2P4V
 
 | | Crystal structure of the transcript cleavage factor, GreB at 2.6A resolution | | Descriptor: | Transcription elongation factor greB | | Authors: | Vassylyeva, M.N, Svetlov, V, Dearborn, A.D, Klyuyev, S, Artsimovitch, I, Vassylyev, D.G. | | Deposit date: | 2007-03-13 | | Release date: | 2008-01-22 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors.
Embo Rep., 8, 2007
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3DBG
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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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3E0J
 | | X-ray structure of the complex of regulatory subunits of human DNA polymerase delta | | Descriptor: | DNA polymerase subunit delta-2, DNA polymerase subunit delta-3 | | Authors: | Baranovskiy, A.G, Babayeva, N.D, Pavlov, Y.I, Vassylyev, D.G, Tahirov, T.H. | | Deposit date: | 2008-07-31 | | Release date: | 2008-12-16 | | Last modified: | 2020-10-21 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | X-ray structure of the complex of regulatory subunits of human DNA polymerase delta.
Cell Cycle, 7, 2008
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2A6H
 | | Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin | | Descriptor: | DNA-directed RNA polymerase alpha chain, DNA-directed RNA polymerase beta chain, DNA-directed RNA polymerase beta' chain, ... | | Authors: | Temiakov, D, Zenkin, N, Vassylyeva, M.N, Perederina, A, Tahirov, T.H, Savkina, M, Zorov, S, Nikiforov, V, Igarashi, N, Matsugaki, N, Wakatsuki, S, Severinov, K, Vassylyev, D.G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-02 | | Release date: | 2005-09-20 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis of transcription inhibition by antibiotic streptolydigin.
Mol.Cell, 19, 2005
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2A69
 | | Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin | | Descriptor: | DNA-directed RNA polymerase alpha chain, DNA-directed RNA polymerase beta chain, DNA-directed RNA polymerase beta' chain, ... | | Authors: | Artsimovitch, I, Vassylyeva, M.N, Svetlov, D, Svetlov, V, Perederina, A, Igarashi, N, Matsugaki, N, Wakatsuki, S, Tahirov, T.H, Vassylyev, D.G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-02 | | Release date: | 2005-09-20 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.
Cell(Cambridge,Mass.), 122, 2005
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2A68
 | | Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic rifabutin | | Descriptor: | DNA-directed RNA polymerase alpha chain, DNA-directed RNA polymerase beta chain, DNA-directed RNA polymerase beta' chain, ... | | Authors: | Artsimovitch, I, Vassylyeva, M.N, Svetlov, D, Svetlov, V, Perederina, A, Igarashi, N, Matsugaki, N, Wakatsuki, S, Tahirov, T.H, Vassylyev, D.G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-01 | | Release date: | 2005-09-20 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.
Cell(Cambridge,Mass.), 122, 2005
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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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1SMY
 | | Structural basis for transcription regulation by alarmone ppGpp | | Descriptor: | DNA-directed RNA polymerase alpha chain, DNA-directed RNA polymerase beta chain, DNA-directed RNA polymerase beta' chain, ... | | Authors: | Artsimovitch, I, Patlan, V, Sekine, S, Vassylyeva, M.N, Hosaka, T, Ochi, K, Yokoyama, S, Vassylyev, D.G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-03-10 | | Release date: | 2004-05-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural basis for transcription regulation by alarmone ppGpp
Cell(Cambridge,Mass.), 117, 2004
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1TJL
 | | Crystal structure of transcription factor DksA from E. coli | | Descriptor: | DnaK suppressor protein, ZINC ION | | Authors: | Perederina, A, Svetlov, V, Vassylyeva, M.N, Artsimovitch, I, Yokoyama, S, Vassylyev, D.G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-06-06 | | Release date: | 2004-09-07 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription
Cell(Cambridge,Mass.), 118, 2004
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1UC9
 | | Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8 | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, lysine biosynthesis enzyme | | Authors: | Sakai, H, Vassylyeva, M.N, Matsuura, T, Sekine, S, Nishiyama, M, Terada, T, Shirouzu, M, Kuramitsu, S, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-04-09 | | Release date: | 2003-09-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.38 Å) | | Cite: | Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8
J.Mol.Biol., 332, 2003
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1UC8
 | | Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8 | | Descriptor: | lysine biosynthesis enzyme | | Authors: | Sakai, H, Vassylyeva, M.N, Matsuura, T, Sekine, S, Nishiyama, M, Terada, T, Shirouzu, M, Kuramitsu, S, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-04-09 | | Release date: | 2003-09-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8
J.Mol.Biol., 332, 2003
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1POY
 | | SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM) | | Descriptor: | SPERMIDINE, SPERMIDINE/PUTRESCINE-BINDING PROTEIN | | Authors: | Sugiyama, S, Vassylyev, D.G, Matsushima, M, Morikawa, K. | | Deposit date: | 1996-02-02 | | Release date: | 1996-07-11 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coli.
