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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 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, P62805, P06899, P04908, P49450 0.071
1 1KX3 X-ray 2.00 2002-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J. 10.1016/S0022-2836(02)00386-8 12079350 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2002 P02281, P06897, P84233, P62799 -
2 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, P62805, P0C0S5, P06899, P04908 -
3 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 Q71DI3, O60814, P04908, P62805 0.224
4 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 Q6AZJ8, P02281, P02302, P62799 0.387
5 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
6 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 P62807, P62805, Q6FI13, P49450 0.512
7 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, P02299, P02283, P84051 0.206
8 3KUY X-ray 2.90 2010-01-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent Davey, G.E., Wu, B., Dong, Y., Surana, U., Davey, C.A. 10.1093/nar/gkp1174 20026584 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P06897, P84233, P62799 -
9 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 Q6AZJ8, P02281, P84233, P62799 0.494
10 1S32 X-ray 2.05 2004-05-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Molecular Recognition of the Nucleosomal 'Supergroove' Edayathumangalam, R.S., Weyermann, P., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1073/pnas.0401743101 15100411 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
11 3MGS X-ray 3.15 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Cesium ions to the Nucleosome Core particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P02281, P84233, P62799 -
12 3LJA X-ray 2.75 2010-04-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome Wu, B., Davey, C.A. 10.1016/j.jmb.2010.03.038 20350553 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P06897, P84233, P62799 -
13 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 P06899, P0C0S5, P68431, P62805 -
14 7VA4 EM 14.00 2022-07-27 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 539 Telomeric tetranucleosome in open state Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P04908, P68431, O60814, P62805 0.043
15 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 P06899, P04908, P68431, P62805 0.109
16 5X7X X-ray 2.18 2017-04-19 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Taguchi, H., Xie, Y., Horikoshi, N., Maehara, K., Harada, A., Nogami, J., Sato, K., Arimura, Y., Osakabe, A., Kujirai, T., Iwasaki, T., Semba, Y., Tachibana, T., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1021/acs.biochem.6b01098 28374988 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P06899, P84243, P04908, P62805 -
17 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 Q71DI3, P62805, P06897, P02281, P22844 -
18 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, P07305, P62805, P06899, P04908 -
19 5XM1 X-ray 3.45 2018-03-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4 Harada, A., Maehara, K., Ono, Y., Taguchi, H., Yoshioka, K., Kitajima, Y., Xie, Y., Sato, Y., Iwasaki, T., Nogami, J., Okada, S., Komatsu, T., Semba, Y., Takemoto, T., Kimura, H., Kurumizaka, H., Ohkawa, Y. 10.1038/s41467-018-03845-1 29643389 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2018 P62806, P84244, Q9D2U9, C0HKE1 -
20 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 P06899, P04908, P68431, P62805 -
21 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 Q71DI3, P0C0S8, P62807, P62805 0.534
22 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 P04908, P68431, Q7Z2G1, P62805 0.398
23 8OX0 EM 2.52 2023-08-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 Structure of apo telomeric nucleosome Hu, H., van Roon, A.M., Ghanim, G.E., Ahsan, B., Oluwole, A.O., Peak-Chew, S.Y., Robinson, C.V., Nguyen, T.H.D. 10.1126/sciadv.adi4148 37624885 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Q93077, P68431, P62807, P62805 0.607
24 3AFA X-ray 2.50 2010-05-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The human nucleosome structure Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H. 10.1073/pnas.1003064107 20498094 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2010 P06899, P04908, P68431, P62805 -
25 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, P07305, P62805, P06899, P04908 -
26 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
27 3W99 X-ray 3.00 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P06899, P04908, P68431, P62805 -
28 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, P06897, P84233, P62799 0.493
29 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, P07305, P62805, O60814, P04908 0.246
30 4WU8 X-ray 2.45 2015-09-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of trPtNAP-NCP145 Chua, E.Y., Davey, G.E., Chin, C.F., Droge, P., Ang, W.H., Davey, C.A. 10.1093/nar/gkv356 25916851 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P06897, P84233, P62799 -
31 6LE9 X-ray 2.60 2020-04-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Soman, A., Liew, C.W., Teo, H.L., Berezhnoy, N.V., Olieric, V., Korolev, N., Rhodes, D., Nordenskiold, L. 10.1093/nar/gkaa289 32374876 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P68431, O60814, P62805 -
32 1P3K X-ray 2.90 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
33 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 P15308, P62799, P84233, Q6DKE3, P02281 0.29
34 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 P62806, P0C0S5, P84233, P02281 -
35 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, P06897, P84233, P62799 0.55
36 5B40 X-ray 3.33 2016-06-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Machida, S., Sekine, S., Nishiyama, Y., Horikoshi, N., Kurumizaka, H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P06899, Q71DI3, P04908, P62805 -
37 5AV9 X-ray 2.20 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
38 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, P62805, P16402, P06899, P04908 -
39 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
40 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 P06899, P04908, P68431, P62805 -
41 6KE9 X-ray 2.22 2020-04-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Soman, A., Liew, C.W., Teo, H.L., Berezhnoy, N.V., Olieric, V., Korolev, N., Rhodes, D., Nordenskiold, L. 10.1093/nar/gkaa289 32374876 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P68431, O60814, P62805 -
42 3REH X-ray 2.50 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P06897, P84233, P62799 -
43 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, P02299, P02283, P84051 0.442
44 3AZJ X-ray 2.89 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
45 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 P0C0S5, P02281, P84233, P62799 0.508
46 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 Q71DI3, P62805, P10412, O60814, P04908 0.302
