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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 9MPP EM 3.10 2025-10-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 166 The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L Yan, Y., Zhou, X.E., Thomas, S.L., Liu, M., Lai, G.Q., Worden, E.J., Jones, P.A., Xu, T.H. 10.1038/s41594-025-01704-4 41174279 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2025 DNA (cytosine-5)-methyltransferase 3A, DNA (cytosine-5)-methyltransferase 3-like DNA modification Q9Y6K1, Q9UJW3 P06897, P84233, P62799, P02281 0.282
1 9E3D EM 3.80 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 320 Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.153
2 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, P62805, P0C0S8 0.506
3 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 modification, DNA repair P29372 P06897, P84233, P62799, P02281 0.466
4 9E0R EM 3.20 2026-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Cryo-EM structure of a single nucleosome (1) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.345
5 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 modification, DNA repair P29372 P06897, P84233, P62799, P02281 0.466
6 9Y4P EM 3.84 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 321 Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 Isoform 7 of DNA (cytosine-5)-methyltransferase 3B, DNA (cytosine-5)-methyltransferase 3A DNA modification, Transcription-associated Q9UBC3, Q9Y6K1 P06897, P62799, P02281, A0A310TTQ1, P84233 -
7 9E3R EM 6.90 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 319 Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.068
8 9E2Q EM 3.14 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 319 Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.145
9 9E2D EM 6.08 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 316 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.083
10 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 modification, DNA repair O15527 P06897, P84233, P62799, P02281 0.424
11 9E00 EM 3.75 2026-02-25 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 321 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, None -
12 9E3U EM 4.90 2026-01-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 165 Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Isoform 3 of DNA (cytosine-5)-methyltransferase 3B, DNA (cytosine-5)-methyltransferase 3A DNA modification, Transcription-associated Q9UBC3, Q9Y6K1 Q71DI3, A0A1B8Y854, P62805, None 0.124
13 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 modification, DNA repair O15527 Q71DI3, P62807, P62805, P0C0S8 0.41
14 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 P02302, P06897, P62799, P02281 0.443
15 9E2R EM 7.71 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 319 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Xie, X., Liu, M., Zhou, X.E., Worden, E., Jones, P. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.072
16 9E05 EM 8.00 2026-02-18 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 321 The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 3 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.159
17 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 P06897, P84233, P62799, P02281 0.403
18 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 modification, DNA repair P29372 P06897, P84233, P62799, P02281 0.515
19 9E09 EM 3.72 2026-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 156 Cryo-EM structure a single nucleosome (2) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9UBC3 Q71DI3, P62805, P06899, P0C0S8 0.316
20 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 modification, DNA repair O15527 P62807, P62805, Q93077, P84243 0.465
21 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 modification, DNA repair O15527 Q71DI3, P62807, P62805, P0C0S8 0.359
22 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 P06897, P84233, A0A8J1LTD2, P02281 -
23 9Q7U EM 3.40 2026-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 162 Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 DNA (cytosine-5)-methyltransferase 3A, Isoform 7 of DNA (cytosine-5)-methyltransferase 3B DNA modification, Transcription-associated Q9Y6K1, Q9UBC3 A0A310TTQ1, P06897, P62799, P02281 -