1V3Y
 
 | | The crystal structure of peptide deformylase from Thermus thermophilus HB8 | | Descriptor: | Peptide deformylase | | Authors: | Kamo, M, Kudo, N, Lee, W.C, Ito, K, Motoshim, H, Tanokura, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-11-07 | | Release date: | 2004-12-28 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.81 Å) | | Cite: | The crystal structure of peptide deformylase from Thermus thermophilus HB8
to be published
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2HI7
 | | Crystal structure of DsbA-DsbB-ubiquinone complex | | Descriptor: | Disulfide bond formation protein B, Thiol:disulfide interchange protein dsbA, UBIQUINONE-1, ... | | Authors: | Inaba, K, Murakami, S, Suzuki, M, Nakagawa, A, Yamashita, E, Okada, K, Ito, K. | | Deposit date: | 2006-06-29 | | Release date: | 2006-12-05 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | Crystal Structure of the DsbB-DsbA Complex Reveals a Mechanism of Disulfide Bond Generation
Cell(Cambridge,Mass.), 127, 2006
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3J9W
 | | Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex | | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein bS16, ... | | Authors: | Sohmen, D, Chiba, S, Shimokawa-Chiba, N, Innis, C.A, Berninghausen, O, Beckmann, R, Ito, K, Wilson, D.N. | | Deposit date: | 2015-03-16 | | Release date: | 2015-04-29 | | Last modified: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
Nat Commun, 6, 2015
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5B3S
 | | Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K) | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Shimada, A, Shinzawa-Ito, K, Yoshikawa, S, Tsukihara, T. | | Deposit date: | 2016-03-11 | | Release date: | 2017-03-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.68 Å) | | Cite: | Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)
To Be Published
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2IPC
 | | Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer | | Descriptor: | Preprotein translocase SecA subunit | | Authors: | Vassylyev, D.G, Mori, H, Vassylyeva, M.N, Tsukazaki, T, Kimura, Y, Tahirov, T.H, Ito, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-10-12 | | Release date: | 2006-11-28 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal Structure of the Translocation ATPase SecA from Thermus thermophilus Reveals a Parallel, Head-to-Head Dimer.
J.Mol.Biol., 364, 2006
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1IRE
 | | Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila | | Descriptor: | COBALT (II) ION, Nitrile Hydratase | | Authors: | Miyanaga, A, Fushinobu, S, Ito, K, Wakagi, T. | | Deposit date: | 2001-10-01 | | Release date: | 2002-10-01 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of cobalt-containing nitrile hydratase.
Biochem.Biophys.Res.Commun., 288, 2001
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5AWH
 | | Rhodobacter sphaeroides Argonaute in complex with guide RNA/target DNA heteroduplex | | Descriptor: | DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3'), MAGNESIUM ION, RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'), ... | | Authors: | Miyoshi, T, Ito, K, Murakami, R, Uchiumi, T. | | Deposit date: | 2015-07-03 | | Release date: | 2016-07-06 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute.
Nat Commun, 7, 2016
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5XRZ
 | | Structure of a ssDNA bound to the inner DNA binding site of RAD52 | | Descriptor: | DNA repair protein RAD52 homolog, POTASSIUM ION, ssDNA (40-MER) | | Authors: | Saotome, M, Saito, K, Yasuda, T, Sugiyama, S, Kurumizaka, H, Kagawa, W. | | Deposit date: | 2017-06-11 | | Release date: | 2018-04-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.6 Å) | | Cite: | Structural Basis of Homology-Directed DNA Repair Mediated by RAD52
iScience, 3, 2018
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1J2T
 | | Creatininase Mn | | Descriptor: | MANGANESE (II) ION, SULFATE ION, ZINC ION, ... | | Authors: | Yoshimoto, T, Tanaka, N, Kanada, N, Inoue, T, Nakajima, Y, Haratake, M, Nakamura, K.T, Xu, Y, Ito, K. | | Deposit date: | 2003-01-11 | | Release date: | 2004-01-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism
J.Mol.Biol., 337, 2004
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1J2U
 | | Creatininase Zn | | Descriptor: | SULFATE ION, ZINC ION, creatinine amidohydrolase | | Authors: | Yoshimoto, T, Tanaka, N, Kanada, N, Inoue, T, Nakajima, Y, Haratake, M, Nakamura, K.T, Xu, Y, Ito, K. | | Deposit date: | 2003-01-11 | | Release date: | 2004-01-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism
J.Mol.Biol., 337, 2004
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7DHW
 | | Crystal structure of myosin-XI motor domain in complex with ADP-ALF4 | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... | | Authors: | Suzuki, K, Haraguchi, T, Tamanaha, M, Yoshimura, K, Imi, T, Tominaga, M, Sakayama, H, Nishiyama, T, Ito, K, Murata, T. | | Deposit date: | 2020-11-17 | | Release date: | 2021-05-19 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.84 Å) | | Cite: | Discovery of ultrafast myosin, its amino acid sequence, and structural features.
Proc.Natl.Acad.Sci.USA, 119, 2022
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1KOL
 | | Crystal structure of formaldehyde dehydrogenase | | Descriptor: | NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SULFATE ION, ZINC ION, ... | | Authors: | Tanaka, N, Kusakabe, Y, Ito, K, Yoshimoto, T, Nakamura, K.T. | | Deposit date: | 2001-12-21 | | Release date: | 2002-12-11 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal Structure of Formaldehyde Dehydrogenase from Pseudomonas putida: the Structural Origin of the Tightly Bound Cofactor in Nicotinoprotein Dehydrogenases
J.mol.biol., 324, 2002
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6JI2
 | | Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex | | Descriptor: | Archaeal ribosomal stalk protein aP1, Elongation factor 1-alpha, GUANOSINE-5'-TRIPHOSPHATE, ... | | Authors: | Maruyama, K, Imai, H, Kawamura, M, Ishino, S, Ishino, Y, Ito, K, Uchiumi, T. | | Deposit date: | 2019-02-20 | | Release date: | 2019-11-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations.