47 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 P06899, P04908, P68431, P62805 -
48 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, P62805, P0C0S5, P06899, P04908 -
49 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 Q57Z31, Q4GYX7, Q389T1, Q57YA3 0.439
50 5B0Z X-ray 1.99 2016-01-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Suzuki, Y., Horikoshi, N., Kato, D., Kurumizaka, H. 10.1016/j.bbrc.2015.12.041 26694698 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P06899, Q71DI3, P04908, P62805 -
51 5DNN X-ray 2.80 2016-09-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes Adhireksan, Z., Palermo, G., Riedel, T., Ma, Z., Muhammad, R., Rothlisberger, U., Dyson, P.J., Davey, C.A. 10.1038/ncomms14860 28358030 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P06897, P84233, P62799 -
52 3AZF X-ray 2.70 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
53 1ZBB X-ray 9.00 2005-07-12 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 347 Structure of the 4_601_167 Tetranucleosome Schalch, T., Duda, S., Sargent, D.F., Richmond, T.J. 10.1038/nature03686 16001076 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2005 P02281, P06897, P84233, P62799 -
54 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 P06899, P68431, P16104, P62805 -
55 9GXA EM 4.01 2025-01-29 H3_H4_tetramer, H3_H4_tetramer 2 cenH3 canonical_H4 alphasat_native 112 CENP-A/H4 di-tetrasome assembled on alpha-satellite DNA. Ali-Ahmad, A., Mors, M., Carrer, M., Li, X., Bilokapic, S., Halic, M., Cascella, M., Sekulic, N. 10.1101/2024.12.31.630874 39803555 Homo sapiens Homo sapiens Xenopus laevis Xenopus laevis Xenopus laevis 2025 P62805, P49450 -
56 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 Q71DI3, P62805, P10412, O60814, P04908 0.101
57 2CV5 X-ray 2.50 2005-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of human nucleosome core particle Tsunaka, Y., Kajimura, N., Tate, S., Morikawa, K. 10.1093/nar/gki663 15951514 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2005 P04908, P68431, O60814, P62805 -
58 6V2K X-ray 2.60 2020-11-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The nucleosome structure after H2A-H2B exchange Hirano, R., Arimura, Y., Kujirai, T., Shibata, M., Okuda, A., Morishima, K., Inoue, R., Sugiyama, M., Kurumizaka, H. 10.1038/s42003-021-01707-z 33580188 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P06899, P04908, P68431, P62805 -
59 3AZG X-ray 2.40 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
60 7NL0 EM 3.50 2021-08-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 131 Cryo-EM structure of the Lin28B nucleosome core particle Roberts, G.A., Ozkan, B., Gachulincova, I., O'Dwyer, M.R., Hall-Ponsele, E., Saxena, M., Robinson, P.J., Soufi, A. 10.1038/s41556-021-00727-5 34354236 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2021 P06899, P04908, P68431, P62805 0.519
61 5XF4 X-ray 2.87 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P06899, P04908, P68431, P62805 -
62 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, P06897, P84233, P62799 0.598
63 1ID3 X-ray 3.10 2001-09-28 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B alphasat_146 146 CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS White, C.L., Suto, R.K., Luger, K. 10.1093/emboj/20.18.5207 11566884 Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae Xenopus laevis 2001 P04911, P61830, P02294, P02309 -
64 6R94 EM 3.50 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP_THF2(-3) Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P06899, P04908, P68431, P62805 0.363
65 5AVC X-ray 2.40 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
66 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 P04908, P68431, Q7Z2G1, P62805 0.445
67 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 Q71DI3, P62805, P10412, O60814, P04908 0.217
68 5B2J X-ray 2.60 2016-06-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146_4CpG 142 Human nucleosome containing CpG methylated DNA Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S. 10.1002/2211-5463.12064 27419055 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P06899, P04908, P68431, P62805 -
69 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, P62805, P06899, P04908 -
70 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
71 6IQ4 X-ray 2.25 2019-10-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Batchelor, L.K., De Falco, L., von Erlach, T., Sharma, D., Adhireksan, Z., Roethlisberger, U., Davey, C.A., Dyson, P.J. 10.1002/anie.201906423 31478581 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P06899, P04908, P68431, P62805 -
72 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 P06897, P02281, P02302, P62799 0.196
73 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 P06899, P04908, P68431, P62805 -
74 5XM0 X-ray 2.87 2018-03-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4 Harada, A., Maehara, K., Ono, Y., Taguchi, H., Yoshioka, K., Kitajima, Y., Xie, Y., Sato, Y., Iwasaki, T., Nogami, J., Okada, S., Komatsu, T., Semba, Y., Takemoto, T., Kimura, H., Kurumizaka, H., Ohkawa, Y. 10.1038/s41467-018-03845-1 29643389 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2018 P62806, P84244, Q9D2U9, C0HKE1 -
75 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, P06897, P84233, P62799 0.508
76 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, P06897, P84233, P62799 0.569
77 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 P62807, P62805, Q6FI13, P49450 0.328
78 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 Q71DI3, P0C0S8, P62807, P62805 0.385
79 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, P06897, P84233, P62799 0.504
80 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
81 3X1S X-ray 2.80 2015-09-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the nucleosome core particle Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bbrc.2015.07.070 26188507 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P04908, P33778, P68431, P62805 -
82 5ZBX X-ray 2.58 2019-02-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Arimura, Y., Tachiwana, H., Takagi, H., Hori, T., Kimura, H., Fukagawa, T., Kurumizaka, H. 10.1038/s41467-019-08314-x 30718488 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P06899, P04908, P68431, P62805 -
83 5CPI X-ray 2.90 2015-10-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_2R 146 Nucleosome containing unmethylated Sat2R DNA Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H. 10.1098/rsob.150128 26446621 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
84 3AYW X-ray 2.90 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
85 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, A2YMC6, A2Y533, None 0.441
86 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 Q71DI3, P0C0S8, P62807, P62805 0.366
87 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 P0C0S6, P84243, P02281, P62799 0.455
