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 |