5Y0D
| Crystal Structure of the human nucleosome containing the H2B E76K mutant | Descriptor: | CHLORIDE ION, DNA (146-MER), Histone H2A type 1-B/E, ... | Authors: | Kurumizaka, H, Arimura, Y, Fujita, R, Noda, M. | Deposit date: | 2017-07-16 | Release date: | 2018-07-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.99 Å) | Cite: | Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome. Nucleic Acids Res., 46, 2018
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5Y0C
| Crystal Structure of the human nucleosome at 2.09 angstrom resolution | Descriptor: | CHLORIDE ION, DNA (146-MER), Histone H2A type 1-B/E, ... | Authors: | Kurumizaka, H, Arimura, Y, Fujita, R, Noda, M. | Deposit date: | 2017-07-16 | Release date: | 2018-07-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.087 Å) | Cite: | Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome. Nucleic Acids Res., 46, 2018
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6AAV
| Crystal structure of alpha-glucosyl transfer enzyme, XgtA at 1.72 angstrom resolution | Descriptor: | Alpha-glucosyltransferase | Authors: | Kurumizaka, H, Arimura, Y, Kirimura, K, Watanabe, R. | Deposit date: | 2018-07-19 | Release date: | 2019-07-24 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.72 Å) | Cite: | Crystal structure of alpha-glucosyl transfer enzyme XgtA from Xanthomonas campestris WU-9701. Biochem.Biophys.Res.Commun., 526, 2020
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6L49
| H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA | Descriptor: | DNA (485-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Takizawa, Y, Ho, C.-H, Tachiwana, H, Matsunami, H, Ohi, M, Wolf, M, Kurumizaka, H. | Deposit date: | 2019-10-16 | Release date: | 2019-12-04 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (18.9 Å) | Cite: | Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome. Structure, 28, 2020
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6KXV
| Crystal structure of a nucleosome containing Leishmania histone H3 | Descriptor: | DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Dacher, M, Taguchi, H, Kujirai, T, Kurumizaka, H. | Deposit date: | 2019-09-13 | Release date: | 2020-07-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.63 Å) | Cite: | Incorporation and influence of Leishmania histone H3 in chromatin. Nucleic Acids Res., 47, 2019
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7YOZ
| Cryo-EM structure of human subnucleosome (intermediate form) | Descriptor: | Histone H3.1, Histone H4, Widom601 DNA FW (145-MER), ... | Authors: | Nozawa, K, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2022-08-02 | Release date: | 2022-11-16 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (4.3 Å) | Cite: | Cryo-electron microscopy structure of the H3-H4 octasome: A nucleosome-like particle without histones H2A and H2B. Proc.Natl.Acad.Sci.USA, 119, 2022
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4YM6
| Crystal structure of the human nucleosome containing 6-4PP (outside) | Descriptor: | 145-MER DNA, Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | 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. | Deposit date: | 2015-03-06 | Release date: | 2015-12-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.514 Å) | Cite: | Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome Sci Rep, 5, 2015
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4YM5
| Crystal structure of the human nucleosome containing 6-4PP (inside) | Descriptor: | 144 mer-DNA, 144-mer DNA, Histone H2A type 1-B/E, ... | Authors: | 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. | Deposit date: | 2015-03-06 | Release date: | 2015-12-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (4.005 Å) | Cite: | Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome Sci Rep, 5, 2015
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4Z5T
| The nucleosome containing human H3.5 | Descriptor: | DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | 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. | Deposit date: | 2015-04-03 | Release date: | 2016-02-10 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis. Epigenetics Chromatin, 9, 2016
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6V2K
| The nucleosome structure after H2A-H2B exchange | Descriptor: | CHLORIDE ION, DNA (146-MER), Histone H2A, ... | Authors: | Arimura, Y, Hirano, R, Kurumizaka, H. | Deposit date: | 2019-11-24 | Release date: | 2020-11-25 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome. Commun Biol, 4, 2021
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6L4A
| H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA | Descriptor: | DNA (485-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Takizawa, Y, Ho, C.-H, Tachiwana, H, Matsunami, H, Ohi, M, Wolf, M, Kurumizaka, H. | Deposit date: | 2019-10-16 | Release date: | 2019-12-04 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (12.3 Å) | Cite: | Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome. Structure, 28, 2020
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4WD3
| Crystal structure of an L-amino acid ligase RizA | Descriptor: | L-amino acid ligase | Authors: | Kagawa, W, Arai, T, Kino, K, Kurumizaka, H. | Deposit date: | 2014-09-06 | Release date: | 2015-09-09 | Last modified: | 2020-01-01 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structure of RizA, an L-amino-acid ligase from Bacillus subtilis. Acta Crystallogr.,Sect.F, 71, 2015