88 4Z5T X-ray 2.80 2016-02-10 octamer 1 H3.5 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The nucleosome containing human H3.5 Urahama, T., Harada, A., Maehara, K., Horikoshi, N., Sato, K., Sato, Y., Shiraishi, K., Sugino, N., Osakabe, A., Tachiwana, H., Kagawa, W., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1186/s13072-016-0051-y 26779285 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P06899, P04908, Q6NXT2, P62805 -
89 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 P06899, P04908, P68431, P62805 0.631
90 8G86 EM 2.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 145 Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome) Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 Q6AZJ8, P02281, P84233, P62799 0.606
91 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 Q71DI3, P62805, P10412, O60814, P04908 0.177
92 5XF6 X-ray 2.63 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P06897, P84233, P62799 -
93 1P3L X-ray 2.40 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
94 3AN2 X-ray 3.60 2011-07-20 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_4_palindorm 121 The structure of the centromeric nucleosome containing CENP-A Tachiwana, H., Kagawa, W., Shiga, T., Osakabe, A., Miya, Y., Saito, K., Hayashi-Takanaka, Y., Oda, T., Sato, M., Park, S.-Y., Kimura, H., Kurumizaka, H. 10.1038/nature10258 21743476 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P62805, P49450 -
95 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 P68431, P62805, P06899, P04908, Q92522 -
96 5AV5 X-ray 2.40 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
97 6IPU X-ray 1.99 2020-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Human nucleosome core particle containing 145 bp of DNA 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 P06899, P04908, P68431, P62805 -
98 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 Q71DI3, P0C0S8, P62807, P62805 0.559
99 1P3M X-ray 2.90 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
100 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 P06899, P84243, P0C0S5, P62805 -
101 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, P06897, P84233, P62799 -
102 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 P04908, P68431, O60814, P62805 0.558
103 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 Q71DI3, O60814, P04908, P62805 0.29
104 1P3F X-ray 2.90 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
105 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 P06899, P04908, P68431, P62805 0.569
106 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, P06897, P84233, P62799 0.563
107 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 Q16778, P68431, P0C5Z0, P62805 0.493
108 5ONW X-ray 2.80 2017-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 146 X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C Frouws, T.D., Barth, P.D., Richmond, T.J. 10.1016/j.jmb.2017.10.029 29113904 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P06897, P84233, P62799 -
109 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 Q71DI3, P62805, P10412, O60814, P04908 0.329
110 4WU9 X-ray 2.60 2015-09-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Structure of cisPtNAP-NCP145 Chua, E.Y., Davey, G.E., Chin, C.F., Droge, P., Ang, W.H., Davey, C.A. 10.1093/nar/gkv356 25916851 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P06897, P84233, P62799 -
111 3W97 X-ray 3.20 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P06899, P04908, P68431, P62805 -
112 3B6G X-ray 3.45 2007-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome core particle treated with oxaliplatin Wu, B., Droge, P., Davey, C.A. 10.1038/nchembio.2007.58 18157123 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2007 P02281, P06897, P84233, P62799 -
113 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 P06899, P04908, P68431, P62805 0.598
114 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 Q71DI3, Q6AZJ8, P02281, P62805 0.258
115 7V9J EM 8.00 2022-07-27 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 399 Telomeric trinucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P04908, P68431, O60814, P62805 0.107
116 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 Q71DI3, P62805, P10412, O60814, P04908 0.105
117 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, P06897, P84233, P62799 0.587
118 5B0Y X-ray 2.56 2016-01-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Suzuki, Y., Horikoshi, N., Kato, D., Kurumizaka, H. 10.1016/j.bbrc.2015.12.041 26694698 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P06899, Q71DI3, P04908, P62805 -
119 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 P06899, P04908, P68431, P62805 -
120 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 P06899, P0C0S5, P68431, P62805 -
121 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 Q71DI3, P62805, P10412, O60814, P04908 0.267
122 3REJ X-ray 2.55 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P06897, P84233, P62799 -
123 5AV6 X-ray 2.20 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
124 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, P06897, P84233, P62799 0.301
125 1AOI X-ray 2.80 1998-09-30 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J. 10.1038/38444 9305837 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 1998 P06897, P02281, P02302, P62799 -
126 3AV2 X-ray 2.80 2011-06-01 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The human nucleosome structure containing the histone variant H3.3 Tachiwana, H., Osakabe, A., Shiga, T., Miya, Y., Kimura, H., Kagawa, W., Kurumizaka, H. 10.1107/S0907444911014818 21636898 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P84243, P04908, P62805 -
127 1EQZ X-ray 2.50 2000-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION Harp, J.M., Hanson, B.L., Timm, D.E., Bunick, G.J. 10.1107/S0907444900011847 11092917 Gallus gallus Gallus gallus Gallus gallus Gallus gallus Xenopus laevis 2000 P0C1H5, P62801, P84229, P02263 -
128 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 Q71DI3, O60814, P04908, P62805 0.281
129 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 Q71DI3, O60814, P04908, P62805 0.221
130 3UTB X-ray 2.20 2012-04-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b) 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, P06897, P84233, P62799 -
131 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, P59259, Q9FJE8, P59226 0.53
132 5AV8 X-ray 2.20 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
133 4J8X X-ray 2.87 2013-05-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P02281, P06897, P84233, P62799 -
134 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 Q6AZJ8, P02281, P84233, P62799 0.209
135 8RGM EM 4.00 2025-01-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 603 145 Cryo-EM structure of nucleosome containing Widom603 DNA Armeev, G.A., Moiseenko, A.V., Motorin, N.A., Afonin, D.A., Zhao, L., Vasilev, V.A., Oleinikov, P.D., Glukhov, G.S., Peters, G.S., Studitsky, V.M., Feofanov, A.V., Shaytan, A.K., Shi, X., Sokolova, O.S. 10.1016/j.str.2025.02.007 40101710 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P06899, P04908, P68431, P62805 0.352