Sci Rep, 9, 2019
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7CSL
 | | Crystal structure of the archaeal EF1A-EF1B complex | | Descriptor: | Elongation factor 1-alpha, Elongation factor 1-beta | | Authors: | Suzuki, T, Ito, K, Miyoshi, T, Murakami, R, Uchiumi, T. | | Deposit date: | 2020-08-15 | | Release date: | 2021-06-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural insights into the Switching Off of the Interaction between the Archaeal Ribosomal Stalk and aEF1A by Nucleotide Exchange Factor aEF1B.
J.Mol.Biol., 433, 2021
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6LCQ
 | | Crystal structure of rice defensin OsAFP1 | | Descriptor: | Defensin-like protein CAL1, PHOSPHATE ION | | Authors: | Ochiai, A, Ogawa, K, Fukuda, M, Suzuki, M, Ito, K, Tanaka, T, Sagehashi, Y, Taniguchi, M. | | Deposit date: | 2019-11-19 | | Release date: | 2020-04-01 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.62 Å) | | Cite: | Crystal structure of rice defensin OsAFP1 and molecular insight into lipid-binding.
J.Biosci.Bioeng., 130, 2020
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3VMF
 | | Archaeal protein | | Descriptor: | Elongation factor 1-alpha, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Kobayashi, K, Saito, K, Ishitani, R, Ito, K, Nureki, O. | | Deposit date: | 2011-12-12 | | Release date: | 2012-07-25 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for translation termination by archaeal RF1 and GTP-bound EF1alpha complex
Nucleic Acids Res., 40, 2012
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6J3L
 | | Solution structure of the N-terminal extended protuberant domain of eukaryotic ribosomal stalk protein P0 | | Descriptor: | 60S acidic ribosomal protein P0 | | Authors: | Choi, K.H.A, Lee, K.M, Yang, L, Wing-Heng Yu, C, Banfield, D.K, Ito, K, Uchiumi, T, Wong, K.B. | | Deposit date: | 2019-01-04 | | Release date: | 2019-09-04 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Structural and Mutagenesis Studies Evince the Role of the Extended Protuberant Domain of Ribosomal Protein uL10 in Protein Translation.
Biochemistry, 58, 2019
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5YT0
 | | Crystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal translation initiation factor aIF5B | | Descriptor: | Archaeal ribosomal stalk protein aP1, GUANOSINE-5'-DIPHOSPHATE, Probable translation initiation factor IF-2 | | Authors: | Murakami, R, Singh, C.R, Morris, J, Tang, L, Harmon, I, Miyoshi, T, Ito, K, Asano, K, Uchiumi, T. | | Deposit date: | 2017-11-16 | | Release date: | 2018-06-27 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | The Interaction between the Ribosomal Stalk Proteins and Translation Initiation Factor 5B Promotes Translation Initiation
Mol. Cell. Biol., 38, 2018
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2CZK
 | | Crystal structure of human myo-inositol monophosphatase 2 (IMPA2) (trigonal form) | | Descriptor: | Inositol monophosphatase 2 | | Authors: | Arai, R, Ito, K, Hanawa-Suetsugu, K, Ohnishi, T, Ohba, H, Yoshikawa, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-13 | | Release date: | 2006-07-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Crystal structure of human myo-inositol monophosphatase 2, the product of the putative susceptibility gene for bipolar disorder, schizophrenia, and febrile seizures
Proteins, 67, 2007
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2DDK
 | | Crystal structure of human myo-inositol monophosphatase 2 (IMPA2) (orthorhombic form) | | Descriptor: | Inositol monophosphatase 2 | | Authors: | Arai, R, Ito, K, Kamo-Uchikubo, T, Bessho, Y, Ohba, H, Ohnishi, T, Yoshikawa, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-01-30 | | Release date: | 2007-02-06 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of human myo-inositol monophosphatase 2, the product of the putative susceptibility gene for bipolar disorder, schizophrenia, and febrile seizures
Proteins, 67, 2007
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2ZTU
 | | T190A mutant of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ | | Descriptor: | D(-)-3-hydroxybutyrate dehydrogenase, MAGNESIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | | Authors: | Nakashima, K, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2008-10-09 | | Release date: | 2009-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor.
J.Biochem., 145, 2009
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2ZTM
 | | T190S mutant of D-3-hydroxybutyrate dehydrogenase | | Descriptor: | (3S)-3-HYDROXYBUTANOIC ACID, D(-)-3-hydroxybutyrate dehydrogenase, MAGNESIUM ION, ... | | Authors: | Nakashima, K, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2008-10-07 | | Release date: | 2009-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor.
J.Biochem., 145, 2009
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3A6J
 | | E122Q mutant creatininase complexed with creatine | | Descriptor: | Creatinine amidohydrolase, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, SULFATE ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-09-02 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
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3A6D
 | | Creatininase complexed with 1-methylguanidine | | Descriptor: | 1-METHYLGUANIDINE, Creatinine amidohydrolase, MANGANESE (II) ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-08-31 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
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3A6F
 | | W174F mutant creatininase, Type II | | Descriptor: | CACODYLATE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-08-31 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
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