Author results

1WY5
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CRYSTAL STRUCTURE OF ISOLUECYL-TRNA LYSIDINE SYNTHETASE
Descriptor:Hypothetical UPF0072 protein AQ_1887
Authors:Nakanishi, K., Fukai, S., Ikeuchi, Y., Soma, A., Sekine, Y., Suzuki, T., Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-02-06
Release date:2005-05-03
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.42 Å)
Cite:Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain.
Proc.Natl.Acad.Sci.Usa, 102, 2005
2CSX
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CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS METHIONYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(MET)
Descriptor:RNA (75-MER), Methionyl-tRNA synthetase
Authors:Nakanishi, K., Ogiso, Y., Nakama, T., Fukai, S., Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-05-23
Release date:2005-09-20
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural basis for anticodon recognition by methionyl-tRNA synthetase.
Nat.Struct.Mol.Biol., 12, 2005
2CT8
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CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS METHIONYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(MET) AND METHIONYL-ADENYLATE ANOLOGUE
Descriptor:RNA (74-MER), Methionyl-tRNA synthetase, 5'-O-[(L-METHIONYL)-SULPHAMOYL]ADENOSINE
Authors:Nakanishi, K., Ogiso, Y., Nakama, T., Fukai, S., Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-05-23
Release date:2005-09-20
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural basis for anticodon recognition by methionyl-tRNA synthetase.
Nat.Struct.Mol.Biol., 12, 2005
3A2K
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CRYSTAL STRUCTURE OF TILS COMPLEXED WITH TRNA
Descriptor:tRNA(Ile)-lysidine synthase, bacterial tRNA
Authors:Nakanishi, K., Bonnefond, L., Ishitani, R., Nureki, O.
Deposit date:2009-05-23
Release date:2009-10-20
Last modified:2018-01-24
Method:X-RAY DIFFRACTION (3.65 Å)
Cite:Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.
Nature, 461, 2009
3HJ7
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CRYSTAL STRUCTURE OF TILS C-TERMINAL DOMAIN
Descriptor:tRNA(Ile)-lysidine synthase, CHLORIDE ION
Authors:Nakanishi, K., Bonnefond, L., Kimura, S., Suzuki, T., Ishitani, R., Nureki, O.
Deposit date:2009-05-21
Release date:2009-10-20
Last modified:2017-11-01
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.
Nature, 461, 2009
4F1N
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CRYSTAL STRUCTURE OF KLUYVEROMYCES POLYSPORUS ARGONAUTE WITH A GUIDE RNA
Descriptor:KpAGO, RNA 5'-R(P*UP*AP*AP*AP*AP*AP*AP*AP*A)-3'
Authors:Nakanishi, K., Weinberg, D.E., Bartel, D.P., Patel, D.J.
Deposit date:2012-05-07
Release date:2012-06-13
Last modified:2012-07-04
Method:X-RAY DIFFRACTION (3.187 Å)
Cite:Structure of yeast Argonaute with guide RNA.
Nature, 486, 2012
4KXT
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STRUCTURE OF HUMAN ARGONAUTE1 IN COMPLEX WITH GUIDE RNA
Descriptor:Protein argonaute-1, RNA
Authors:Nakanishi, K., Patel, D.J.
Deposit date:2013-05-28
Release date:2013-07-31
Method:X-RAY DIFFRACTION (2.294 Å)
Cite:Eukaryote-Specific Insertion Elements Control Human ARGONAUTE Slicer Activity.
Cell Rep, 3, 2013
3RV0
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CRYSTAL STRUCTURE OF K. POLYSPORUS DCR1 WITHOUT THE C-TERMINAL DSRBD
Descriptor:K. polysporus Dcr1, MAGNESIUM ION
Authors:Nakanishi, K., Weinberg, D.E., Bartel, D.P., Patel, D.J.
Deposit date:2011-05-05
Release date:2011-08-03
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (2.29 Å)
Cite:The inside-out mechanism of dicers from budding yeasts.
Cell(Cambridge,Mass.), 146, 2011
3RV1
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CRYSTAL STRUCTURE OF THE N-TERMINAL AND RNASE III DOMAINS OF K. POLYSPORUS DCR1 E224Q MUTANT
Descriptor:K. polysporus Dcr1
Authors:Nakanishi, K., Weinberg, D.E., Bartel, D.P., Patel, D.J.
Deposit date:2011-05-05
Release date:2011-08-03
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.975 Å)
Cite:The inside-out mechanism of dicers from budding yeasts.
Cell(Cambridge,Mass.), 146, 2011
1TFK
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RIBONUCLEASE FROM ESCHERICHIA COLI COMPLEXED WITH ITS INHIBTOR PROTEIN
Descriptor:Colicin D, Colicin D immunity protein, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Authors:Yajima, S., Nakanishi, K., Takahashi, K., Ogawa, T., Kezuka, Y., Hidaka, M., Nonaka, T., Ohsawa, K., Masaki, H.
Deposit date:2004-05-27
Release date:2005-03-01
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Relation between tRNase activity and the structure of colicin D according to X-ray crystallography
Biochem.Biophys.Res.Commun., 322, 2004
1TFO
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RIBONUCLEASE FROM ESCHERICHIA COLI COMPLEXED WITH ITS INHIBITOR PROTEIN
Descriptor:Colicin D, Colicin D immunity protein
Authors:Yajima, S., Nakanishi, K., Takahashi, K., Ogawa, T., Kezuka, Y., Hidaka, M., Nonaka, T., Ohsawa, K., Masaki, H.
