8IC9
 
 | | Lys48-linked K48C-diubiquitin | | Descriptor: | Polyubiquitin-B, Ubiquitin | | Authors: | Hiranyakorn, M, Yagi-Utsumi, M, Yanaka, S, Ohtsuka, N, Momiyama, N, Satoh, T, Kato, K. | | Deposit date: | 2023-02-11 | | Release date: | 2023-04-26 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.25 Å) | | Cite: | Mutational and Environmental Effects on the Dynamic Conformational Distributions of Lys48-Linked Ubiquitin Chains.
Int J Mol Sci, 24, 2023
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5Y7O
 | | Crystal structure of folding sensor region of UGGT from Thermomyces dupontii | | Descriptor: | UGGT | | Authors: | Satoh, T, Song, C, Zhu, T, Toshimori, T, Murata, K, Hayashi, Y, Kamikubo, H, Uchihashi, T, Kato, K. | | Deposit date: | 2017-08-17 | | Release date: | 2017-09-27 | | Last modified: | 2017-11-01 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT.
Sci Rep, 7, 2017
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8KB7
 | | Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2, ... | | Authors: | Satoh, T, Umezawa, F, Yagi, H, Kato, K. | | Deposit date: | 2023-08-04 | | Release date: | 2024-08-07 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2)
To Be Published
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5Y7F
 | | Crystal structure of catalytic domain of UGGT (UDP-bound form) from Thermomyces dupontii | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CALCIUM ION, UGGT, ... | | Authors: | Satoh, T, Song, C, Zhu, T, Toshimori, T, Murata, K, Hayashi, Y, Kamikubo, H, Uchihashi, T, Kato, K. | | Deposit date: | 2017-08-17 | | Release date: | 2017-09-27 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT.
Sci Rep, 7, 2017
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1X60
 | | Solution structure of the peptidoglycan binding domain of B. subtilis cell wall lytic enzyme CwlC | | Descriptor: | Sporulation-specific N-acetylmuramoyl-L-alanine amidase | | Authors: | Mishima, M, Shida, T, Yabuki, K, Kato, K, Sekiguchi, J, Kojima, C. | | Deposit date: | 2005-05-17 | | Release date: | 2005-08-09 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of the Peptidoglycan Binding Domain of Bacillus subtilis Cell Wall Lytic Enzyme CwlC: Characterization of the Sporulation-Related Repeats by NMR(,)
Biochemistry, 44, 2005
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5DKY
 | | Crystal structure of glucosidase II alpha subunit (DNJ-bound from) | | Descriptor: | 1-DEOXYNOJIRIMYCIN, Alpha glucosidase-like protein | | Authors: | Satoh, T, Toshimori, T, Yan, G, Yamaguchi, T, Kato, K. | | Deposit date: | 2015-09-04 | | Release date: | 2016-01-27 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control.
Sci Rep, 6, 2016
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5GIJ
 | | Crystal structure of TDR-TDIF complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Leucine-rich repeat receptor-like protein kinase TDR, ... | | Authors: | Morita, J, Kato, K, Ishitani, R, Nishimasu, H, Nureki, O. | | Deposit date: | 2016-06-23 | | Release date: | 2016-08-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide
Nat Commun, 7, 2016
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5H7K
 | | Crystal structure of Elongation factor 2 GDP-form | | Descriptor: | Elongation factor 2, GUANOSINE-5'-DIPHOSPHATE | | Authors: | Tanzawa, T, Kato, K, Uchiumi, T, Yao, M. | | Deposit date: | 2016-11-18 | | Release date: | 2018-02-21 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.599 Å) | | Cite: | The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion
Nucleic Acids Res., 46, 2018
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5H7L
 | | Complex of Elongation factor 2-50S ribosomal protein L12 | | Descriptor: | 50S ribosomal protein L12, Elongation factor 2, PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER | | Authors: | Tanzawa, T, Kato, K, Uchiumi, T, Yao, M. | | Deposit date: | 2016-11-18 | | Release date: | 2018-02-21 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion
Nucleic Acids Res., 46, 2018
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6KRU
 | | Crystal structure of mouse IgG2b Fc | | Descriptor: | Ig gamma-2B chain C region, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | | Authors: | Taniguchi, Y, Satoh, T, Yagi, H, Kato, K. | | Deposit date: | 2019-08-22 | | Release date: | 2020-01-22 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q.
