Author results

1GLN
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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
1ILE
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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
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
1V2X
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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
3AII
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ARCHAEAL NON-DISCRIMINATING GLUTAMYL-TRNA SYNTHETASE FROM METHANOTHERMOBACTER THERMAUTOTROPHICUS
Descriptor:Glutamyl-tRNA synthetase, ACETIC ACID, 1,2-ETHANEDIOL, ...
Authors:Nureki, O., Ishitani, R.
Deposit date:2010-05-14
Release date:2010-08-04
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation
Nucleic Acids Res., 2010
1IRX
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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
1UET
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DIVERGENT EVOLUTIONS OF TRINUCLEOTIDE POLYMERIZATION REVEALED BY AN ARCHAEAL CCA-ADDING ENZYME STRUCTURE
Descriptor:tRNA nucleotidyltransferase, ACETATE ION, CALCIUM ION, ...
Authors:Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-05-21
Release date:2003-12-02
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure.
Embo J., 22, 2003
1UEU
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DIVERGENT EVOLUTIONS OF TRINUCLEOTIDE POLYMERIZATION REVEALED BY AN ARCHAEAL CCA-ADDING ENZYME STRUCTURE
Descriptor:tRNA nucleotidyltransferase, ACETATE ION, MAGNESIUM ION, ...
Authors:Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-05-21
Release date:2003-12-02
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure.
Embo J., 22, 2003
1UEV
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DIVERGENT EVOLUTIONS OF TRINUCLEOTIDE POLYMERIZATION REVEALED BY AN ARCHAEAL CCA-ADDING ENZYME STRUCTURE
Descriptor:tRNA nucleotidyltransferase, MAGNESIUM ION, CALCIUM ION, ...
Authors:Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2003-05-21
Release date:2003-12-02
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure.
Embo J., 22, 2003
2D6F
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CRYSTAL STRUCTURE OF GLU-TRNA(GLN) AMIDOTRANSFERASE IN THE COMPLEX WITH TRNA(GLN)
Descriptor:tRNA, Glutamyl-tRNA(Gln) amidotransferase subunit D, Glutamyl-tRNA(Gln) amidotransferase subunit E, ...
Authors:Nureki, O.
Deposit date:2005-11-13
Release date:2006-07-11
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (3.15 Å)
Cite:Structural basis of RNA-dependent recruitment of glutamine to the genetic code
Science, 312, 2006
2ZY9
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IMPROVED CRYSTAL STRUCTURE OF MAGNESIUM TRANSPORTER MGTE
Descriptor:Mg2+ transporter MgtE, MAGNESIUM ION
Authors:Nureki, O., Ishitani, R., Hattori, M.
Deposit date:2009-01-19
Release date:2009-12-01
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.94 Å)
Cite:Mg(2+)-dependent gating of bacterial MgtE channel underlies Mg(2+) homeostasis
Embo J., 28, 2009
1J09
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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
1N75
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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
1N77
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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
1N78
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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
1IVS
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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
2DB3
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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
3AQO
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STRUCTURE AND FUNCTION OF A MEMBRANE COMPONENT SECDF THAT ENHANCES PROTEIN EXPORT
Descriptor:Probable SecDF protein-export membrane protein
Authors:Echizen, Y., Tsukazaki, T., Ishitani, R., Nureki, O.
Deposit date:2010-11-16
Release date:2011-05-18
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structure and function of a membrane component SecDF that enhances protein export.
Nature, 474, 2011
3VU8
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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
3UG9
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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
5XW6
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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, N-ACETYL-D-GLUCOSAMINE, 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
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
5Y5I
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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
5Y5J
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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
5Y5K
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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
5Y5L
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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