7YVS
 
 | | Complex structure of Clostridioides difficile binary toxin unfolded CDTa-bound CDTb-pore (short). | | Descriptor: | ADP-ribosylating binary toxin binding subunit CdtB, ADP-ribosylating binary toxin enzymatic subunit CdtA, CALCIUM ION | | Authors: | Yamada, T, Kawamoto, A, Yoshida, T, Sato, Y, Kato, T, Tsuge, H. | | Deposit date: | 2022-08-19 | | Release date: | 2022-10-26 | | Last modified: | 2022-11-02 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile.
Nat Commun, 13, 2022
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2Z6E
 | | Crystal Structure of Human DAAM1 FH2 | | Descriptor: | Disheveled-associated activator of morphogenesis 1 | | Authors: | Yamashita, M, Higashi, T, Sato, Y, Shirakawa, R, Kita, T, Horiuchi, H, Fukai, S, Nureki, O. | | Deposit date: | 2007-07-31 | | Release date: | 2008-05-27 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of human DAAM1 formin homology 2 domain
Genes Cells, 12, 2007
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6IXF
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6IXE
 | | Crystal structure of SeMet apo SH3BP5 (I41) | | Descriptor: | SH3 domain-binding protein 5, SUCCINIC ACID | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | | Deposit date: | 2018-12-10 | | Release date: | 2019-03-20 | | Last modified: | 2019-03-27 | | Method: | X-RAY DIFFRACTION (3.35 Å) | | Cite: | Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5.
Life Sci Alliance, 2, 2019
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6IXV
 | | Crystal structure of SH3BP5-Rab11a | | Descriptor: | PHOSPHATE ION, Ras-related protein Rab-11A, SH3 domain-binding protein 5 | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | | Deposit date: | 2018-12-12 | | Release date: | 2019-03-20 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (3.8 Å) | | Cite: | Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5.
Life Sci Alliance, 2, 2019
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6IXG
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5YOY
 | | Crystal structure of the human tumor necrosis factor in complex with golimumab Fv | | Descriptor: | Golimumab heavy chain variable region, Golimumab light chain variable region, Tumor necrosis factor | | Authors: | Ono, M, Horita, S, Sato, Y, Nomura, Y, Iwata, S, Nomura, N. | | Deposit date: | 2017-10-31 | | Release date: | 2018-05-09 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.727 Å) | | Cite: | Structural basis for tumor necrosis factor blockade with the therapeutic antibody golimumab
Protein Sci., 27, 2018
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5XIS
 | | Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I | | Descriptor: | E3 ubiquitin-protein ligase RNF168, MAGNESIUM ION, Ubiquitin-40S ribosomal protein S27a, ... | | Authors: | Takahashi, T.S, Sato, Y, Fukai, S. | | Deposit date: | 2017-04-27 | | Release date: | 2018-03-07 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.
Nat Commun, 9, 2018
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5XIU
 | | Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin | | Descriptor: | 1,2-ETHANEDIOL, E3 ubiquitin-protein ligase RNF168, Ubiquitin-40S ribosomal protein S27a | | Authors: | Takahashi, T.S, Sato, Y, Fukai, S. | | Deposit date: | 2017-04-27 | | Release date: | 2018-03-07 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.
Nat Commun, 9, 2018
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5YDK
 | | Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form | | Descriptor: | E3 ubiquitin-protein ligase RNF168, GLYCEROL, Ubiquitin-40S ribosomal protein S27a | | Authors: | Takahashi, T.S, Sato, Y, Fukai, S. | | Deposit date: | 2017-09-13 | | Release date: | 2018-03-07 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.505 Å) | | Cite: | Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168
Nat Commun, 9, 2018
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5YJ9
 | | Crystal structure of Tribolium castaneum PINK1 kinase domain in complex with AMP-PNP | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, Serine/threonine-protein kinase PINK1, ... | | Authors: | Okatsu, K, Sato, Y, Fukai, S. | | Deposit date: | 2017-10-09 | | Release date: | 2018-07-25 | | Method: | X-RAY DIFFRACTION (2.53 Å) | | Cite: | Structural insights into ubiquitin phosphorylation by PINK1.
