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5XRZ
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STRUCTURE OF A SSDNA BOUND TO THE INNER DNA BINDING SITE OF RAD52
Descriptor:DNA repair protein RAD52 homolog, ssDNA (40-MER), POTASSIUM ION
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:2018-11-28
Method:X-RAY DIFFRACTION (3.6 Å)
Cite:Structural Basis of Homology-Directed DNA Repair Mediated by RAD52
iScience, 3, 2018
5XS0
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STRUCTURE OF A SSDNA BOUND TO THE OUTER DNA BINDING SITE OF RAD52
Descriptor:DNA repair protein RAD52 homolog, ssDNA (5'-D(*CP*CP*CP*CP*CP*C)-3'), ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3'), ...
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:2018-11-28
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structural Basis of Homology-Directed DNA Repair Mediated by RAD52
iScience, 3, 2018
5XV8
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SOLUTION STRUCTURE OF THE COMPLEX BETWEEN UVSSA ACIDIC REGION AND TFIIH P62 PH DOMAIN
Descriptor:UV-stimulated scaffold protein A, General transcription factor IIH subunit 1
Authors:Okuda, M., Nishimura, Y.
Deposit date:2017-06-27
Release date:2017-11-08
Last modified:2017-12-27
Method:SOLUTION NMR
Cite:Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways
Nucleic Acids Res., 45, 2017
5Y95
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HADDOCK MODEL OF MSIN3B PAH1 DOMAIN
Descriptor:Paired amphipathic helix protein Sin3b, propan-2-yl (3R,6S,9aS)-3-ethyl-8-(3-methylbutyl)-6-(2-methylsulfanylethyl)-4,7-bis(oxidanylidene)-9,9a-dihydro-6H-pyrazino[2,1-c][1,2,4]oxadiazine-1-carboxylate
Authors:Kurita, J., Hirao, Y., Nishimura, Y.
Deposit date:2017-08-22
Release date:2017-10-04
Last modified:2017-12-06
Method:SOLUTION NMR
Cite:A mimetic of the mSin3-binding helix of NRSF/REST ameliorates abnormal pain behavior in chronic pain models.
Bioorg. Med. Chem. Lett., 27, 2017
5GSE
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CRYSTAL STRUCTURE OF UNUSUAL NUCLEOSOME
Descriptor:Histone H3.1, Histone H4, Histone H2A type 1-B/E, ...
Authors:Kato, D., Osakabe, A., Arimura, Y., Park, S.Y., Kurumizaka, H.
Deposit date:2016-08-16
Release date:2017-05-03
Method:X-RAY DIFFRACTION (3.14 Å)
Cite:Crystal structure of the overlapping dinucleosome composed of hexasome and octasome
Science, 356, 2017
5GOW
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SOLUTION STRUCTURE OF THE COMPLEX BETWEEN DP1 ACIDIC REGION AND TFIIH P62 PH DOMAIN
Descriptor:DP1, General transcription factor IIH subunit 1
Authors:Okuda, M., Nishimura, Y.
Deposit date:2016-07-29
Release date:2016-12-07
Last modified:2016-12-14
Method:SOLUTION NMR
Cite:The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH
J. Mol. Biol., 428, 2016
2RVQ
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SOLUTION STRUCTURE OF THE ISOLATED HISTONE H2A-H2B HETERODIMER
Descriptor:Histone H2A type 1-B/E, Histone H2B type 1-J
Authors:Moriwaki, Y., Yamane, T., Ohtomo, H., Ikeguchi, M., Kurita, J., Sato, M., Nagadoi, A., Shimojo, H., Nishimura, Y.
Deposit date:2016-03-28
Release date:2016-05-25
Method:SOLUTION NMR
Cite:Solution structure of the isolated histone H2A-H2B heterodimer
Sci Rep, 6, 2016
2RVL
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SOLUTION STRUCTURE OF THE CHROMODOMAIN OF HP1ALPHA WITH THE N-TERMINAL TAIL
Descriptor:Chromobox protein homolog 5
Authors:Kawaguchi, A., Nishimura, Y.
Deposit date:2015-12-18
Release date:2016-03-16
Method:SOLUTION NMR
Cite:Extended string-like binding of the phosphorylated HP1 alpha N-terminal tail to the lysine 9-methylated histone H3 tail
Sci Rep, 6, 2016
2RVM
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SOLUTION STRUCTURE OF THE CHROMODOMAIN OF HP1ALPHA WITH THE PHOSPHORYLATED N-TERMINAL TAIL
Descriptor:Chromobox protein homolog 5
Authors:Kawaguchi, A., Nishimura, Y.