Deposit date:2004-05-27
Release date:2005-03-01
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Relation between tRNase activity and the structure of colicin D according to X-ray crystallography
Biochem.Biophys.Res.Commun., 322, 2004
3W4I
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CRYSTAL STRUCTURE OF HUMAN DAAO IN COMPLEX WITH COUMPOUND 8
Descriptor:D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, pyridine-2,3-diol
Authors:Hondo, T., Warizaya, M., Niimi, T., Namatame, I., Yamaguchi, T., Nakanishi, K., Hamajima, T., Harada, K., Sakashita, H., Matsumoto, Y., Orita, M., Watanabe, T., Takeuchi, M.
Deposit date:2013-01-09
Release date:2013-05-29
Last modified:2017-11-22
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:4-Hydroxypyridazin-3(2H)-one Derivatives as Novel d-Amino Acid Oxidase Inhibitors.
J.Med.Chem., 56, 2013
3W4J
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CRYSTAL STRUCTURE OF HUMAN DAAO IN COMPLEX WITH COUMPOUND 12
Descriptor:D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, 3-hydroxy-5-(2-phenylethyl)pyridin-2(1H)-one
Authors:Hondo, T., Warizaya, M., Niimi, T., Namatame, I., Yamaguchi, T., Nakanishi, K., Hamajima, T., Harada, K., Sakashita, H., Matsumoto, Y., Orita, M., Watanabe, T., Takeuchi, M.
Deposit date:2013-01-09
Release date:2013-05-29
Last modified:2017-11-22
Method:X-RAY DIFFRACTION (2.74 Å)
Cite:4-Hydroxypyridazin-3(2H)-one Derivatives as Novel d-Amino Acid Oxidase Inhibitors.
J.Med.Chem., 56, 2013
3W4K
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CRYSTAL STRUCTURE OF HUMAN DAAO IN COMPLEX WITH COUMPOUND 13
Descriptor:D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, 3-hydroxy-6-(2-phenylethyl)pyridazin-4(1H)-one
Authors:Hondo, T., Warizaya, M., Niimi, T., Namatame, I., Yamaguchi, T., Nakanishi, K., Hamajima, T., Harada, K., Sakashita, H., Matsumoto, Y., Orita, M., Watanabe, T., Takeuchi, M.
Deposit date:2013-01-09
Release date:2013-05-29
Last modified:2018-07-04
Method:X-RAY DIFFRACTION (2.86 Å)
Cite:4-Hydroxypyridazin-3(2H)-one Derivatives as Novel d-Amino Acid Oxidase Inhibitors.
J.Med.Chem., 56, 2013
5VXB
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CRYSTAL STRUCTURE OF CAULOBACTER CRESCENTUS PROXP-ALA AT 1.69 ANGSTROM
Descriptor:ProXp-ala
Authors:Foster, M.P., Musier-Forsyth, K., Nakanishi, K., Ma, X.
Deposit date:2017-05-23
Release date:2017-08-09
Last modified:2017-09-20
Method:X-RAY DIFFRACTION (1.69 Å)
Cite:Conformational and chemical selection by a trans-acting editing domain.
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
5THE
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CRYSTAL STRUCTURE OF THE C-TERMINAL LOBE OF A BUDDING YEAST ARGONAUTE
Descriptor:Uncharacterized protein, RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')
Authors:Dayeh, D.M., Nakanishi, K.
Deposit date:2016-09-29
Release date:2018-03-14
Last modified:2018-05-09
Method:X-RAY DIFFRACTION (2.097 Å)
Cite:Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA target cleavage.
J. Biol. Chem., 293, 2018
5VM9
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HUMAN ARGONAUTE3 BOUND TO GUIDE RNA
Descriptor:Protein argonaute-3, RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3'), RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')
Authors:Park, M.S., Nakanishi, K.
Deposit date:2017-04-26
Release date:2017-10-18
Last modified:2017-12-06
Method:X-RAY DIFFRACTION (3.28 Å)
Cite:Human Argonaute3 has slicer activity.
Nucleic Acids Res., 45, 2017
1G0D
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CRYSTAL STRUCTURE OF RED SEA BREAM TRANSGLUTAMINASE
Descriptor:PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE, SULFATE ION
Authors:Noguchi, K., Ishikawa, K., Yokoyama, K., Ohtsuka, T., Nio, N., Suzuki, E.
Deposit date:2000-10-06
Release date:2001-05-23
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal structure of red sea bream transglutaminase.
J.Biol.Chem., 276, 2001
5ZNM
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COLICIN D CENTRAL DOMAIN AND C-TERMINAL TRNASE DOMAIN
Descriptor:Colicin-D, SULFATE ION, GLYCEROL
Authors:Chang, J.W., Sato, Y., Ogawa, T., Arakawa, T., Fukai, S., Fushinobu, S., Masaki, H.
Deposit date:2018-04-10
Release date:2018-08-29
Last modified:2018-10-31
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell
J. Biochem., 164, 2018