Sci Rep, 8, 2018
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5ZNM
 | | Colicin D Central Domain and C-terminal tRNase domain | | Descriptor: | Colicin-D, GLYCEROL, SULFATE ION | | 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: | 2024-03-27 | | 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
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3A1K
 | | Crystal structure of Rhodococcus sp. N771 Amidase | | Descriptor: | Amidase | | Authors: | Ohtaki, A, Noguchi, K, Sato, Y, Murata, K, Odaka, M, Yohda, M. | | Deposit date: | 2009-04-09 | | Release date: | 2009-11-03 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.17 Å) | | Cite: | Structure and characterization of amidase from Rhodococcus sp. N-771: Insight into the molecular mechanism of substrate recognition
Biochim.Biophys.Acta, 1804, 2010
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3A36
 | | Structural insight into the membrane insertion of tail-anchored proteins by Get3 | | Descriptor: | ATPase GET3, ZINC ION | | Authors: | Yamagata, A, Mimura, H, Sato, Y, Yamashita, M, Yoshikawa, A, Fukai, S. | | Deposit date: | 2009-06-10 | | Release date: | 2010-01-12 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural insight into the membrane insertion of tail-anchored proteins by Get3
Genes Cells, 15, 2010
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3A1I
 | | Crystal structure of Rhodococcus sp. N-771 Amidase complexed with Benzamide | | Descriptor: | Amidase, BENZAMIDE | | Authors: | Ohtaki, A, Noguchi, K, Sato, Y, Murata, K, Odaka, M, Yohda, M. | | Deposit date: | 2009-04-03 | | Release date: | 2009-10-27 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.32 Å) | | Cite: | Structure and Characterization of Amidase from Rhodococcus sp. N-771: Insight into the Molecular Mechanism of Substrate Recognition
Biochim.Biophys.Acta, 2009
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3A37
 | | Structural insight into the membrane insertion of tail-anchored proteins by Get3 | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ATPase GET3, ZINC ION | | Authors: | Yamagata, A, Mimura, H, Sato, Y, Yamashita, M, Yoshikawa, A, Fukai, S. | | Deposit date: | 2009-06-10 | | Release date: | 2010-01-12 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structural insight into the membrane insertion of tail-anchored proteins by Get3
Genes Cells, 15, 2010
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3D24
 | | Crystal structure of ligand-binding domain of estrogen-related receptor alpha (ERRalpha) in complex with the peroxisome proliferators-activated receptor coactivator-1alpha box3 peptide (PGC-1alpha) | | Descriptor: | Peroxisome proliferator-activated receptor gamma coactivator 1-alpha, Steroid hormone receptor ERR1 | | Authors: | Moras, D, Greschik, H, Flaig, R, Sato, Y, Rochel, N, Structural Proteomics in Europe (SPINE) | | Deposit date: | 2008-05-07 | | Release date: | 2008-06-10 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.11 Å) | | Cite: | Communication between the ERR{alpha} Homodimer Interface and the PGC-1{alpha} Binding Surface via the Helix 8-9 Loop.
J.Biol.Chem., 283, 2008
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5XWU
 | | Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | | Deposit date: | 2017-06-30 | | Release date: | 2018-06-06 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (3.162 Å) | | Cite: | Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.
Nat Commun, 9, 2018
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5XWS
 | | Crystal structure of SALM5 LRR-Ig | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Leucine-rich repeat and fibronectin type-III domain-containing protein 5 | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | | Deposit date: | 2017-06-30 | | Release date: | 2018-06-06 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (3.084 Å) | | Cite: | Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.
Nat Commun, 9, 2018
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5XWT
 | | Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig | | 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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | | Deposit date: | 2017-06-30 | | Release date: | 2018-06-06 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (4.178 Å) | | Cite: | Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.
Nat Commun, 9, 2018
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6A6I
 | | Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin | | Descriptor: | CHLORIDE ION, Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant, ... | | Authors: | Takahashi, T.S, Sato, Y, Fukai, S. | | Deposit date: | 2018-06-28 | | Release date: | 2019-02-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis of ubiquitin recognition by the winged-helix domain of Cockayne syndrome group B protein.
Nucleic Acids Res., 47, 2019
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3VDR
 | | Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+) | | Descriptor: | (3R)-3-hydroxybutanoic acid, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, ACETOACETIC ACID, ... | | Authors: | Hoque, M.M, Shimizu, S, Juan, E.C.M, Sato, Y, Hossain, M.T, Yamamoto, T, Imamura, S, Amano, H, Suzuki, K, Sekiguchi, T, Tsunoda, M, Takenaka, A. | | Deposit date: | 2012-01-06 | | Release date: | 2012-02-08 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.
Acta Crystallogr.,Sect.F, 65, 2009
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5B3N
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8JH0
 | | Crystal structure of the light-driven sodium pump IaNaR | | Descriptor: | RETINAL, Xanthorhodopsin | | Authors: | Hashimoto, T, Kato, K, Tanaka, Y, Yao, M, Kikukawa, T. | | Deposit date: | 2023-05-22 | | Release date: | 2023-11-01 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2.79 Å) | | Cite: | Multistep conformational changes leading to the gate opening of light-driven sodium pump rhodopsin.
J.Biol.Chem., 299, 2023
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1WYD
 | | Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CHLORIDE ION, SULFATE ION, ... | | Authors: | Maeda, Y, Hossain, M.T, Ubukata, S, Suzuki, K, Sekiguchi, T, Takenaka, A. | | Deposit date: | 2005-02-12 | | Release date: | 2006-07-04 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons
ACTA CRYSTALLOGR.,SECT.D, 63, 2007
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