J.Biol.Chem., 271, 1996
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1IVS
 | | CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE | | Descriptor: | N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE, Valyl-tRNA synthetase, tRNA (Val) | | Authors: | Fukai, S, Nureki, O, Sekine, S.-I, Shimada, A, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-03-29 | | Release date: | 2003-02-11 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
RNA, 9, 2003
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1B7Y
 | | PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE | | Descriptor: | ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE], MAGNESIUM ION, PROTEIN (PHENYLALANYL-TRNA SYNTHETASE) | | Authors: | Reshetnikova, L, Moor, N, Lavrik, O, Vassylyev, D.G. | | Deposit date: | 1999-01-26 | | Release date: | 2000-01-26 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.
J.Mol.Biol., 287, 1999
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1B70
 | | PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE | | Descriptor: | MAGNESIUM ION, PHENYLALANINE, PHENYLALANYL-TRNA SYNTHETASE | | Authors: | Reshetnikova, L, Moor, N, Lavrik, O, Vassylyev, D.G. | | Deposit date: | 1999-01-26 | | Release date: | 2000-02-09 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue
J.Mol.Biol., 287, 1999
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1HJR
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1AT9
 | | STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY | | Descriptor: | BACTERIORHODOPSIN, RETINAL | | Authors: | Kimura, Y, Vassylyev, D.G, Miyazawa, A, Kidera, A, Matsushima, M, Mitsuoka, K, Murata, K, Hirai, T, Fujiyoshi, Y. | | Deposit date: | 1997-08-20 | | Release date: | 1998-09-16 | | Last modified: | 2024-06-05 | | Method: | ELECTRON CRYSTALLOGRAPHY (2.8 Å) | | Cite: | Surface of bacteriorhodopsin revealed by high-resolution electron crystallography.
Nature, 389, 1997
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1VMO
 | | CRYSTAL STRUCTURE OF VITELLINE MEMBRANE OUTER LAYER PROTEIN I (VMO-I): A FOLDING MOTIF WITH HOMOLOGOUS GREEK KEY STRUCTURES RELATED BY AN INTERNAL THREE-FOLD SYMMETRY | | Descriptor: | VITELLINE MEMBRANE OUTER LAYER PROTEIN I | | Authors: | Shimizu, T, Vassylyev, D.G, Kido, S, Doi, Y, Morikawa, K. | | Deposit date: | 1994-01-06 | | Release date: | 1994-05-31 | | Last modified: | 2024-06-05 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of vitelline membrane outer layer protein I (VMO-I): a folding motif with homologous Greek key structures related by an internal three-fold symmetry.
EMBO J., 13, 1994
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1VFG
 | | Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog | | Descriptor: | DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, RNA (75-MER), poly A polymerase | | Authors: | Tomita, K, Fukai, S, Ishitani, R, Ueda, T, Takeuchi, N, Vassylyev, D.G, Nureki, O, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-04-13 | | Release date: | 2004-08-10 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural basis for template-independent RNA polymerization.
Nature, 430, 2004
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1IPA
 | | 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: | 2023-12-27 | | 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
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1IYW
 | | Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase | | Descriptor: | Valyl-tRNA Synthetase | | Authors: | Fukai, S, Nureki, O, Sekine, S, Shimada, A, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-09-10 | | Release date: | 2003-06-17 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (4 Å) | | Cite: | Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
RNA, 9, 2003
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1ILE
 | | ISOLEUCYL-TRNA SYNTHETASE | | Descriptor: | ISOLEUCYL-TRNA SYNTHETASE, ZINC ION | | Authors: | Nureki, O, Vassylyev, D.G, Tateno, M, Shimada, A, Nakama, T, Fukai, S, Konno, M, Schimmel, P, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1998-02-24 | | Release date: | 1999-04-13 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Enzyme structure with two catalytic sites for double-sieve selection of substrate.
Science, 280, 1998
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1FL0
 | | CRYSTAL STRUCTURE OF THE EMAP2/RNA-BINDING DOMAIN OF THE P43 PROTEIN FROM HUMAN AMINOACYL-TRNA SYNTHETASE COMPLEX | | Descriptor: | ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II | | Authors: | Renault, L, Kerjan, P, Pasqualato, S, Menetrey, J, Robinson, J.-C, Kawaguchi, S, Vassylyev, D.G, Yokoyama, S, Mirande, M, Cherfils, J. | | Deposit date: | 2000-08-11 | | Release date: | 2000-12-06 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry.
EMBO J., 20, 2001
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1FUT
 | | CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ITS FREE FORM AND IN COMPLEX WITH 2'GMP | | Descriptor: | GUANOSINE-2'-MONOPHOSPHATE, RIBONUCLEASE F1 | | Authors: | Katayanagi, K, Vassylyev, D.G, Ishikawa, K, Morikawa, K. | | Deposit date: | 1993-01-18 | | Release date: | 1993-10-31 | | Last modified: | 2019-12-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structures of ribonuclease F1 of Fusarium moniliforme in its free form and in complex with 2'GMP.
J.Mol.Biol., 230, 1993
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