	-
70	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
71	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
72	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
73	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
74	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
75	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
76	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
77	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
78	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
79	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
80	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
81	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
82	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	-
83	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
84	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
85	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
86	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
87	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
88	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
89	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
90	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
91	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
92	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
93	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	-
94	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
95	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
96	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
97	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	-
98	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
99	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
100	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
101	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
102	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
103	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
104	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
105	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
106	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
107	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
108	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
109	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
110	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
111	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
112	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
113	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
114	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
115	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
116	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
117	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
118	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
119	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
120	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
121	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
122	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
123	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
124	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
125	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
126	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
127	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
128	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
129	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
130	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
131	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	-
132	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	-
133	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
134	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
135	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
136	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
137	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
138	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	-
139	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
140	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
141	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	-
142	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
143	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
144	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
145	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	-
146	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
147	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	-
148	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
149	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
150	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
151	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	-
152	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
153	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
154	6UPK	EM	4.90	2019-12-11	hexamer	1	canonical_H3	canonical_H4	canonical_H2A	canonical_H2B		601_modified	72	Structure of FACT_subnucleosome complex 1	Liu, Y., Zhou, K., Zhang, N., Wei, H., Tan, Y.Z., Zhang, Z., Carragher, B., Potter, C.S., D'Arcy, S., Luger, K.	10.1038/s41586-019-1820-0	31775157	Homo sapiens	Homo sapiens	Homo sapiens	Homo sapiens	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
155	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
156	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	-
157	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
158	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
159	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
160	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
161	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
162	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
163	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
164	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
165	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
166	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
167	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	-
168	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
169	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
170	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	-
171	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	-
172	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	-
173	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	-
174	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	-
175	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
176	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
177	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
178	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
179	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
180	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
181	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
182	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	-
183	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
184	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
185	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
186	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
187	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
188	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
189	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
190	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
191	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
192	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	-
193	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
194	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
195	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
196	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
197	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
198	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
199	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
200	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
201	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
202	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
203	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
204	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
205	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
206	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
207	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
208	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	-
209	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
210	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
211	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
212	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
213	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
214	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
215	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
216	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
217	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
218	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
219	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
220	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	-
221	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
222	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
223	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
224	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
225	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
226	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
227	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
228	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
229	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
230	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
231	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
232	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
233	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
234	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
235	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
236	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
237	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
238	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	-
239	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
240	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
241	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	-
242	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	-
243	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
244	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
245	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
246	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
247	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
248	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
249	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
250	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
251	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
252	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
253	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
254	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
255	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
256	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
257	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
258	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
259	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
260	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
261	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
262	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
263	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
264	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
265	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
266	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
267	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
268	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
269	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
270	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
271	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
272	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
273	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
274	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
275	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
276	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
277	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
278	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
279	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
280	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
281	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
282	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
283	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
284	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
285	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
286	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
287	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
288	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
289	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
290	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
291	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
292	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
293	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
294	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
295	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
296	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
297	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
298	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
299	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
300	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
301	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
302	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
303	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
304	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
305	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
306	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
307	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
308	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
309	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
310	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
311	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
312	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
313	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
314	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
315	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
316	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	-
317	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
318	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
319	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
320	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
321	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
322	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
323	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
324	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
325	6NQA	EM	3.54	2019-02-20	octamer	1	canonical_H3	canonical_H4	canonical_H2A	canonical_H2B		601	146	Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex	Worden, E.J., Hoffmann, N.A., Hicks, C.W., Wolberger, C.	10.1016/j.cell.2019.02.002	30765112	Xenopus laevis	Xenopus laevis	Xenopus laevis	Xenopus laevis	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
326	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
327	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
328	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
329	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
330	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
331	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
332	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
333	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
334	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
335	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
336	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
337	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
338	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
339	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
340	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
341	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
342	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
343	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
344	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
345	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
346	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
347	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
348	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
349	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
350	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
351	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
352	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
353	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
354	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
355	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
356	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
357	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	-
358	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
359	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
360	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
361	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
362	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
363	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	-
364	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
365	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
366	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
367	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
368	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
369	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	-
370	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
371	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
372	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
373	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
374	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
375	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
376	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
377	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	-
378	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
379	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
380	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	-
381	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
382	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	-
383	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
384	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
385	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
386	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
387	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
388	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
389	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
390	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
391	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
392	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
393	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
394	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	-
395	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
396	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
397	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
398	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
399	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
400	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
401	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
402	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
403	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
404	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
405	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
406	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
407	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
408	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
409	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
410	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
411	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
412	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
413	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
414	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
415	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
416	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
417	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
418	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
419	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
420	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
421	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
422	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
423	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
424	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
425	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
426	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
427	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
428	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
429	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
430	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
431	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
432	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
433	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
434	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
435	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
436	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
437	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
438	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
439	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
440	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
441	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
442	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
443	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
444	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
445	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	-
446	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	-
447	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
448	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
449	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
450	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
451	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
452	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
453	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
454	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
455	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
456	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
457	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
458	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
459	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
460	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
461	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
462	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
463	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
464	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
465	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	-
466	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
467	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
468	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
469	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
470	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
471	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
472	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
473	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
474	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
475	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
476	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
477	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
478	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
479	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
480	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
481	6NZO	EM	3.80	2019-08-28	octamer	1	canonical_H3	canonical_H4	canonical_H2A	canonical_H2B		601	145	Set2 bound to nucleosome	Bilokapic, S., Halic, M.	10.1038/s41467-019-11726-4	31439846	Xenopus laevis	Xenopus laevis	Saccharomyces cerevisiae	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
482	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
483	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
484	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
485	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
486	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
487	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
488	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	-
489	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
490	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
491	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
492	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
493	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	-
494	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
495	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
496	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
497	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
498	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
499	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
500	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
501	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
502	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
503	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
504	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
505	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
506	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
507	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
508	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
509	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
510	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
511	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
512	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
513	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
514	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
515	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
516	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
517	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
518	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
519	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
520	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
521	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
522	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
523	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
524	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
525	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
526	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
527	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
528	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
529	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
530	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	-
531	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
532	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
533	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
534	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
535	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	-
536	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	-
537	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
538	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
539	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
540	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
541	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	-
542	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
543	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	-
544	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
545	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
546	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
547	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
548	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
549	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
550	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
551	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
552	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
553	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

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