Search results:

Click PDB ID or Title to access structure information.
PDBID Method Resolution Release Date NLP types # NLPs H3 H4 H2A H2B H1 Dna variant Dna length Title Authors DOI Publication H3 taxa H4 taxa H2A taxa H2B taxa H1 taxa Release Year Interactors Interactor categories Interactor UIDS Histone UIDS Q-score
0 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
1 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
2 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
3 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
4 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
5 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
6 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
7 7YRG EM 4.20 2023-12-13 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 histone methyltransferase Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. 10.1016/j.molcel.2023.07.001 37536340 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P02281, P84233, P0C0S5, P62799 0.227
8 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
9 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
10 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
11 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 -
12 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
13 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
14 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
15 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
16 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
17 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
18 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
19 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
20 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
21 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
22 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
23 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
24 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 -
25 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
26 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
27 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
28 7YRD EM 3.20 2023-08-16 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 histone methyltransferase Huang, L., Wang, Y., Long, H., Zhu, H., Wen, Z., Zhang, L., Zhang, W., Guo, Z., Wang, L., Tang, F., Hu, J., Bao, K., Zhu, P., Li, G., Zhou, Z. 10.1016/j.molcel.2023.07.001 37536340 Xenopus laevis Xenopus laevis Homo sapiens Xenopus laevis Xenopus laevis 2023 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B Histone_methylation_H4K20_writer, Histone PTM writers, Transcription-associated, Heterochromatin-associated, DNA repair Q4FZB7 P06899, P0C0S5, Q71DI3, P62805 0.484
29 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
30 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
31 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
32 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
33 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
34 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
35 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
36 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
37 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
38 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
39 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