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: | 2017-11-29 | | 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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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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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: | 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
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1V2X | | TRMH | | Descriptor: | tRNA (Gm18) methyltransferase, PHOSPHATE ION, S-ADENOSYLMETHIONINE | | 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: | 2013-06-26 | | 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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3AII | |
1IRX | | CRYSTAL STRUCTURE OF CLASS I LYSYL-TRNA SYNTHETASE | | Descriptor: | lysyl-tRNA synthetase, ZINC ION | | 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: | 2011-07-13 | | 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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1UET | |
1UEU | |
1UEV | |
2D6F | |
2ZY9 | |
1J09 | | CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH ATP AND GLU | | Descriptor: | Glutamyl-tRNA synthetase, MAGNESIUM ION, GLUTAMIC ACID, ... | | 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: | 2011-07-13 | | 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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1N75 | | CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH ATP. | | Descriptor: | Glutamyl-tRNA synthetase, MAGNESIUM ION, ADENOSINE-5'-TRIPHOSPHATE | | 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: | 2011-07-13 | | 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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1N77 | | CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU) AND ATP. | | Descriptor: | tRNA(Glu), 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: | 2011-07-13 | | 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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1N78 | | CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU) AND GLUTAMOL-AMP. | | Descriptor: | tRNA(Glu), 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: | 2011-07-13 | | 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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1IVS | | CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE | | Descriptor: | tRNA (Val), Valyl-tRNA synthetase, N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE | | 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: | 2011-07-13 | | 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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2DB3 | | STRUCTURAL BASIS FOR RNA UNWINDING BY THE DEAD-BOX PROTEIN DROSOPHILA VASA | | Descriptor: | 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3', ATP-dependent RNA helicase vasa, MAGNESIUM ION, ... | | Authors: | Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-12-14 | | Release date: | 2006-05-02 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
Cell(Cambridge,Mass.), 125, 2006
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3AQO | |
3VU8 | | METIONYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH METHIONYL-ADENYLATE ANALOGUE | | Descriptor: | Methionine--tRNA ligase, ZINC ION, N-[METHIONYL]-N'-[ADENOSYL]-DIAMINOSULFONE | | Authors: | Konno, M., Kato-Murayama, M., Toma-Fukai, S., Uchikawa, E., Nureki, O., Yokoyama, S. | | Deposit date: | 2012-06-22 | | Release date: | 2013-06-26 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases
To be Published
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3UG9 | | CRYSTAL STRUCTURE OF THE CLOSED STATE OF CHANNELRHODOPSIN | | Descriptor: | Archaeal-type opsin 1, Archaeal-type opsin 2, RETINAL, ... | | Authors: | Kato, H.E., Ishitani, R., Nureki, O. | | Deposit date: | 2011-11-02 | | Release date: | 2012-01-25 | | Last modified: | 2017-08-09 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of the channelrhodopsin light-gated cation channel
Nature, 482, 2012
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5XW6 | | CRYSTAL STRUCTURE OF THE CHICKEN ATP-GATED P2X7 RECEPTOR CHANNEL IN THE PRESENCE OF COMPETITIVE ANTAGONIST TNP-ATP AT 3.1 ANGSTROMS | | Descriptor: | P2X purinoceptor, 2-acetamido-2-deoxy-beta-D-glucopyranose, SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE | | Authors: | Kasuya, G., Hattori, M., Nureki, O. | | Deposit date: | 2017-06-29 | | Release date: | 2017-10-25 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Structural insights into the competitive inhibition of the ATP-gated P2X receptor channel
Nat Commun, 8, 2017
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5Y5I | | TIME-RESOLVED SFX STRUCTURE OF CYTOCHROME P450NOR: 20 MS AFTER PHOTO-IRRADIATION OF CAGED NO IN THE PRESENCE OF NADH (NO-BOUND STATE), LIGHT DATA | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE, ... | | Authors: | Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2018-09-19 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5J | | TIME-RESOLVED SFX STRUCTURE OF CYTOCHROME P450NOR: DARK-2 DATA IN THE PRESENCE OF NADH (RESTING STATE) | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL | | Authors: | Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5K | | TIME-RESOLVED SFX STRUCTURE OF CYTOCHROME P450NOR : 20 MS AFTER PHOTO-IRRADIATION OF CAGED NO IN THE ABSENCE OF NADH (NO-BOUND STATE), LIGHT DATA | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE | | Authors: | Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2018-09-19 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5L | | TIME-RESOLVED SFX STRUCTURE OF CYTOCHROME P450NOR: DARK-2 DATA IN THE ABSENCE OF NADH (RESTING STATE) | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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