3LNQ
 
 | | Structure of Aristaless homeodomain in complex with DNA | | Descriptor: | 5'-D(*CP*CP*CP*TP*AP*AP*TP*TP*AP*AP*AP*CP*CP*C)-3', 5'-D(*GP*GP*GP*TP*TP*TP*AP*AP*TP*TP*AP*GP*GP*G)-3', ACETATE ION, ... | | Authors: | Takamura, Y, Miyazono, K, Nagata, K, Saigo, K, Kojima, T, Tanokura, M. | | Deposit date: | 2010-02-02 | | Release date: | 2010-04-28 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless
Embo J., 29, 2010
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8HYL
 | | Crystal structure of DO1 Fv-clasp fragment | | Descriptor: | VH-SARAH, VL-SARAH | | Authors: | Anan, Y, Lu, P, Nagata, K, Itakura, M, Uchida, K. | | Deposit date: | 2023-01-06 | | Release date: | 2024-02-14 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Molecular and structural basis of anti-DNA antibody specificity for pyrrolated proteins.
Commun Biol, 7, 2024
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4H7F
 | | Crystal structure of haloalkane dehalogenase LinB V134I mutant from Sphingobium sp. MI1205 | | Descriptor: | CALCIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Okai, M, Ohtsuka, J, Imai, L.F, Mase, T, Moriuchi, R, Tsuda, M, Nagata, K, Nagata, Y, Tanokura, M. | | Deposit date: | 2012-09-20 | | Release date: | 2013-06-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.
J.Bacteriol., 195, 2013
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4H7E
 | | Crystal structure of haloalkane dehalogenase LinB V112A mutant from Sphingobium sp. MI1205 | | Descriptor: | CALCIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Okai, M, Ohtsuka, J, Imai, L.F, Mase, T, Moriuchi, R, Tsuda, M, Nagata, K, Nagata, Y, Tanokura, M. | | Deposit date: | 2012-09-20 | | Release date: | 2013-06-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.
J.Bacteriol., 195, 2013
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4H77
 | | Crystal structure of haloalkane dehalogenase LinB from Sphingobium sp. MI1205 | | Descriptor: | CALCIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Okai, M, Ohtsuka, J, Imai, F.L, Mase, T, Moriuchi, R, Tsuda, M, Nagata, K, Nagata, Y, Tanokura, M. | | Deposit date: | 2012-09-20 | | Release date: | 2013-06-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.
J.Bacteriol., 195, 2013
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4H7J
 | | Crystal structure of haloalkane dehalogenase LinB H247A mutant from Sphingobium sp. MI1205 | | Descriptor: | CALCIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Okai, M, Ohtsuka, J, Imai, L.F, Mase, T, Moriuchi, R, Tsuda, M, Nagata, K, Nagata, Y, Tanokura, M. | | Deposit date: | 2012-09-20 | | Release date: | 2013-06-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.
J.Bacteriol., 195, 2013
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5WVU
 | | Crystal structure of carboxypeptidase from Thermus thermophilus | | Descriptor: | GLYCEROL, Thermostable carboxypeptidase 1, ZINC ION | | Authors: | Okai, M, Nagata, K, Tanokura, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2016-12-29 | | Release date: | 2017-02-22 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase.
Biochem. Biophys. Res. Commun., 484, 2017
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4H7H
 | | Crystal structure of haloalkane dehalogenase LinB T135A mutant from Sphingobium sp. MI1205 | | Descriptor: | CALCIUM ION, CHLORIDE ION, Haloalkane dehalogenase | | Authors: | Okai, M, Ohtsuka, J, Imai, L.F, Mase, T, Moriuchi, R, Tsuda, M, Nagata, K, Nagata, Y, Tanokura, M. | | Deposit date: | 2012-09-20 | | Release date: | 2013-06-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.
J.Bacteriol., 195, 2013
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4H7D
 | | Crystal structure of haloalkane dehalogenase LinB T81A mutant from Sphingobium sp. MI1205 | | Descriptor: | CALCIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Okai, M, Ohtsuka, J, Imai, L.F, Mase, T, Moriuchi, R, Tsuda, M, Nagata, K, Nagata, Y, Tanokura, M. | | Deposit date: | 2012-09-20 | | Release date: | 2013-06-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.