136 3KWQ X-ray 3.50 2010-05-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Watanabe, S., Resch, M., Lilyestrom, W., Clark, N., Hansen, J.C., Peterson, C., Luger, K. 10.1016/j.bbagrm.2010.01.009 20100606 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 P02281, P06897, P84233, P62799 -
137 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 Q71DI3, Q6AZJ8, A0A8J1LZU9, P62805 0.39
138 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 P04908, P68431, P62807, P62805 0.43
139 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
140 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 Q71DI3, P62805, P10412, O60814, P04908 0.138
141 5Y0D X-ray 1.99 2018-07-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of the human nucleosome containing the H2B E76K 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 P06899, P04908, P68431, P62805 -
142 4YM5 X-ray 4.00 2015-12-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 143 Crystal structure of the human nucleosome containing 6-4PP (inside) Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H. 10.1038/srep16330 26573481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
143 3W96 X-ray 3.00 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P06899, P04908, P68431, P62805 -
144 5B24 X-ray 3.60 2016-03-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 144 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Horikoshi, N., Tachiwana, H., Kagawa, W., Osakabe, A., Matsumoto, S., Iwai, S., Sugasawa, K., Kurumizaka, H. 10.1016/j.bbrc.2016.01.170 26837048 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P06899, P04908, P68431, P62805 -
145 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, P07305, P62805, P06899, P04908 -
146 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 Q16778, P68431, P0C5Z0, P62805 0.365
147 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 Q71DI3, P0C0S8, P02281, P62805 0.375
148 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, A0A8C1JQV0, H2QSF5, A0A2Y9FT95, P06899 -
149 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 P06899, P04908, P68431, P62805 0.256
150 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, P06897, P84233, P62799 -
151 4XZQ X-ray 2.40 2015-10-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Chatterjee, N., North, J.A., Dechassa, M.L., Manohar, M., Prasad, R., Luger, K., Ottesen, J.J., Poirier, M.G., Bartholomew, B. 10.1128/MCB.00441-15 26416878 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P06897, P84233, P62799 -
152 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 Q71DI3, Q6AZJ8, A0A8J1LZU9, P62805 0.402
153 6KVD X-ray 2.21 2019-12-18 octamer 1 canonical_H3 canonical_H4 H2A.J canonical_H2B alphasat_146 146 Crystal structure of human nucleosome containing H2A.J Tanaka, H., Sato, S., Koyama, M., Kujirai, T., Kurumizaka, H. 10.1093/jb/mvz109 31793981 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P06899, P68431, Q9BTM1, P62805 -
154 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, P06897, P84233, P62799 0.55
155 3AZL X-ray 2.70 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
156 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 Q71DI3, P62805, P10412, O60814, P04908 0.203
157 4J8U X-ray 2.38 2013-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P02281, P06897, P84233, P62799 -
158 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, P06897, P84233, P62799 -
159 6KXV X-ray 3.63 2020-07-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of a nucleosome containing Leishmania histone H3 Dacher, M., Tachiwana, H., Horikoshi, N., Kujirai, T., Taguchi, H., Kimura, H., Kurumizaka, H. 10.1093/nar/gkz1040 31722422 Leishmania major Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P06899, P04908, Q4QHB5, P62805 -
160 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, P06897, P84233, P62799 0.186
161 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 A0A1B2JD99, A0A1B2JA70, A0A1B2JB78, A0A1B2JBS1 0.45
162 5Y0C X-ray 2.09 2018-07-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of the human nucleosome at 2.09 angstrom resolution 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 P06899, P04908, P68431, P62805 -
163 3X1T X-ray 2.81 2015-09-23 octamer 1 canonical_H3 canonical_H4 H2A.1 H2B.1 alphasat_146 146 Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bbrc.2015.07.070 26188507 Homo sapiens Homo sapiens Mus musculus Mus musculus Xenopus laevis 2015 P70696, P68431, Q8CGP4, P62805 -
164 3AZH X-ray 3.49 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
165 7V90 EM 3.50 2022-07-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 Telomeric mononucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P04908, P68431, O60814, P62805 0.459
166 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 P06899, P04908, P68431, P62805 0.59
167 5JRG X-ray 2.50 2017-03-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 144 Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Osakabe, A., Arimura, Y., Matsumoto, S., Horikoshi, N., Sugasawa, K., Kurumizaka, H. 10.1038/srep41783 28139742 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P06899, P04908, P68431, P62805 -
168 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 P06899, P04908, P68431, P62805 0.453
169 1KX4 X-ray 2.60 2002-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 X-Ray Structure of the Nucleosome Core Particle, NCP146b, at 2.6 A Resolution Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J. 10.1016/S0022-2836(02)00386-8 12079350 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2002 P02281, P06897, P84233, P62799 -
170 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 P36012, Q6CK59, Q6CMU6, Q6CK60 0.623
171 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, P06897, P84233, P62799 0.528
172 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 Q71DI3, P0C0S8, P62807, P62805 0.537
173 5B2I X-ray 3.00 2016-06-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146_4CpG 146 Human nucleosome containing CpG unmethylated DNA Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S. 10.1002/2211-5463.12064 27419055 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P06899, P04908, P68431, P62805 -
174 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 Q71DI3, P62805, P10412, O60814, P04908 0.351
175 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, P07305, P62805, P06899, P04908 -
176 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 Q6AZJ8, P02281, P84233, P62799 -
177 4J8W X-ray 2.41 2013-04-17 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P02281, P06897, P84233, P62799 -
178 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, A2YMC6, A2Y533, None 0.401
