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5Y0D
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BU of 5y0d by Molmil
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
5Y0C
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BU of 5y0c by Molmil
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
5XM0
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BU of 5xm0 by Molmil
The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4
Descriptor: DNA (146-MER), Histone H2A type 1-B, Histone H2B type 3-A, ...
Authors:Taguchi, H, Horikoshi, N, Kurumizaka, H.
Deposit date:2017-05-12
Release date:2018-03-07
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.874 Å)
Cite:Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration.
Nat Commun, 9, 2018
5XRZ
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BU of 5xrz by Molmil
Structure of a ssDNA bound to the inner DNA binding site of RAD52
Descriptor: DNA repair protein RAD52 homolog, POTASSIUM ION, ssDNA (40-MER)
Authors:Saotome, M, Saito, K, Yasuda, T, Sugiyama, S, Kurumizaka, H, Kagawa, W.
Deposit date:2017-06-11
Release date:2018-04-25
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (3.6 Å)
Cite:Structural Basis of Homology-Directed DNA Repair Mediated by RAD52
iScience, 3, 2018
6IR9
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BU of 6ir9 by Molmil
RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome
Descriptor: DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ...
Authors:Ehara, H, Kujirai, T, Fujino, Y, Shirouzu, M, Kurumizaka, H, Sekine, S.
Deposit date:2018-11-12
Release date:2019-02-20
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science, 363, 2019
6INQ
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BU of 6inq by Molmil
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
Descriptor: DNA (198-MER), DNA (31-MER), DNA-directed RNA polymerase subunit, ...
Authors:Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H.
Deposit date:2018-10-26
Release date:2019-04-03
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (6.9 Å)
Cite:Structural basis of the nucleosome transition during RNA polymerase II passage.
Science, 362, 2018
4WD3
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BU of 4wd3 by Molmil
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
1B22
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BU of 1b22 by Molmil
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
1AA3
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BU of 1aa3 by Molmil
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
6V2K
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BU of 6v2k by Molmil
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
2EO0
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BU of 2eo0 by Molmil
Crystal Structure of Holliday Junction Resolvase ST1444
Descriptor: Hypothetical protein ST1444
Authors:Sarai, N, Kagawa, W, Kurumizaka, H, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2007-03-28
Release date:2007-10-02
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal Structure of Holliday Junction Resolvase ST1444
To be published
5GXQ
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BU of 5gxq by Molmil
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
5JRB
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BU of 5jrb by Molmil
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
5JRG
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BU of 5jrg by Molmil
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
5GTC
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BU of 5gtc by Molmil
Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle
Descriptor: CHLORIDE ION, DNA (146-MER), Histone H2A type 1-B/E, ...
Authors:Arimura, Y, Kato, D, Suto, H, Kurumizaka, H, Kawashima, S.A, Yamatsugu, K, Kanai, M.
Deposit date:2016-08-19
Release date:2017-06-28
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin.
J. Am. Chem. Soc., 139, 2017
5GSE
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BU of 5gse by Molmil
Crystal structure of unusual nucleosome
Descriptor: DNA (250-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ...
Authors:Kato, D, Osakabe, A, Arimura, Y, Park, S.Y, Kurumizaka, H.
Deposit date:2016-08-16
Release date:2017-05-03
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.14 Å)
Cite:Crystal structure of the overlapping dinucleosome composed of hexasome and octasome
Science, 356, 2017
8KB5
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BU of 8kb5 by Molmil
Cryo-EM structure of the human nucleosome containing H3.8
Descriptor: DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ...
Authors:Hirai, H, Kujirai, T, Takizawa, Y, Kurumizaka, H.
Deposit date:2023-08-03
Release date:2023-10-18
Last modified:2023-12-27
Method:ELECTRON MICROSCOPY (2.26133 Å)
Cite:Cryo-EM and biochemical analyses of the nucleosome containing the human histone H3 variant H3.8.
J.Biochem., 174, 2023
1UFI
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BU of 1ufi by Molmil
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
1V5W
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BU of 1v5w by Molmil
Crystal structure of the human Dmc1 protein
Descriptor: Meiotic recombination protein DMC1/LIM15 homolog
Authors:Kinebuchi, T, Kagawa, W, Enomoto, R, Ikawa, S, Shibata, T, Kurumizaka, H, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-11-26
Release date:2004-05-18
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein dmc1
Mol.Cell, 14, 2004
3W99
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BU of 3w99 by Molmil
Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region
Descriptor: 146-mer DNA, Histone H2A type 1-B/E, Histone H2B type 1-J, ...
Authors:Iwasaki, W, Miya, Y, Horikoshi, N, Osakabe, A, Tachiwana, H, Shibata, T, Kagawa, W, Kurumizaka, H.
Deposit date:2013-04-01
Release date:2013-08-28
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3 Å)
Cite:Contribution of histone N-terminal tails to the structure and stability of nucleosomes
FEBS Open Bio, 3, 2013
3W98
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BU of 3w98 by Molmil
Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region
Descriptor: 146-mer DNA, Histone H2A type 1-B/E, Histone H2B type 1-J, ...
Authors:Iwasaki, W, Miya, Y, Horikoshi, N, Osakabe, A, Tachiwana, H, Shibata, T, Kagawa, W, Kurumizaka, H.
Deposit date:2013-04-01
Release date:2013-08-28
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.42 Å)
Cite:Contribution of histone N-terminal tails to the structure and stability of nucleosomes
FEBS Open Bio, 3, 2013
3VH0
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BU of 3vh0 by Molmil
Crystal structure of E. coli YncE complexed with DNA
Descriptor: DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*TP*CP*AP*G)-3'), Uncharacterized protein YncE
Authors:Kagawa, W, Sagawa, T, Niki, H, Kurumizaka, H.
Deposit date:2011-08-23
Release date:2011-11-16
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural basis for the DNA-binding activity of the bacterial beta-propeller protein YncE
Acta Crystallogr.,Sect.D, 67, 2011
3VGZ
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BU of 3vgz by Molmil
Crystal structure of E. coli YncE
Descriptor: Uncharacterized protein YncE
Authors:Kagawa, W, Sagawa, T, Niki, H, Kurumizaka, H.
Deposit date:2011-08-23
Release date:2011-11-16
Last modified:2011-12-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structural basis for the DNA-binding activity of the bacterial beta-propeller protein YncE
Acta Crystallogr.,Sect.D, 67, 2011
8YBK
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BU of 8ybk by Molmil
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
Last modified:2024-09-11
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, 29, 2024
8YBJ
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BU of 8ybj by Molmil
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
Last modified:2024-09-11
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, 29, 2024

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