8I5F
 
 | | Crystal structure of the DHR-2 domain of DOCK10 in complex with Cdc42 (T17N mutant) | | Descriptor: | Cell division control protein 42 homolog, Dedicator of cytokinesis protein 10 | | Authors: | Kukimoto-Niino, M, Mishima-Tsumagari, C, Fukui, Y, Yokoyama, S, Shirouzu, M. | | Deposit date: | 2023-01-25 | | Release date: | 2023-03-15 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural basis for the dual GTPase specificity of the DOCK10 guanine nucleotide exchange factor.
Biochem.Biophys.Res.Commun., 653, 2023
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8I5V
 | | DOCK10 mutant L1903Y complexed with Rac1 | | Descriptor: | Dedicator of cytokinesis protein 10, Ras-related C3 botulinum toxin substrate 1, SULFATE ION | | Authors: | Kukimoto-Niino, M, Mishima-Tsumagari, C, Ihara, K, Fukui, Y, Yokoyama, S, Shirouzu, M. | | Deposit date: | 2023-01-26 | | Release date: | 2023-03-15 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.726 Å) | | Cite: | Structural basis for the dual GTPase specificity of the DOCK10 guanine nucleotide exchange factor.
Biochem.Biophys.Res.Commun., 653, 2023
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1J1V
 | | Crystal structure of DnaA domainIV complexed with DnaAbox DNA | | Descriptor: | 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3', 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3', Chromosomal replication initiator protein dnaA | | Authors: | Fujikawa, N, Kurumizaka, H, Nureki, O, Terada, T, Shirouzu, M, Katayama, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-12-18 | | Release date: | 2003-04-22 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural basis of replication origin recognition by the DnaA protein
NUCLEIC ACIDS RES., 31, 2003
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1JZQ
 | | Isoleucyl-tRNA synthetase Complexed with Isoleucyl-adenylate analogue | | Descriptor: | Isoleucyl-tRNA synthetase, N-[ISOLEUCINYL]-N'-[ADENOSYL]-DIAMINOSUFONE, ZINC ION | | Authors: | Nakama, T, Nureki, O, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-09-17 | | Release date: | 2001-12-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase.
J.Biol.Chem., 276, 2001
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4WR5
 | | Crystal Structure of GST Mutated with Halogenated Tyrosine (7cGST-1) | | Descriptor: | GLUTATHIONE, Glutathione S-transferase class-mu 26 kDa isozyme, SULFATE ION | | Authors: | Akasaka, R, Kawazoe, M, Tomabechi, Y, Ohtake, K, Itagaki, T, Takemoto, C, Shirouzu, M, Yokoyama, S, Sakamoto, K. | | Deposit date: | 2014-10-23 | | Release date: | 2015-08-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Protein stabilization utilizing a redefined codon
Sci Rep, 5, 2015
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4WR4
 | | Crystal Structure of GST Mutated with Halogenated Tyrosine (7bGST-1) | | Descriptor: | GLUTATHIONE, Glutathione S-transferase class-mu 26 kDa isozyme, SULFATE ION | | Authors: | Akasaka, R, Kawazoe, M, Tomabechi, Y, Ohtake, K, Itagaki, T, Takemoto, C, Shirouzu, M, Yokoyama, S, Sakamoto, K. | | Deposit date: | 2014-10-23 | | Release date: | 2015-08-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Protein stabilization utilizing a redefined codon
Sci Rep, 5, 2015
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4WQS
 | | Thermus thermophilus RNA polymerase backtracked complex | | Descriptor: | DNA (28-MER), DNA (5'-D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)-3'), DNA-directed RNA polymerase subunit alpha, ... | | Authors: | Murayama, Y, Sekine, S, Yokoyama, S. | | Deposit date: | 2014-10-22 | | Release date: | 2015-02-18 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (4.306 Å) | | Cite: | The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions.
Mol.Cell, 57, 2015
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4WQT
 | | Thermus thermophilus RNA polymerase complexed with an RNA cleavage stimulating factor (a GreA/Gfh1 chimeric protein) | | Descriptor: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | | Authors: | Murayama, Y, Sekine, S, Yokoyama, S. | | Deposit date: | 2014-10-22 | | Release date: | 2015-02-18 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (4.4 Å) | | Cite: | The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions.
Mol.Cell, 57, 2015
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3WPQ
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3WHE
 | | A new conserved neutralizing epitope at the globular head of hemagglutinin in H3N2 influenza viruses | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Hemagglutinin, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Fujii, Y, Sumida, T, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2013-08-25 | | Release date: | 2014-04-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (4 Å) | | Cite: | Conserved neutralizing epitope at globular head of hemagglutinin in H3N2 influenza viruses.
J.Virol., 88, 2014
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3WU5
 | | Reduced E.coli Lon Proteolytic domain | | Descriptor: | Lon protease, SULFATE ION | | Authors: | Nishii, W, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Muramatsu, T, Yokoyama, S. | | Deposit date: | 2014-04-22 | | Release date: | 2014-11-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.
Nat. Chem. Biol., 11, 2015
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3WJ9
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3WU3
 | | Reduced-form structure of E.coli Lon Proteolytic domain | | Descriptor: | Lon protease, SULFATE ION | | Authors: | Nishii, W, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Muramatsu, T, Yokoyama, S. | | Deposit date: | 2014-04-22 | | Release date: | 2014-11-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.82 Å) | | Cite: | A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.