Deposit date:2015-12-18
Release date:2016-03-16
Method:SOLUTION NMR
Cite:Extended string-like binding of the phosphorylated HP1 alpha N-terminal tail to the lysine 9-methylated histone H3 tail
Sci Rep, 6, 2016
2RVN
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SOLUTION STRUCTURE OF THE CHROMODOMAIN OF HP1A WITH THE PHOSPHORYLATED N-TERMINAL TAIL COMPLEXED WITH H3K9ME3 PEPTIDE
Descriptor:Chromobox protein homolog 5, 18-mer peptide of Histone H3
Authors:Kawaguchi, A., Nishimura, Y.
Deposit date:2015-12-18
Release date:2016-03-16
Method:SOLUTION NMR
Cite:Extended string-like binding of the phosphorylated HP1 alpha N-terminal tail to the lysine 9-methylated histone H3 tail
Sci Rep, 6, 2016
2RVB
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SOLUTION STRUCTURE OF THE COMPLEX BETWEEN XPC ACIDIC DOMAIN AND TFIIH P62 PH DOMAIN
Descriptor:DNA repair protein complementing XP-C cells, General transcription factor IIH subunit 1
Authors:Okuda, M., Nishimura, Y.
Deposit date:2015-07-01
Release date:2015-09-09
Last modified:2017-06-07
Method:SOLUTION NMR
Cite:Structural Insight into the Mechanism of TFIIH Recognition by the Acidic String of the Nucleotide Excision Repair Factor XPC.
Structure, 23, 2015
2RUK
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SOLUTION STRUCTURE OF THE COMPLEX BETWEEN P53 TRANSACTIVATION DOMAIN 2 AND TFIIH P62 PH DOMAIN
Descriptor:Cellular tumor antigen p53, General transcription factor IIH subunit 1
Authors:Okuda, M., Nishimura, Y.
Deposit date:2014-09-24
Release date:2014-10-15
Method:SOLUTION NMR
Cite:Extended String Binding Mode of the Phosphorylated Transactivation Domain of Tumor Suppressor p53
J.Am.Chem.Soc., 2014
3WEX
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CRYSTAL STRUCTURE OF HLA-DP5 IN COMPLEX WITH CRY J 1-DERIVED PEPTIDE (RESIDUES 214-222)
Descriptor:MHC class II antigen, N-ACETYL-D-GLUCOSAMINE
Authors:Kusano, S., Kukimoto-Niino, M., Shirouzu, M., Yokoyama, S.
Deposit date:2013-07-16
Release date:2014-07-23
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural basis for the specific recognition of the major antigenic peptide from the Japanese cedar pollen allergen Cry j 1 by HLA-DP5
J. Mol. Biol., 426, 2014
3J3Z
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STRUCTURE OF MA28-7 NEUTRALIZING ANTIBODY FAB FRAGMENT FROM ELECTRON CRYO-MICROSCOPY OF ENTEROVIRUS 71 COMPLEXED WITH A FAB FRAGMENT
Descriptor:MA28-7 neutralizing antibody light chain, MA28-7 neutralizing antibody heavy chain
Authors:Lee, H., Cifuente, J.O., Ashley, R.E., Conway, J.F., Makhov, A.M., Tano, Y., Shimizu, H., Nishimura, Y., Hafenstein, S.
Deposit date:2013-05-21
Release date:2013-08-28
Last modified:2018-07-18
Method:ELECTRON MICROSCOPY (23.4 Å)
Cite:A strain-specific epitope of enterovirus 71 identified by cryo-electron microscopy of the complex with fab from neutralizing antibody.
J.Virol., 87, 2013
4J6R
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CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC23 IN COMPLEX WITH HIV-1 GP120
Descriptor:Envelope glycoprotein gp160, HEAVY CHAIN OF ANTIBODY VRC23, LIGHT CHAIN OF ANTIBODY VRC23, ...
Authors:Zhou, T., Moquin, S., Kwong, P.D.
Deposit date:2013-02-11
Release date:2013-05-08
Last modified:2018-01-24
Method:X-RAY DIFFRACTION (1.64 Å)
Cite:Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization.
Science, 340, 2013
4JB9
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CRYSTAL STRUCTURE OF ANTIBODY VRC06 IN COMPLEX WITH HIV-1 GP120 CORE
Descriptor:clade A/E 93TH057 HIV-1 gp120 core, antibody VRC06 heavy chain, antibody VRC06 light chain, ...