179 4J8V X-ray 2.58 2013-05-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Meier, S.M., Hanif, M., Adhireksan, Z., Pichler, V., Novak, M., Jirkovsky, E., Jakupec, M.A., Arion, V.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 10.1039/C3SC22294B 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2013 P02281, P06897, P84233, P62799 -
180 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 P68431, P62805, P16403, P06899, P04908 0.352
181 3AZK X-ray 3.20 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
182 3REK X-ray 2.60 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P06897, P84233, P62799 -
183 5B1M X-ray 2.34 2017-02-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The mouse nucleosome structure containing H3.1 Ueda, J., Harada, A., Urahama, T., Machida, S., Maehara, K., Hada, M., Makino, Y., Nogami, J., Horikoshi, N., Osakabe, A., Taguchi, H., Tanaka, H., Tachiwana, H., Yao, T., Yamada, M., Iwamoto, T., Isotani, A., Ikawa, M., Tachibana, T., Okada, Y., Kimura, H., Ohkawa, Y., Kurumizaka, H., Yamagata, K. 10.1016/j.celrep.2016.12.065 28099840 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2017 P68433, P62806, Q9D2U9, C0HKE1 -
184 3KXB X-ray 3.20 2010-06-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Watanabe, S., Resch, M., Lilyestrom, W., Clark, N., Hansen, J.C., Peterson, C., Luger, K. 10.1016/j.bbagrm.2010.01.009 20100606 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P02281, P84233, P62799 -
185 5GSU X-ray 3.10 2017-02-15 octamer 1 canonical_H3 canonical_H4 H2A.1 H2B.1 alphasat_146 146 Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B Padavattan, S., Thiruselvam, V., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bpc.2016.11.013 27992841 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 Q96QV6, P68431, Q96A08, P62805 -
186 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 P62799, P84233, P06897, P02281, P22844 -
187 3AV1 X-ray 2.50 2011-06-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The human nucleosome structure containing the histone variant H3.2 Tachiwana, H., Osakabe, A., Shiga, T., Miya, Y., Kimura, H., Kagawa, W., Kurumizaka, H. 10.1107/S0907444911014818 21636898 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, Q71DI3, P04908, P62805 -
188 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 Q6AZJ8, A0A310TTQ1, P02281, P62799 0.434
189 3AZI X-ray 2.70 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
190 6T79 EM 3.20 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 145 Structure of a human nucleosome at 3.2 A resolution Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Q71DI3, O60814, P04908, P62805 0.47
191 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 P06899, P68431, P16104, P62805 -
192 5Z23 X-ray 2.73 2019-02-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Arimura, Y., Tachiwana, H., Takagi, H., Hori, T., Kimura, H., Fukagawa, T., Kurumizaka, H. 10.1038/s41467-019-08314-x 30718488 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P06899, P04908, P68431, P62805 -
193 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 A8BI78, A8BUJ9, A8BHS7, E2RU29 0.427
194 1KX5 X-ray 1.94 2002-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J. 10.1016/S0022-2836(02)00386-8 12079350 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2002 P02281, P06897, P84233, P62799 -
195 5XF5 X-ray 2.82 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P06899, P04908, P68431, P62805 -
196 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 Q6AZJ8, P02281, P84233, P62799 0.198
197 6JR0 X-ray 2.50 2019-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the human nucleosome phased with 12 selenium atoms Saotome, M., Horikoshi, N., Urano, K., Kujirai, T., Yuzurihara, H., Kurumizaka, H., Kagawa, W. 10.1107/S2059798319012713 31588924 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P06899, P04908, P68431, P62805 -
198 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 Q71DI3, P62805, P10412, O60814, P04908 0.236
199 3X1V X-ray 2.92 2015-09-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 146 Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bbrc.2015.07.070 26188507 Homo sapiens Homo sapiens Homo sapiens Mus musculus Xenopus laevis 2015 P70696, P04908, P68431, P62805 -
200 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 Q71DI3, O60814, P04908, P62805 0.274
201 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 Q71DI3, P62805, P10412, O60814, P04908 0.268
202 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 P06899, P68431, Q71UI9, P62805 -
203 5GT3 X-ray 2.91 2017-02-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 146 Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b Padavattan, S., Thiruselvam, V., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bpc.2016.11.013 27992841 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P20671, P68431, Q96A08, P62805 -
204 3WKJ X-ray 2.80 2014-04-09 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 145 The nucleosome containing human TSH2B Urahama, T., Horikoshi, N., Osakabe, A., Tachiwana, H., Kurumizaka, H. 10.1107/S2053230X14004695 24699735 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2014 P04908, P68431, Q96A08, P62805 -
205 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 Q71DI3, P62805, P10412, O60814, P04908 0.208
206 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 P06899, P04908, P68431, P62805 -
207 7V9K EM 8.10 2022-07-27 octamer, octamer, octamer, octamer 4 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 539 Telomeric tetranucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P04908, P68431, O60814, P62805 0.076
208 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 Q71DI3, P62805, P10412, O60814, P04908 0.109
209 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 Q6AZJ8, A0A310TTQ1, A0A1B8Y854, P62798 0.322
210 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 O23629, Q9LHQ5, P59259, P59226 0.545
211 6R0C EM 4.20 2019-09-25 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B Human-D02 142 Human-D02 Nucleosome Core Particle with biotin-streptavidin label Wilson, M.D., Renault, L., Maskell, D.P., Ghoneim, M., Pye, V.E., Nans, A., Rueda, D.S., Cherepanov, P., Costa, A. 10.1038/s41467-019-12007-w 31519882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P84243, P0C0S8, P62807, P62805 0.373
212 3AZE X-ray 3.00 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
213 4XUJ X-ray 3.18 2016-01-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound Hanif, M., Meier, S.M., Adhireksan, Z., Henke, H., Martic, S., Labib, M., Kandioller, W., Jakupec, M.A., Kraatz, H.B., Davey, C.A., Keppler, B.K., Hartinger, C.G. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P06897, P84233, P62799 -
214 5GXQ X-ray 2.85 2017-04-19 octamer 1 H3.6 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The crystal structure of the nucleosome containing H3.6 Taguchi, H., Xie, Y., Horikoshi, N., Maehara, K., Harada, A., Nogami, J., Sato, K., Arimura, Y., Osakabe, A., Kujirai, T., Iwasaki, T., Semba, Y., Tachibana, T., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1021/acs.biochem.6b01098 28374988 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P06899, P04908, P62805, A0A1X8XL64 -
