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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 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
1 8X2X EM 3.80 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P0AEX9, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.261
2 1F66 X-ray 2.60 2000-11-27 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z Suto, R.K., Clarkson, M.J., Tremethick, D.J., Luger, K. 10.1038/81971 11101893 Xenopus laevis Mus musculus Homo sapiens Xenopus laevis Xenopus laevis 2000 P02281, P84233, P62806, P0C0S5 -
3 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
4 6JOU X-ray 2.17 2020-03-25 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 Crystal structure of the human nucleosome containing H2A.Z.1 S42R Horikoshi, N., Kujirai, T., Sato, K., Kimura, H., Kurumizaka, H. 10.1016/j.bbrc.2019.06.012 31186139 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P68431, P06899, P0C0S5, P62805 -
5 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
6 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
7 8X31 EM 6.20 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.123
8 8X30 EM 4.30 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 Structure of piccolo NuA4 and H2A.Z nucleosome 2:1 complex Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6 Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, Q540A3, P38806, P47128 Q12692, P02309, P02293, P61830 0.165
9 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
10 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
11 5B31 X-ray 2.20 2016-08-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A,H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Horikoshi, N., Arimura, Y., Taguchi, H., Kurumizaka, H. 10.1098/rsob.160127 27358293 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P68431, P06899, P0C0S5, P04908, P62805 -
12 5B33 X-ray 2.92 2016-08-03 octamer 1 H3.3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the H2AZ nucleosome with H3.3. Horikoshi, N., Arimura, Y., Taguchi, H., Kurumizaka, H. 10.1098/rsob.160127 27358293 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P84243, P0C0S5, P06899, P62805 -
13 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
14 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
15 3WA9 X-ray 3.07 2013-12-18 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The nucleosome containing human H2A.Z.1 Horikoshi, N., Sato, K., Shimada, K., Arimura, Y., Osakabe, A., Tachiwana, H., Hayashi-Takanaka, Y., Iwasaki, W., Kagawa, W., Harata, M., Kimura, H., Kurumizaka, H. 10.1107/S090744491302252X 24311584 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P68431, P06899, P0C0S5, P62805 -
16 8X2Y EM 4.10 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class1 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P0AEX9, P08515, P38806 Q12692, P02309, P02293, P61830 0.229
17 3WAA X-ray 3.20 2013-12-18 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The nucleosome containing human H2A.Z.2 Horikoshi, N., Sato, K., Shimada, K., Arimura, Y., Osakabe, A., Tachiwana, H., Hayashi-Takanaka, Y., Iwasaki, W., Kagawa, W., Harata, M., Kimura, H., Kurumizaka, H. 10.1107/S090744491302252X 24311584 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P68431, P06899, Q71UI9, P62805 -
18 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
19 5Z30 X-ray 2.45 2018-07-18 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T., Kurumizaka, H. 10.1093/nar/gky661 30053102 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2018 P68431, P06899, P0C0S5, P62805 -
20 5B32 X-ray 2.35 2016-08-03 octamer 1 H3.3 canonical_H4 canonical_H2A,H2A.Z canonical_H2B alphasat_146 146 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Horikoshi, N., Arimura, Y., Taguchi, H., Kurumizaka, H. 10.1098/rsob.160127 27358293 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P84243, P06899, P0C0S5, P04908, P62805 -
21 8X2Z EM 3.90 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.237
22 8X32 EM 4.40 2025-03-19 octamer 1 canonical_H3 canonical_H4 H2A.Z canonical_H2B alphasat_146 146 The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ Complex with Ac-CoA at resetting state Wang, L., Zhang, H., Jia, Q., Li, W., Yang, C., Ma, L., Li, M., Lu, Y., Zhu, H., Zhu, P. 10.1073/pnas.2414490122 40100634 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2025 Histone acetyltransferase, Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6, glutathione transferase,Enhancer of polycomb-like protein, Chromatin modification-related protein Histone PTM writers, NuA4, Cell cycle, Transcription-associated, Histone_acetylation_writer Q08649, P47128, Q540A3, P38806 Q12692, P02309, P02293, P61830 0.114
23 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