Author results

1GD7
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CRYSTAL STRUCTURE OF A BIFUNCTIONAL PROTEIN (CSAA) WITH EXPORT-RELATED CHAPERONE AND TRNA-BINDING ACTIVITIES.
Descriptor:CSAA PROTEIN
Authors:Shibata, T., Inoue, Y., Vassylyev, D.G., Kawaguchi, S., Yokoyama, S., Muller, J., Linde, D., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2000-09-22
Release date:2001-09-22
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus.
EMBO J., 20, 2001
1RRB
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THE RAS-BINDING DOMAIN OF RAF-1 FROM RAT, NMR, 1 STRUCTURE
Descriptor:RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE
Authors:Terada, T., Ito, Y., Shirouzu, M., Tateno, M., Hashimoto, K., Kigawa, T., Ebisuzaki, T., Takio, K., Shibata, T., Yokoyama, S., Smith, B.O., Laue, E.D., Cooper, J.A., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:1998-03-26
Release date:1999-03-30
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Nuclear magnetic resonance and molecular dynamics studies on the interactions of the Ras-binding domain of Raf-1 with wild-type and mutant Ras proteins.
J.Mol.Biol., 286, 1999
2RPD
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MHR1P-BOUND SSDNA
Descriptor:DNA (5'-D(*DTP*DAP*DCP*DG)-3')
Authors:Masuda, T., Ito, Y., Shibata, T., Mikawa, T.
Deposit date:2008-05-15
Release date:2009-05-26
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:A non-canonical DNA structure enables homologous recombination in various genetic systems
J.Biol.Chem., 284, 2009
2RPE
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HSRAD51-BOUND SSDNA
Descriptor:DNA (5'-D(*DTP*DAP*DCP*DG)-3')
Authors:Masuda, T., Ito, Y., Shibata, T., Mikawa, T.
Deposit date:2008-05-15
Release date:2009-05-26
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:A non-canonical DNA structure enables homologous recombination in various genetic systems
J.Biol.Chem., 284, 2009
2RPF
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RECO-BOUND SSDNA
Descriptor:DNA (5'-D(*DTP*DAP*DCP*DG)-3')
Authors:Masuda, T., Ito, Y., Shibata, T., Mikawa, T.
Deposit date:2008-05-15
Release date:2009-05-26
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:A non-canonical DNA structure enables homologous recombination in various genetic systems
J.Biol.Chem., 284, 2009
2RPH
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RECT-BOUND SSDNA
Descriptor:DNA (5'-D(*DTP*DAP*DCP*DG)-3')
Authors:Masuda, T., Ito, Y., Shibata, T., Mikawa, T.
Deposit date:2008-05-15
Release date:2009-05-26
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:A non-canonical DNA structure enables homologous recombination in various genetic systems
J.Biol.Chem., 284, 2009
4TWZ
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CRYSTAL STRUCTURE ANALYSIS OF E COLI. RECA PROTEIN
Descriptor:Protein RecA, MAGNESIUM ION
Authors:Hikima, T., Hiraki, T., Furuse, M., Ikawa, S., Iwasaki, W., Shibata, T., Kamiya, N.
Deposit date:2014-07-02
Release date:2015-07-08
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair
Nucleic Acids Res., 43, 2015
1IPA
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CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE
Descriptor:RNA 2'-O-RIBOSE METHYLTRANSFERASE
Authors:Nureki, O., Shirouzu, M., Hashimoto, K., Ishitani, R., Terada, T., Tamakoshi, M., Oshima, T., Chijimatsu, M., Takio, K., Vassylyev, D.G., Shibata, T., Inoue, Y., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2001-05-02
Release date:2002-07-10
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:An enzyme with a deep trefoil knot for the active-site architecture.
Acta Crystallogr.,Sect.D, 58, 2002
1J1H
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SOLUTION STRUCTURE OF A TMRNA-BINDING PROTEIN, SMPB, FROM THERMUS THERMOPHILUS
Descriptor:Small Protein B
Authors:Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M., Terada, T., Shirouzu, M., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., Kawai, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2002-12-04
Release date:2003-02-11
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus
FEBS Lett., 535, 2003
3GJJ
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CRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 7,8-DIHYDROPYRIDOL[2,3-D]PYRIMIDIN-2-ONE
Descriptor:5'-D(*CP*GP*CP*GP*AP*AP*TP*(B7C)P*CP*GP*CP*G)-3', 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
Authors:Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L., Williams, D.M.
Deposit date:2009-03-09
Release date:2010-03-31
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
3GJK
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CRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 7,8-DIHYDROPYRIDOL[2,3-D]PYRIMIDIN-2-ONE
Descriptor:5'-D(*CP*GP*CP*GP*AP*A)-3', 5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3', POTASSIUM ION
Authors:Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L., Williams, D.M.