J.Bacteriol., 195, 2013
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4H7I
 | | Crystal structure of haloalkane dehalogenase LinB L138I mutant from Sphingobium sp. MI1205 | | Descriptor: | CALCIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Okai, M, Ohtsuka, J, Imai, L.F, Mase, T, Moriuchi, R, Tsuda, M, Nagata, K, Nagata, Y, Tanokura, M. | | Deposit date: | 2012-09-20 | | Release date: | 2013-06-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.
J.Bacteriol., 195, 2013
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4H7K
 | | Crystal structure of haloalkane dehalogenase LinB I253M mutant from Sphingobium sp. MI1205 | | Descriptor: | CALCIUM ION, CHLORIDE ION, Haloalkane dehalogenase | | Authors: | Okai, M, Ohtsuka, J, Imai, L.F, Mase, T, Moriuchi, R, Tsuda, M, Nagata, K, Nagata, Y, Tanokura, M. | | Deposit date: | 2012-09-20 | | Release date: | 2013-06-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.
J.Bacteriol., 195, 2013
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3LQB
 | | Crystal structure of the hatching enzyme ZHE1 from the zebrafish Danio rerio | | Descriptor: | 1,2-ETHANEDIOL, LOC792177 protein, SULFATE ION, ... | | Authors: | Tanokura, M, Okada, A, Nagata, K, Yasumasu, S, Ohtsuka, J, Iuchi, I. | | Deposit date: | 2010-02-08 | | Release date: | 2010-09-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Crystal structure of zebrafish hatching enzyme 1 from the zebrafish Danio rerio
J.Mol.Biol., 402, 2010
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7VQ0
 | | Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Maeda, R, Fujita, J, Konishi, Y, Kazuma, Y, Yamazaki, H, Anzai, I, Yamaguchi, K, Kasai, K, Nagata, K, Yamaoka, Y, Miyakawa, K, Ryo, A, Shirakawa, K, Makino, F, Matsuura, Y, Inoue, T, Imura, A, Namba, K, Takaori-Kondo, A. | | Deposit date: | 2021-10-18 | | Release date: | 2022-07-20 | | Method: | ELECTRON MICROSCOPY (3.03 Å) | | Cite: | A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.
Commun Biol, 5, 2022
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3AI1
 | | The crystal structure of L-sorbose reductase from Gluconobacter frateurii complexed with NADPH and L-sorbose reveals the structure bases of its catalytic mechanism and high substrate selectivity | | Descriptor: | NADPH-sorbose reductase | | Authors: | Kubota, K, Nagata, K, Okai, M, Miyazono, K, Tanokura, M. | | Deposit date: | 2010-05-06 | | Release date: | 2011-02-09 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.38 Å) | | Cite: | The Crystal Structure of l-Sorbose Reductase from Gluconobacter frateurii Complexed with NADPH and l-Sorbose
J.Mol.Biol., 407, 2011
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3APO
 | | Crystal structure of full-length ERdj5 | | Descriptor: | DnaJ homolog subfamily C member 10 | | Authors: | Inaba, K, Suzuki, M, Nagata, K. | | Deposit date: | 2010-10-20 | | Release date: | 2011-04-20 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis of an ERAD pathway mediated by the ER-resident protein disulfide reductase ERdj5.
Mol.Cell, 41, 2011
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3APS
 | | Crystal structure of Trx4 domain of ERdj5 | | Descriptor: | DnaJ homolog subfamily C member 10, GLYCEROL, SULFATE ION | | Authors: | Inaba, K, Suzuki, M, Nagata, K. | | Deposit date: | 2010-10-20 | | Release date: | 2011-04-20 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural basis of an ERAD pathway mediated by the ER-resident protein disulfide reductase ERdj5.
Mol.Cell, 41, 2011
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1MKN
 | | N-TERMINAL HALF OF MIDKINE | | Descriptor: | PROTEIN (MIDKINE) | | Authors: | Iwasaki, W, Nagata, K, Hatanaka, H, Ogura, K, Inui, T, Kimura, T, Muramatsu, T, Yoshida, K, Tasumi, M, Inagaki, F. | | Deposit date: | 1999-03-16 | | Release date: | 1999-03-23 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of midkine, a new heparin-binding growth factor.
