1GLN
| ARCHITECTURES OF CLASS-DEFINING AND SPECIFIC DOMAINS OF GLUTAMYL-TRNA SYNTHETASE | Descriptor: | GLUTAMYL-TRNA SYNTHETASE | Authors: | Nureki, O, Vassylyev, D.G, Katayanagi, K, Shimizu, T, Sekine, S, Kigawa, T, Miyazawa, T, Yokoyama, S, Morikawa, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 1994-07-20 | Release date: | 1995-10-15 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science, 267, 1995
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1V2X
| TrmH | Descriptor: | PHOSPHATE ION, S-ADENOSYLMETHIONINE, tRNA (Gm18) methyltransferase | Authors: | Nureki, O, Watanabe, K, Fukai, S, Ishii, R, Endo, Y, Hori, H, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-10-17 | Release date: | 2004-05-04 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme STRUCTURE, 12, 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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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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3AII
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8XBH
| Human GPR34 -Gi complex bound to M1 | Descriptor: | (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, ... | Authors: | Kawahara, R, Shihoya, W, Nureki, O. | Deposit date: | 2023-12-06 | Release date: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.83 Å) | Cite: | Cryo-EM structure of the Human GPR34-Gi complex bound to S3E-LysoPS To Be Published
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8XBI
| Human GPR34 -Gi complex bound to M1, receptor focused | Descriptor: | (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid, Probable G-protein coupled receptor 34 | Authors: | Kawahara, R, Shihoya, W, Nureki, O. | Deposit date: | 2023-12-06 | Release date: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (3.06 Å) | Cite: | Cryo-EM structure of the Human GPR34-Gi complex bound to S3E-LysoPS To Be Published
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1UET
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1UEU
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1UEV
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2D6F
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1IRX
| Crystal structure of class I lysyl-tRNA synthetase | Descriptor: | ZINC ION, lysyl-tRNA synthetase | Authors: | Nureki, O, Terada, T, Ishitani, R, Ambrogelly, A, Ibba, M, Soll, D, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2001-10-25 | Release date: | 2002-04-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat.Struct.Biol., 9, 2002
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2ZY9
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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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8XGR
| ETB-eGt complex bound to endothelin-1 | Descriptor: | Camelid antibody VHH fragment, Endothelin receptor type B, Endothelin-1, ... | Authors: | Oshima, H.S, Sano, F.K, Akasaka, H, Iwama, A, Shihoya, W, Nureki, O. | Deposit date: | 2023-12-15 | Release date: | 2024-04-03 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Optimizing cryo-EM structural analysis of G i -coupling receptors via engineered G t and Nb35 application. Biochem.Biophys.Res.Commun., 693, 2024
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1N75
| Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP. | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Glutamyl-tRNA synthetase, MAGNESIUM ION | 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 (1.9 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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1N78
| Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP. | Descriptor: | GLUTAMOL-AMP, Glutamyl-tRNA synthetase, MAGNESIUM ION, ... | 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: | 2002-11-13 | Release date: | 2003-02-25 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 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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1N77
| Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and ATP. | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Glutamyl-tRNA synthetase, MAGNESIUM ION, ... | 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: | 2002-11-13 | Release date: | 2003-02-25 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.4 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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5CZZ
| Crystal structure of Staphylococcus aureus Cas9 in complex with sgRNA and target DNA (TTGAAT PAM) | Descriptor: | 1,2-ETHANEDIOL, CRISPR-associated endonuclease Cas9, DNA (28-MER), ... | Authors: | Nishimasu, H, Ishitani, R, Nureki, O. | Deposit date: | 2015-08-01 | Release date: | 2015-09-02 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal Structure of Staphylococcus aureus Cas9. Cell, 162, 2015
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5D4J
| Chloride-bound form of a copper nitrite reductase from Alcaligenes faecals | Descriptor: | ACETIC ACID, CHLORIDE ION, COPPER (II) ION, ... | Authors: | Fukuda, Y, Tse, K.M, Nakane, T, Nakatsu, T, Suzuki, M, Sugahara, M, Inoue, S, Yumoto, F, Matsugaki, N, Nango, E, Tono, K, Joti, Y, Kameshima, T, Song, C, Yabashi, M, Nureki, O, Murphy, M.E.P, Inoue, T, Iwata, S, Mizohata, E. | Deposit date: | 2015-08-07 | Release date: | 2016-03-09 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography Proc.Natl.Acad.Sci.USA, 113, 2016
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5D4H
| High-resolution nitrite complex of a copper nitrite reductase determined by synchrotron radiation crystallography | Descriptor: | ACETIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | Authors: | Fukuda, Y, Tse, K.M, Nakane, T, Nakatsu, T, Suzuki, M, Sugahara, M, Inoue, S, Masuda, T, Yumoto, F, Matsugaki, N, Nango, E, Tono, K, Joti, Y, Kameshima, T, Song, C, Hatsui, T, Yabashi, M, Nureki, O, Murphy, M.E.P, Inoue, T, Iwata, S, Mizohata, E. | Deposit date: | 2015-08-07 | Release date: | 2016-03-09 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.3 Å) | Cite: | Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography Proc.Natl.Acad.Sci.USA, 113, 2016
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1A8H
| METHIONYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS | Descriptor: | METHIONYL-TRNA SYNTHETASE, ZINC ION | Authors: | Sugiura, I, Nureki, O, Ugaji, Y, Kuwabara, S, Lober, B, Giege, R, Moras, D, Yokoyama, S, Konno, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 1998-03-26 | Release date: | 1999-05-04 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules. Structure, 8, 2000
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1B7F
| SXL-LETHAL PROTEIN/RNA COMPLEX | Descriptor: | PROTEIN (SXL-LETHAL PROTEIN), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3') | Authors: | Handa, N, Nureki, O, Kurimoto, K, Kim, I, Sakamoto, H, Shimura, Y, Muto, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 1999-01-23 | Release date: | 1999-05-03 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature, 398, 1999
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2RRN
| Solution structure of SecDF periplasmic domain P4 | Descriptor: | Probable SecDF protein-export membrane protein | Authors: | Tanaka, T, Tsukazaki, T, Echizen, Y, Nureki, O, Kohno, T. | Deposit date: | 2011-01-30 | Release date: | 2011-05-18 | Last modified: | 2024-05-01 | Method: | SOLUTION NMR | Cite: | Structure and function of a membrane component SecDF that enhances protein export Nature, 474, 2011
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7BTW
| The mitochondrial SAM complex from S.cere | Descriptor: | Mitochondrial outer membrane beta-barrel protein, SAM37 isoform 1, Sorting assembly machinery 35 kDa subunit | Authors: | Takeda, H, Tsutsumi, A, Nishizawa, T, Nureki, O, Kikkawa, M, Endo, T. | Deposit date: | 2020-04-03 | Release date: | 2021-01-20 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Mitochondrial sorting and assembly machinery operates by beta-barrel switching. Nature, 590, 2021
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