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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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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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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8H0V
| RNA polymerase II transcribing a chromatosome (type I) | Descriptor: | DNA (261-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | Authors: | Hirano, R, Ehara, H, Tomoya, K, Takizawa, Y, Sekine, S, Kurumizaka, H. | Deposit date: | 2022-09-30 | Release date: | 2022-12-07 | Method: | ELECTRON MICROSCOPY (3.8 Å) | Cite: | Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1. Nat Commun, 13, 2022
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8H0W
| RNA polymerase II transcribing a chromatosome (type II) | Descriptor: | DNA (261-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | Authors: | Hirano, R, Ehara, H, Tomoya, K, Takizawa, Y, Sekine, S, Kurumizaka, H. | Deposit date: | 2022-09-30 | Release date: | 2022-12-07 | Method: | ELECTRON MICROSCOPY (4.6 Å) | Cite: | Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1. Nat Commun, 13, 2022
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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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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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8H1P
| Cryo-EM structure of the human RAD52 protein | Descriptor: | DNA repair protein RAD52 homolog | Authors: | Kinoshita, C, Takizawa, Y, Saotome, M, Ogino, S, Kurumizaka, H, Kagawa, W. | Deposit date: | 2022-10-03 | Release date: | 2023-02-08 | Last modified: | 2023-03-22 | Method: | ELECTRON MICROSCOPY (3.48 Å) | Cite: | The cryo-EM structure of full-length RAD52 protein contains an undecameric ring. Febs Open Bio, 13, 2023
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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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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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8JND
| The cryo-EM structure of the nonameric 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: | 2023-06-06 | Release date: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.66 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site Nature, 2024
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8JNE
| The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without 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: | 2023-06-06 | Release date: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (4.68 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site Nature, 2024
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8JNF
| The cryo-EM structure of the RAD51 filament bound to the nucleosome | 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: | 2023-06-06 | Release date: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (6.91 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site Nature, 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 | Method: | ELECTRON MICROSCOPY (4.12 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site Nature, 2024
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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 | Method: | ELECTRON MICROSCOPY (4.24 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site Nature, 2024
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8XBV
| The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the sticky end of the nucleosome | Descriptor: | DNA (5'-D(P*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*A)-3'), DNA (5'-D(P*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*G)-3'), 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 | Method: | ELECTRON MICROSCOPY (7.61 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site Nature, 2024
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8XBW
| The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome | Descriptor: | DNA (5'-D(P*AP*CP*CP*GP*CP*TP*TP*AP*AP*AP*CP*GP*CP*AP*CP*GP*TP*A)-3'), DNA (5'-D(P*TP*AP*CP*GP*TP*GP*CP*GP*TP*TP*TP*AP*AP*GP*CP*GP*GP*T)-3'), 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 | Method: | ELECTRON MICROSCOPY (2.89 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site Nature, 2024
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8XBX
| The cryo-EM structure of the RAD51 L2 loop bound to the linker DNA with the blunt end of the nucleosome | Descriptor: | DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP*G)-3'), DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP*T)-3'), 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 | Method: | ELECTRON MICROSCOPY (4.36 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site Nature, 2024
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8XBY
| The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the blunt end of the nucleosome | Descriptor: | DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP*G)-3'), DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP*T)-3'), 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 | Method: | ELECTRON MICROSCOPY (7.8 Å) | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site Nature, 2024
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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: | 2011-07-13 | 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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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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2EO0
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5GXQ
| The crystal structure of the nucleosome containing H3.6 | Descriptor: | DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Taguchi, H, Xie, Y, Horikoshi, N, Kurumizaka, H. | Deposit date: | 2016-09-19 | Release date: | 2017-04-19 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8 Biochemistry, 56, 2017
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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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