Deposit date:2009-03-09
Release date:2010-03-31
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
3GJL
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CRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 7,8-DIHYDROPYRIDOL[2,3-D]PYRIMIDIN-2-ONE
Descriptor:5'-D(*CP*GP*CP*GP*AP*A)-3', 5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3', SODIUM ION
Authors:Takenaka, A., Juan, E.C.M., Shimizu, S., Haraguchi, T., Xiao, M., Kurose, T., Ohkubo, A., Sekine, M., Shibata, T., Millington, C.L., Williams, D.M.
Deposit date:2009-03-09
Release date:2010-03-31
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
4R07
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CRYSTAL STRUCTURE OF HUMAN TLR8 IN COMPLEX WITH ORN06
Descriptor:Toll-like receptor 8, URIDINE, 3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate), ...
Authors:Tanji, H., Ohto, U., Shibata, T., Taoka, M., Yamauchi, Y., Isobe, T., Miyake, K., Shimizu, T.
Deposit date:2014-07-30
Release date:2015-01-14
Last modified:2015-02-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:Toll-like receptor 8 senses degradation products of single-stranded RNA
Nat.Struct.Mol.Biol., 22, 2015
1AA3
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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
1EW1
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RECA PROTEIN-BOUND SINGLE-STRANDED DNA
Descriptor:DNA (5'-D(*TP*AP*CP*G)-3')
Authors:Nishinaka, T., Ito, Y., Yokoyama, S., Shibata, T.
Deposit date:2000-04-21
Release date:2000-05-08
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:An extended DNA structure through deoxyribose-base stacking induced by RecA protein.
Proc.Natl.Acad.Sci.USA, 94, 1997
1V5W
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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:2011-07-13
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
1V8I
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CRYSTAL STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE
Descriptor:ADP-ribose pyrophosphatase
Authors:Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-09
Release date:2004-10-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.76 Å)
Cite:Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
J.Biol.Chem., 279, 2004
1V8L
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STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE COMPLEXED WITH ADP-RIBOSE
Descriptor:ADP-ribose pyrophosphatase, ADENOSINE-5-DIPHOSPHORIBOSE
Authors:Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-10
Release date:2004-10-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
J.Biol.Chem., 279, 2004
1V8M
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CRYSTAL STRUCTURE ANALYSIS OF ADP-RIBOSE PYROPHOSPHATASE COMPLEXED WITH ADP-RIBOSE AND GD
Descriptor:ADP-ribose pyrophosphatase, ADENOSINE-5-DIPHOSPHORIBOSE, GADOLINIUM ATOM
Authors:Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-12
Release date:2004-10-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
J.Biol.Chem., 279, 2004
1V8N
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CRYSTAL STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE COMPLEXED WITH ZN
Descriptor:ADP-ribose pyrophosphatase, ZINC ION
Authors:Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-12
Release date:2004-10-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
J.Biol.Chem., 279, 2004
1V8R
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CRYSTAL STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE COMPLEXED WITH ADP-RIBOSE AND ZN
Descriptor:ADP-ribose pyrophosphatase, ZINC ION, ADENOSINE-5-DIPHOSPHORIBOSE
Authors:Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-14
Release date:2005-02-22
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
J.Biol.Chem., 279, 2004
1V8S
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CRYSTAL STRUCTURE ANALUSIS OF THE ADP-RIBOSE PYROPHOSPHATASE COMPLEXED WITH AMP AND MG
Descriptor:ADP-ribose pyrophosphatase, MAGNESIUM ION, ADENOSINE MONOPHOSPHATE
Authors:Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-14
Release date:2004-10-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
J.Biol.Chem., 279, 2004
1V8T
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CRYSTAL STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE COMPLEXED WITH RIBOSE-5'-PHOSPHATE AND ZN
Descriptor:ADP-ribose pyrophosphatase, RIBOSE-5-PHOSPHATE, ZINC ION
Authors:Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-14
Release date:2004-10-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
J.Biol.Chem., 279, 2004
1V8U
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CRYSTAL STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE OF E82Q MUTANT WITH SO4 AND MG
Descriptor:ADP-ribose pyrophosphatase, MAGNESIUM ION, SULFATE ION
Authors:Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-15
Release date:2004-10-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
J.Biol.Chem., 279, 2004
1V8V
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CRYSTAL STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE OF E86Q MUTANT, COMPLEXED WITH ADP-RIBOSE AND MG
Descriptor:ADP-ribose pyrophosphatase, MAGNESIUM ION, ADENOSINE-5-DIPHOSPHORIBOSE
Authors:Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-15
Release date:2004-10-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.97 Å)
Cite:Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
J.Biol.Chem., 279, 2004