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6KVD
| Crystal structure of human nucleosome containing H2A.J | Descriptor: | CHLORIDE ION, DNA (146-MER), Histone H2A.J, ... | Authors: | Tanaka, H, Koyama, M, Sato, S, Kujirai, T, Kurumizaka, H. | Deposit date: | 2019-09-04 | Release date: | 2019-12-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.21 Å) | Cite: | Biochemical and structural analyses of the nucleosome containing human histone H2A.J. J.Biochem., 167, 2020
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7C0M
| Human cGAS-nucleosome complex | Descriptor: | Cyclic GMP-AMP synthase, DNA (145-MER), Histone H2A type 1-B/E, ... | Authors: | Kujirai, T, Zierhut, C, Takizawa, Y, Kim, R, Negishi, L, Uruma, N, Hirai, S, Funabiki, H, Kurumizaka, H. | Deposit date: | 2020-05-01 | Release date: | 2020-09-16 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | Structural basis for the inhibition of cGAS by nucleosomes. Science, 370, 2020
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1B22
| RAD51 (N-TERMINAL DOMAIN) | Descriptor: | DNA REPAIR PROTEIN RAD51 | Authors: | Aihara, H, Ito, Y, Kurumizaka, H, Yokoyama, S, Shibata, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 1998-12-04 | Release date: | 1999-12-03 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR. J.Mol.Biol., 290, 1999
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1AA3
| C-TERMINAL DOMAIN OF THE E. COLI RECA, NMR, MINIMIZED AVERAGE STRUCTURE | Descriptor: | RECA | Authors: | Aihara, H, Ito, Y, Kurumizaka, H, Terada, T, Yokoyama, S, Shibata, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 1997-01-22 | Release date: | 1997-07-23 | Last modified: | 2024-04-10 | Method: | SOLUTION NMR | Cite: | An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing. J.Mol.Biol., 274, 1997
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5JRG
| Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) | Descriptor: | CHLORIDE ION, DNA (145-MER), Histone H2A type 1-B/E, ... | Authors: | Osakabe, A, Arimura, Y, Horikoshi, N, Kurumizaka, H. | Deposit date: | 2016-05-06 | Release date: | 2017-03-08 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Polymorphism of apyrimidinic DNA structures in the nucleosome Sci Rep, 7, 2017
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5JRB
| Rad52(1-212) K102A/K133A/E202A mutant | Descriptor: | DNA repair protein RAD52 homolog | Authors: | Saotome, M, Saito, K, Kurumizaka, H, Kagawa, W. | Deposit date: | 2016-05-06 | Release date: | 2016-08-10 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.405 Å) | Cite: | Structure of the human DNA-repair protein RAD52 containing surface mutations. Acta Crystallogr.,Sect.F, 72, 2016
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2EO0
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7DBH
| The mouse nucleosome structure containing H3mm18 | Descriptor: | DNA (126-MER), Histone H2A type 1-B, Histone H2B type 3-A, ... | Authors: | Hirai, S, Takizawa, Y, Kujirai, T, Kurumizaka, H. | Deposit date: | 2020-10-20 | Release date: | 2022-01-19 | Last modified: | 2024-05-29 | Method: | ELECTRON MICROSCOPY (3.6 Å) | Cite: | Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant. Nucleic Acids Res., 50, 2022
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8YBJ
| Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Kimura, T, Hirai, S, Kujirai, T, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2024-02-14 | Release date: | 2024-07-24 | Method: | ELECTRON MICROSCOPY (2.38 Å) | Cite: | Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K. Genes Cells, 2024
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8YBK
| Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Kimura, T, Hirai, S, Kujirai, T, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2024-02-14 | Release date: | 2024-07-24 | Method: | ELECTRON MICROSCOPY (2.69 Å) | Cite: | Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K. Genes Cells, 2024
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1UFI
| Crystal structure of the dimerization domain of human CENP-B | Descriptor: | Major centromere autoantigen B | Authors: | Tawaramoto, M.S, Kurumizaka, H, Tanaka, Y, Park, S.-Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-05-30 | Release date: | 2004-02-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Crystal structure of the human centromere protein B (CENP-B) dimerization domain at 1.65-A resolution J.Biol.Chem., 278, 2003
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8XBU
| The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding | Descriptor: | DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-12-07 | Release date: | 2024-03-27 | Last modified: | 2024-05-08 | Method: | ELECTRON MICROSCOPY (4.24 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature, 628, 2024
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8XBT
| The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding | Descriptor: | DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-12-07 | Release date: | 2024-03-27 | Last modified: | 2024-05-08 | Method: | ELECTRON MICROSCOPY (4.12 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature, 628, 2024
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