215 2F8N X-ray 2.90 2006-05-23 octamer 1 canonical_H3 canonical_H4 macroH2A,canonical_H2A canonical_H2B alphasat_146 145 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Chakravarthy, S., Luger, K. 0 Xenopus laevis Xenopus laevis Homo sapiens,Mus musculus Xenopus laevis Xenopus laevis 2006 P62799, P84233, Q8CGP6, P02281, Q9D2U9, O75367 -
216 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 P06899, P04908, P68431, P62805 0.724
217 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, P06897, P84233, P62799 0.339
218 1M19 X-ray 2.30 2003-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1016/S0022-2836(02)01407-9 12559907 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2003 P06897, P02281, P02302, P62799 -
219 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 P62806, A0A8X6EH29, Q9D2U9, C0HKE1 0.506
220 1P3G X-ray 2.70 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
221 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 P62799, P02281, P06897, P49450 -
222 3REL X-ray 2.70 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146b 146 2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Triamminechloroplatinum(II) Chloride Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P06897, P84233, P62799 -
223 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, P07305, P62805, P06899, P04908 -
224 1U35 X-ray 3.00 2005-09-27 octamer 1 canonical_H3 canonical_H4 macroH2A canonical_H2B alphasat_146 145 Crystal structure of the nucleosome core particle containing the histone domain of macroH2A Chakravarthy, S., Gundimella, S.K., Caron, C., Perche, P.Y., Pehrson, J.R., Khochbin, S., Luger, K. 10.1128/MCB.25.17.7616-7624.2005 16107708 Mus musculus Mus musculus Homo sapiens Mus musculus Xenopus laevis 2005 P68433, P62806, Q9D2U9, O75367 -
225 6JR1 X-ray 2.40 2019-10-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal structure of the human nucleosome phased with 16 selenium atoms Saotome, M., Horikoshi, N., Urano, K., Kujirai, T., Yuzurihara, H., Kurumizaka, H., Kagawa, W. 10.1107/S2059798319012713 31588924 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P06899, P04908, P68431, P62805 -
226 1P3P X-ray 2.70 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
227 4KGC X-ray 2.69 2014-03-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM Adhireksan, Z., Davey, G.E., Campomanes, P., Groessl, M., Clavel, C.M., Yu, H., Nazarov, A.A., Yeo, C.H., Ang, W.H., Droge, P., Rothlisberger, U., Dyson, P.J., Davey, C.A. 10.1038/ncomms4462 24637564 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2014 Q6AZJ8, P02281, P84233, P62799 -
228 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 P06899, P84243, P04908, P62805 0.655
229 5CPK X-ray 2.63 2015-10-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_2L 139 Nucleosome containing methylated Sat2L DNA Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H. 10.1098/rsob.150128 26446621 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
230 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 P06899, P68431, P0C0S8, P62805 0.588
231 4Z66 X-ray 2.50 2015-10-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Chatterjee, N., North, J.A., Dechassa, M.L., Manohar, M., Prasad, R., Luger, K., Ottesen, J.J., Poirier, M.G., Bartholomew, B. 10.1128/MCB.00441-15 26416878 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P06897, P84233, P62799 -
232 5ONG X-ray 2.80 2017-11-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 146 X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Frouws, T.D., Barth, P.D., Richmond, T.J. 10.1016/j.jmb.2017.10.029 29113904 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P06897, P84233, P62799 -
233 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 P06899, P04908, P68431, P62805 -
234 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 P68431, P62805, P06899, P04908, Q92522 -
235 3MNN X-ray 2.50 2011-04-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Wu, B., Ong, M.S., Groessl, M., Adhireksan, Z., Hartinger, C.G., Dyson, P.J., Davey, C.A. 10.1002/chem.201100298 21344528 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2011 P02281, P06897, P84233, P62799 -
236 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 P06899, P04908, P68431, P62805 0.085
237 5GT0 X-ray 2.82 2017-02-15 octamer 1 canonical_H3 canonical_H4 H2A.1 canonical_H2B alphasat_146 146 Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a Padavattan, S., Thiruselvam, V., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bpc.2016.11.013 27992841 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 Q96QV6, P62807, P68431, P62805 -
238 3C1B X-ray 2.20 2008-10-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure Lu, X., Simon, M.D., Chodaparambil, J.V., Hansen, J.C., Shokat, K.M., Luger, K. 10.1038/nsmb.1489 18794842 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2008 Q28D68, P06897, P84233, P62799 -
239 5XF3 X-ray 2.60 2017-10-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Davey, G.E., Adhireksan, Z., Ma, Z., Riedel, T., Sharma, D., Padavattan, S., Rhodes, D., Ludwig, A., Sandin, S., Murray, B.S., Dyson, P.J., Davey, C.A. 10.1038/s41467-017-01680-4 29146919 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2017 P06899, P04908, P68431, P62805 -
240 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, P02299, P02283, P84051 0.409
241 3A6N X-ray 2.70 2010-05-26 octamer 1 TS_H3.4 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 The nucleosome containing a testis-specific histone variant, human H3T Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H. 10.1073/pnas.1003064107 20498094 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2010 Q16695, P04908, P06899, P62805 -
242 3C1C X-ray 3.15 2008-10-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure Lu, X., Simon, M.D., Chodaparambil, J.V., Hansen, J.C., Shokat, K.M., Luger, K. 10.1038/nsmb.1489 18794842 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus laevis 2008 Q28D68, P06897, P84233, P62799 -
243 4YM6 X-ray 3.51 2015-12-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 144 Crystal structure of the human nucleosome containing 6-4PP (outside) Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H. 10.1038/srep16330 26573481 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
244 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 Q71DI3, P0C0S8, P62807, P62805 0.453
245 3AZN X-ray 3.00 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
246 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 P06899, Q71DI3, P04908, P62805 0.602
247 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 P06899, P04908, P68431, P62805 -
248 1M18 X-ray 2.45 2003-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1016/S0022-2836(02)01407-9 12559907 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2003 P06897, P02281, P02302, P62799 -