EMBO J., 16, 1997
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8J4H
 | | X-ray structure of a ferric ion-binding protein A (FbpA) from Vibrio metschnikovii in complex with Danshensu (DSS) | | Descriptor: | (2~{R})-3-[3,4-bis(oxidanyl)phenyl]-2-oxidanyl-propanoic acid, Ferric iron ABC transporter iron-binding protein | | Authors: | Lu, P, Jiang, J, Nagata, K. | | Deposit date: | 2023-04-20 | | Release date: | 2024-01-10 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | Molecular mechanism of Fe 3+ binding inhibition to Vibrio metschnikovii ferric ion-binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu.
Protein Sci., 33, 2024
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8J4J
 | | X-ray structure of a ferric ion-binding protein A (FbpA) from Vibrio metschnikovii in complex with ferric ion | | Descriptor: | CARBONATE ION, FE (III) ION, Ferric iron ABC transporter iron-binding protein | | Authors: | Lu, P, Jiang, J, Nagata, K. | | Deposit date: | 2023-04-20 | | Release date: | 2024-01-10 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Molecular mechanism of Fe 3+ binding inhibition to Vibrio metschnikovii ferric ion-binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu.
Protein Sci., 33, 2024
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1MKC
 | | C-TERMINAL DOMAIN OF MIDKINE | | Descriptor: | PROTEIN (MIDKINE) | | Authors: | Iwasaki, W, Nagata, K, Hatanaka, H, Ogura, K, Inui, T, Kimura, T, Muramatsu, T, Yoshida, K, Tasumi, M, Inagaki, F. | | Deposit date: | 1999-03-16 | | Release date: | 1999-03-23 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of midkine, a new heparin-binding growth factor.
EMBO J., 16, 1997
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3APQ
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3MGF
 | | Crystal Structure of Monomeric Kusabira-Orange (MKO), Orange-Emitting GFP-like Protein, at pH 7.5 | | Descriptor: | Fluorescent protein | | Authors: | Ebisawa, T, Yamamura, A, Ohtsuka, J, Kameda, Y, Hayakawa, K, Nagata, K, Tanokura, M. | | Deposit date: | 2010-04-06 | | Release date: | 2011-03-16 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure of Monomeric Kusabira-Orange (MKO), Orange-Emitting GFP-like Protein, at pH 7.5
To be Published
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2RQY
 | | Solution structure and dynamics of mouse ARMET | | Descriptor: | Putative uncharacterized protein | | Authors: | Hoseki, J, Sasakawa, H, Yamaguchi, Y, Maeda, M, Kubota, H, Kato, K, Nagata, K. | | Deposit date: | 2010-01-26 | | Release date: | 2010-04-21 | | Last modified: | 2022-03-16 | | Method: | SOLUTION NMR | | Cite: | Solution structure and dynamics of mouse ARMET.
Febs Lett., 584, 2010
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6AGZ
 | | Crystal structure of Old Yellow Enzyme from Pichia sp. AKU4542 | | Descriptor: | FLAVIN MONONUCLEOTIDE, Old Yellow Enzyme | | Authors: | Horita, S, Kataoka, M, Kitamura, N, Nakagawa, T, Miyakawa, T, Ohtsuka, J, Nagata, K, Shimizu, S, Tanokura, M. | | Deposit date: | 2018-08-15 | | Release date: | 2019-06-26 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds.
Biosci.Biotechnol.Biochem., 83, 2019
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2EB1
 | | Crystal Structure of the C-Terminal RNase III Domain of Human Dicer | | Descriptor: | Endoribonuclease Dicer, MAGNESIUM ION | | Authors: | Takeshita, D, Zenno, S, Lee, W.C, Nagata, K, Saigo, K, Tanokura, M. | | Deposit date: | 2007-02-05 | | Release date: | 2007-11-06 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Homodimeric Structure and Double-stranded RNA Cleavage Activity of the C-terminal RNase III Domain of Human Dicer
J.Mol.Biol., 374, 2007
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