Authors:Kwon, Y.D., Zhou, T., Srivatsan, S., Kwong, P.D.
Deposit date:2013-02-19
Release date:2013-05-08
Last modified:2016-10-19
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization.
Science, 340, 2013
2RSN
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SOLUTION STRUCTURE OF THE CHROMODOMAIN OF CHP1 IN COMPLEX WITH H3K9ME3 PEPTIDE
Descriptor:Chromo domain-containing protein 1, peptide from Histone H3
Authors:Shimojo, H., Nishimura, Y.
Deposit date:2012-04-18
Release date:2012-08-29
Method:SOLUTION NMR
Cite:Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing
Mol.Cell, 47, 2012
2RSO
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SOLUTION STRUCTURE OF THE CHROMODOMAIN OF SWI6
Descriptor:Chromatin-associated protein swi6
Authors:Shimojo, H., Nishimura, Y.
Deposit date:2012-04-18
Release date:2012-08-29
Method:SOLUTION NMR
Cite:Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing
Mol.Cell, 47, 2012
3APM
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CRYSTAL STRUCTURE OF THE HUMAN SNP PAD4 PROTEIN
Descriptor:Protein-arginine deiminase type-4
Authors:Horikoshi, N., Tachiwana, H., Saito, K., Osakabe, A., Sato, M., Yamada, M., Akashi, S., Nishimura, Y., Kagawa, W., Kurumizaka, H.
Deposit date:2010-10-19
Release date:2011-01-26
Last modified:2012-04-11
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene
Acta Crystallogr.,Sect.D, 67, 2011
3APN
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CRYSTAL STRUCTURE OF THE HUMAN WILD-TYPE PAD4 PROTEIN
Descriptor:Protein-arginine deiminase type-4
Authors:Horikoshi, N., Tachiwana, H., Saito, K., Osakabe, A., Sato, M., Yamada, M., Akashi, S., Nishimura, Y., Kagawa, W., Kurumizaka, H.
Deposit date:2010-10-19
Release date:2011-01-26
Last modified:2012-04-11
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene
Acta Crystallogr.,Sect.D, 67, 2011
3D79
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CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN PH0734.1 FROM HYPERTHERMOPHILIC ARCHAEA PYROCOCCUS HORIKOSHII OT3
Descriptor:Putative uncharacterized protein PH0734
Authors:Nishimura, Y., Miyazono, K., Sawano, Y., Makino, T., Nagata, K., Tanokura, M.
Deposit date:2008-05-20
Release date:2008-12-09
Last modified:2017-10-25
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3.
Proteins, 73, 2008
2RLT
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PHOSPHORYLATED CPI-17 (22-120)
Descriptor:Protein phosphatase 1 regulatory subunit 14A
Authors:Eto, M.
Deposit date:2007-08-11
Release date:2008-07-15
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Phosphorylation-induced conformational switching of CPI-17 produces a potent myosin phosphatase inhibitor.
Structure, 15, 2007
2RNZ
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SOLUTION STRUCTURE OF THE PRESUMED CHROMODOMAIN OF THE YEAST HISTONE ACETYLTRANSFERASE, ESA1
Descriptor:Histone acetyltransferase ESA1
Authors:Shimojo, H., Sano, N., Moriwaki, Y., Okuda, M., Horikoshi, M., Nishimura, Y.
Deposit date:2008-03-01
Release date:2008-04-29
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain
J.Mol.Biol., 378, 2008
2RO0
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SOLUTION STRUCTURE OF THE KNOTTED TUDOR DOMAIN OF THE YEAST HISTONE ACETYLTRANSFERASE, ESA1
Descriptor:Histone acetyltransferase ESA1
Authors:Shimojo, H., Sano, N., Moriwaki, Y., Okuda, M., Horikoshi, M., Nishimura, Y.
Deposit date:2008-03-01
Release date:2008-04-29
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain
J.Mol.Biol., 378, 2008
2Z33
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SOLUTION STRUCTURE OF THE DNA COMPLEX OF PHOB DNA-BINDING/TRANSACTIVATION DOMAIN
Descriptor:5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3', 5'-D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3', Phosphate regulon transcriptional regulatory protein phoB
Authors:Yamane, T., Okamura, H., Ikeguchi, M., Nishimura, Y., Kidera, A.
Deposit date:2007-05-31
Release date:2008-04-22
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment.
Proteins, 71, 2008
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