249 3B6F X-ray 3.45 2007-12-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome core particle treated with cisplatin Wu, B., Droge, P., Davey, C.A. 10.1038/nchembio.2007.58 18157123 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2007 P02281, P06897, P84233, P62799 -
250 5DNM X-ray 2.81 2016-09-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex Adhireksan, Z., Palermo, G., Riedel, T., Ma, Z., Muhammad, R., Rothlisberger, U., Dyson, P.J., Davey, C.A. 10.1038/ncomms14860 28358030 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P06897, P84233, P62799 -
251 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 P06899, P04908, P68431, P62805 -
252 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 P62806, P84244, Q6ZWY9, C0HKE1 0.6
253 1M1A X-ray 2.65 2003-02-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K. 10.1016/S0022-2836(02)01407-9 12559907 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2003 P06897, P02281, P02302, P62799 -
254 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, P06897, P84233, P62799 0.685
255 2PYO X-ray 2.43 2007-11-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Drosophila nucleosome core Clapier, C.R., Chakravarthy, S., Petosa, C., Fernandez-Tornero, C., Luger, K., Muller, C.W. 10.1002/prot.21720 17957772 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2007 P84040, P02299, P02283, P84051 -
256 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 Q9LD28, O23629, P59259, P59226 0.5
257 5F99 X-ray 2.63 2016-02-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B MMTV 147 X-ray Structure of the MMTV-A Nucleosome Core Particle Frouws, T.D., Duda, S.C., Richmond, T.J. 10.1073/pnas.1524607113 26787910 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P06897, P84233, P62799 -
258 6R93 EM 4.00 2019-06-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Cryo-EM structure of NCP-6-4PP Matsumoto, S., Cavadini, S., Bunker, R.D., Grand, R.S., Potenza, A., Rabl, J., Yamamoto, J., Schenk, A.D., Schubeler, D., Iwai, S., Sugasawa, K., Kurumizaka, H., Thoma, N.H. 10.1038/s41586-019-1259-3 31142837 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 P06899, P04908, P68431, P62805 0.352
259 2FJ7 X-ray 3.20 2006-09-26 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_A16 147 Crystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element Bao, Y., White, C.L., Luger, K. 10.1016/j.jmb.2006.06.051 16860337 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2006 P02281, P06897, P84233, P62799 -
260 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 P06899, P0C0S5, P68431, P62805 -
261 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 P06899, P04908, P68431, P62805 0.419
262 6L9H X-ray 2.60 2020-04-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 145 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Soman, A., Liew, C.W., Teo, H.L., Berezhnoy, N.V., Olieric, V., Korolev, N., Rhodes, D., Nordenskiold, L. 10.1093/nar/gkaa289 32374876 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 P04908, P68431, O60814, P62805 -
263 5CPJ X-ray 3.15 2015-10-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_2R 140 Nucleosome containing methylated Sat2R DNA Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y., Kurumizaka, H. 10.1098/rsob.150128 26446621 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
264 7V9C EM 4.50 2022-07-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 273 Telomeric Dinucleosome in open state Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P04908, P68431, O60814, P62805 0.109
265 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 Q71DI3, P0C0S8, P62807, P62805 0.526
266 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 P06899, P04908, P68431, P62805 0.32
267 2NZD X-ray 2.65 2007-04-10 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome core particle containing 145 bp of DNA Ong, M.S., Richmond, T.J., Davey, C.A. 10.1016/j.jmb.2007.02.062 17379244 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2007 P02281, P06897, P84233, P62799 -
268 8VLR EM 2.60 2025-01-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A H2B.1 alphasat_146 136 Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Shen, X.Y., Chen, C.X., Wang, Y., Zheng, W., Zheng, J.H., Jones, A.E., Zhu, B., Zhang, H., Lyons, C., Rijal, A., Moley, J.A., Cao, G.S., Liu, K., Winn, R., McGinty, R.K., Zhang, K., Wang, H.B. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 P04908, P68431, Q96A08, P62805 0.602
269 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 P62806, A0A8X6EH29, Q9D2U9, C0HKE1 0.391
270 3AZM X-ray 2.89 2011-09-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Iwasaki, W., Tachiwana, H., Kawaguchi, K., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1021/bi201021h 21812398 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2011 P06899, P04908, P68431, P62805 -
271 1P3O X-ray 2.75 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
272 5AVB X-ray 2.40 2015-12-23 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 human nucleosome core particle Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., Yokoyama, S. 10.1038/srep17204 26607036 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2015 P06899, P04908, P68431, P62805 -
273 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 Q6AZJ8, P02281, P84233, P62799 0.167
274 4YS3 X-ray 3.00 2015-10-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Chatterjee, N., North, J.A., Dechassa, M.L., Manohar, M., Prasad, R., Luger, K., Ottesen, J.J., Poirier, M.G., Bartholomew, B. 10.1128/MCB.00441-15 26416878 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2015 P02281, P06897, P84233, P62799 -
275 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, P06897, P84233, P62799 0.235
276 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 P06899, P04908, P68431, P62805 -
277 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
278 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, P07305, P62805, P06899, P04908 -
279 7V96 EM 3.92 2022-07-27 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 275 Telomeric Dinucleosome Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P04908, P68431, O60814, P62805 0.4
280 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, P06897, P84233, P62799 0.356
281 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, P07305, P62805, P06899, P04908 -
282 1P3A X-ray 3.00 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
283 6K1J X-ray 2.85 2020-01-15 octamer 1 canonical_H3 canonical_H4 H2A.X canonical_H2B alphasat_147 145 Human nucleosome core particle with H2A.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 P06899, P68431, P16104, P62805 -
284 5CP6 X-ray 2.60 2016-06-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] Ma, Z., Palermo, G., Adhireksan, Z., Murray, B.S., von Erlach, T., Dyson, P.J., Rothlisberger, U., Davey, C.A. 10.1002/anie.201602145 27184539 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2016 P02281, P06897, P84233, P62799 -