Nat. Chem. Biol., 11, 2015
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6JP2
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1D9A
 | | SOLUTION STRUCTURE OF THE SECOND RNA-BINDING DOMAIN (RBD2) OF HU ANTIGEN C (HUC) | | Descriptor: | HU ANTIGEN C | | Authors: | Inoue, M, Muto, Y, Sakamoto, H, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1999-10-26 | | Release date: | 2000-04-07 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | NMR studies on functional structures of the AU-rich element-binding domains of Hu antigen C.
Nucleic Acids Res., 28, 2000
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1D8Z
 | | SOLUTION STRUCTURE OF THE FIRST RNA-BINDING DOMAIN (RBD1) OF HU ANTIGEN C (HUC) | | Descriptor: | HU ANTIGEN C | | Authors: | Inoue, M, Muto, Y, Sakamoto, H, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1999-10-26 | | Release date: | 2000-04-07 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | NMR studies on functional structures of the AU-rich element-binding domains of Hu antigen C.
Nucleic Acids Res., 28, 2000
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3GQB
 | | Crystal Structure of the A3B3 complex from V-ATPase | | Descriptor: | V-type ATP synthase alpha chain, V-type ATP synthase beta chain | | Authors: | Meher, M, Akimoto, S, Iwata, M, Nagata, K, Hori, Y, Yoshida, M, Yokoyama, S, Iwata, S, Yokoyama, K. | | Deposit date: | 2009-03-24 | | Release date: | 2009-11-24 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of A(3)B(3) complex of V-ATPase from Thermus thermophilus.
Embo J., 28, 2009
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1EF5
 | | SOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF RGL | | Descriptor: | RGL | | Authors: | Kigawa, T, Endo, M, Ito, Y, Shirouzu, M, Kikuchi, A, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2000-02-07 | | Release date: | 2000-02-23 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the Ras-binding domain of RGL.
FEBS Lett., 441, 1998
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5KNC
 | | Crystal structure of the 3 ADP-bound V1 complex | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... | | Authors: | Suzuki, K, Mizutani, K, Maruyama, S, Shimono, K, Imai, F.L, Muneyuki, E, Kakinuma, Y, Ishizuka-Katsura, Y, Shirouzu, M, Yokoyama, S, Yamato, I, Murata, T. | | Deposit date: | 2016-06-28 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.015 Å) | | Cite: | Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor
Nat Commun, 7, 2016
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5KNB
 | | Crystal structure of the 2 ADP-bound V1 complex | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... | | Authors: | Suzuki, K, Mizutani, K, Maruyama, S, Shimono, K, Imai, F.L, Muneyuki, E, Kakinuma, Y, Ishizuka-Katsura, Y, Shirouzu, M, Yokoyama, S, Yamato, I, Murata, T. | | Deposit date: | 2016-06-28 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.251 Å) | | Cite: | Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor
Nat Commun, 7, 2016
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5KND
 | | Crystal structure of the Pi-bound V1 complex | | Descriptor: | 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, GLYCEROL, MAGNESIUM ION, ... | | Authors: | Suzuki, K, Mizutani, K, Maruyama, S, Shimono, K, Imai, F.L, Muneyuki, E, Kakinuma, Y, Ishizuka-Katsura, Y, Shirouzu, M, Yokoyama, S, Yamato, I, Murata, T. | | Deposit date: | 2016-06-28 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.888 Å) | | Cite: | Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor
Nat Commun, 7, 2016
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1MG8
 | | NMR structure of ubiquitin-like domain in murine Parkin | | Descriptor: | Parkin | | Authors: | Tashiro, M, Okubo, S, Shimotakahara, S, Hatanaka, H, Yasuda, H, Kainosho, M, Yokoyama, S, Shindo, H, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-08-15 | | Release date: | 2003-04-08 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | NMR structure of ubiquitin-like domain in PARKIN: Gene product of familial Parkinson's disease.
J.Biomol.NMR, 25, 2003
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1J09
 | | Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, GLUTAMIC ACID, Glutamyl-tRNA synthetase, ... | | Authors: | Sekine, S, Nureki, O, Dubois, D.Y, Bernier, S, Chenevert, R, Lapointe, J, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-11-12 | | Release date: | 2003-02-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding
EMBO J., 22, 2003
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1S0V
 | | Structural basis for substrate selection by T7 RNA polymerase | | Descriptor: | 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3', 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3', 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3', ... | | Authors: | Temiakov, D, Patlan, V, Anikin, M, McAllister, W.T, Yokoyama, S, Vassylyev, D.G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-01-05 | | Release date: | 2004-02-24 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Structural basis for substrate selection by t7 RNA polymerase.
Cell(Cambridge,Mass.), 116, 2004
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2EF1
 | | Crystal structure of the extracellular domain of human CD38 | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ADP-ribosyl cyclase 1 | | Authors: | Kukimoto-Niino, M, Nureki, O, Murayama, K, Shirouzu, M, Katada, T, Hara-Yokoyama, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-02-20 | | Release date: | 2007-02-27 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of the extracellular domain of human CD38
To be Published
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