285 3MGP X-ray 2.44 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Cobalt ions to the Nucleosome Core Particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P02281, P84233, P62799 -
286 3O62 X-ray 3.22 2011-01-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link Todd, R.C., Lippard, S.J. 10.1016/j.chembiol.2010.10.018 21168769 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2011 P02281, P06897, P84233, P62799 -
287 3LEL X-ray 2.95 2010-05-19 octamer, octamer 2 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 147 Structural Insight into the Sequence-Dependence of Nucleosome Positioning Wu, B., Mohideen, K., Vasudevan, D., Davey, C.A. 10.1016/j.str.2010.01.015 20399189 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P02281, P84233, P62799 -
288 5OMX X-ray 2.32 2017-11-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 X-ray Structure of the H2A-N38C Nucleosome Core Particle Frouws, T.D., Barth, P.D., Richmond, T.J. 10.1016/j.jmb.2017.10.029 29113904 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2017 P02281, P06897, P84233, P62799 -
289 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 P84040, P02259, P02283, P84051, P02299 -
290 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 Q6AZJ8, P02281, P84233, P62799 0.378
291 3MGQ X-ray 2.65 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Nickel ions to the Nucleosome Core Particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P02281, P84233, P62799 -
292 2NQB X-ray 2.30 2007-09-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Drosophila Nucleosome Structure Chakravarthy, S., Luger, K. 0 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Xenopus laevis 2007 P84040, P02299, P02283, P84051 -
293 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 P06899, Q71DI3, P04908, P62805 0.579
294 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 P0C0S6, P02281, P02302, P62799 0.391
295 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 P84040, P02259, P02283, P84051, P02299 -
296 5AY8 X-ray 2.80 2016-04-06 octamer 1 H3.Y canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal structure of human nucleosome containing H3.Y Kujirai, T., Horikoshi, N., Sato, K., Maehara, K., Machida, S., Osakabe, A., Kimura, H., Ohkawa, Y., Kurumizaka, H. 10.1093/nar/gkw202 27016736 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2016 P06899, P04908, P0DPK2, P62805 -
297 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 Q6AZJ8, P02281, P84233, P62799 -
298 6O1D EM 3.40 2019-05-22 octamer 1 cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_native 145 Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA 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 P06899, P04908, P62805, P49450 0.482
299 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, P06897, P84233, P62799 -
300 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 Q71DI3, P0C0S8, P62807, P62805 0.454
301 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 Q71DI3, P62805, P10412, O60814, P04908 0.084
302 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 Q71DI3, P62805, P10412, O60814, P04908 0.269
303 5B1L X-ray 2.35 2017-02-15 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 The mouse nucleosome structure containing H3t Ueda, J., Harada, A., Urahama, T., Machida, S., Maehara, K., Hada, M., Makino, Y., Nogami, J., Horikoshi, N., Osakabe, A., Taguchi, H., Tanaka, H., Tachiwana, H., Yao, T., Yamada, M., Iwamoto, T., Isotani, A., Ikawa, M., Tachibana, T., Okada, Y., Kimura, H., Ohkawa, Y., Kurumizaka, H., Yamagata, K. 10.1016/j.celrep.2016.12.065 28099840 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2017 P68433, P62806, Q9D2U9, C0HKE1 -
304 1P3B X-ray 3.00 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
305 3X1U X-ray 3.25 2015-09-23 octamer 1 canonical_H3 canonical_H4 H2A.1 canonical_H2B alphasat_146 146 Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T. 10.1016/j.bbrc.2015.07.070 26188507 Homo sapiens Homo sapiens Mus musculus Homo sapiens Xenopus laevis 2015 P33778, P68431, Q8CGP4, P62805 -
306 3WTP X-ray 2.67 2014-12-03 octamer 1 H3.3,cenH3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Arimura, Y., Shirayama, K., Horikoshi, N., Fujita, R., Taguchi, H., Kagawa, W., Fukagawa, T., Almouzni, G., Kurumizaka, H. 10.1038/srep07115 25408271 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2014 P84243, P62805, P06899, P04908, P49450 -
307 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 Q93077, P68431, P62807, P62805 0.525
308 1P34 X-ray 2.70 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
309 3W98 X-ray 3.42 2013-08-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 145 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Iwasaki, W., Miya, Y., Horikoshi, N., Osakabe, A., Taguchi, H., Tachiwana, H., Shibata, T., Kagawa, W., Kurumizaka, H. 10.1016/j.fob.2013.08.007 24251097 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2013 P06899, P04908, P68431, P62805 -
310 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 Q16778, P68431, Q71UI9, P62805 0.311
311 7V9S EM 11.00 2022-07-27 octamer, octamer, octamer 3 canonical_H3 canonical_H4 canonical_H2A canonical_H2B telomeric_human 388 Telomeric trinucleosome in open state Soman, A., Wong, S.Y., Korolev, N., Surya, W., Lattmann, S., Vogirala, V.K., Chen, Q., Berezhnoy, N.V., van Noort, J., Rhodes, D., Nordenskiold, L. 10.1038/s41586-022-05236-5 36104563 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 P04908, P68431, O60814, P62805 0.093
312 3MGR X-ray 2.30 2010-06-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 147 Binding of Rubidium ions to the Nucleosome Core Particle Mohideen, K., Muhammad, R., Davey, C.A. 10.1093/nar/gkq420 20494975 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2010 Q6AZJ8, P02281, P84233, P62799 -
313 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 Q71DI3, P62805, P10412, O60814, P04908 0.27
314 1P3I X-ray 2.30 2004-02-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_146 146 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L., Luger, K. 10.1038/sj.emboj.7600046 14739929 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2004 P02281, P06897, P84233, P62799 -
315 3REI X-ray 2.65 2012-03-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride Wu, B., Davey, G.E., Nazarov, A.A., Dyson, P.J., Davey, C.A. 10.1093/nar/gkr491 21724603 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2012 P02281, P06897, P84233, P62799 -
316 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 Q71DI3, P62805, P10412, O60814, P04908 0.264
317 3UTA X-ray 2.07 2012-04-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B alphasat_147 145 Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) 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, P06897, P84233, P62799 -
318 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, P06897, P84233, P62799 0.525