Int J Mol Sci, 21, 2019
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6KRV
 | | Crystal structure of mouse IgG2b Fc complexed with B domain of Protein A | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Ig gamma-2B chain C region, ... | | Authors: | Taniguchi, Y, Satoh, T, Yagi, H, Kato, K. | | Deposit date: | 2019-08-22 | | Release date: | 2020-01-22 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q.
Int J Mol Sci, 21, 2019
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8IDS
 | | Crystal structure of Bacillus sp. AHU2216 GH13_31 Alpha-glucosidase E256Q/N258P in complex with maltotriose | | Descriptor: | Alpha-glucosidase, CALCIUM ION, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | | Authors: | Auiewiriyanukul, W, Saburi, W, Yu, J, Kato, K, Yao, M, Mori, H. | | Deposit date: | 2023-02-14 | | Release date: | 2023-05-03 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Alteration of Substrate Specificity and Transglucosylation Activity of GH13_31 alpha-Glucosidase from Bacillus sp. AHU2216 through Site-Directed Mutagenesis of Asn258 on beta → alpha Loop 5.
Molecules, 28, 2023
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8IBK
 | | Crystal structure of Bacillus sp. AHU2216 GH13_31 Alpha-glucosidase E256Q/N258G in complex with maltotriose | | Descriptor: | Alpha-glucosidase, CALCIUM ION, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | | Authors: | Auiewiriyanukul, W, Saburi, W, Yu, J, Kato, K, Yao, M, Mori, H. | | Deposit date: | 2023-02-10 | | Release date: | 2023-05-03 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.69 Å) | | Cite: | Alteration of Substrate Specificity and Transglucosylation Activity of GH13_31 alpha-Glucosidase from Bacillus sp. AHU2216 through Site-Directed Mutagenesis of Asn258 on beta → alpha Loop 5.
Molecules, 28, 2023
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5XJE
 | | Crystal structure of fucosylated IgG1 Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa | | Descriptor: | CHLORIDE ION, Immunoglobulin gamma-1 heavy chain, Low affinity immunoglobulin gamma Fc region receptor III-A, ... | | Authors: | Sakae, Y, Satoh, T, Yagi, H, Yanaka, S, Yamaguchi, T, Isoda, Y, Iida, S, Okamoto, Y, Kato, K. | | Deposit date: | 2017-05-01 | | Release date: | 2017-11-01 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fc gamma receptor IIIa.
Sci Rep, 7, 2017
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5XJF
 | | Crystal structure of fucosylated IgG Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ... | | Authors: | Sakae, Y, Satoh, T, Yagi, H, Yanaka, S, Yamaguchi, T, Isoda, Y, Iida, S, Okamoto, Y, Kato, K. | | Deposit date: | 2017-05-01 | | Release date: | 2017-11-01 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fc gamma receptor IIIa.
Sci Rep, 7, 2017
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5Y9N
 | | Crystal structure of Pyrococcus furiosus PbaA (monoclinic form), an archaeal homolog of proteasome-assembly chaperone | | Descriptor: | CHLORIDE ION, PbaA | | Authors: | Yagi-Utsumi, M, Sikdar, A, Kozai, T, Inoue, R, Sugiyama, M, Uchihashi, T, Satoh, T, Kato, K. | | Deposit date: | 2017-08-26 | | Release date: | 2018-01-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Conversion of functionally undefined homopentameric protein PbaA into a proteasome activator by mutational modification of its C-terminal segment conformation
Protein Eng. Des. Sel., 31, 2018
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5X6C
 | | Crystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, O-phosphoserine--tRNA(Cys) ligase, SULFATE ION, ... | | Authors: | Chen, M, Kato, K, Yao, M. | | Deposit date: | 2017-02-21 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.101 Å) | | Cite: | Structural basis for tRNA-dependent cysteine biosynthesis
Nat Commun, 8, 2017
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5X6B
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1WZ1
 | | Crystal structure of the Fv fragment complexed with dansyl-lysine | | Descriptor: | Ig heavy chain, Ig light chain, N~6~-{[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}-L-LYSINE | | Authors: | Nakasako, M, Oka, T, Mashumo, M, Takahashi, H, Shimada, I, Yamaguchi, Y, Kato, K, Arata, Y. | | Deposit date: | 2005-02-21 | | Release date: | 2006-01-31 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten
J.Mol.Biol., 351, 2005
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7Y8Q
 | | Amyloid-beta assemblage on GM1-containing membranes | | Descriptor: | Amyloid-beta protein 40 | | Authors: | Yagi-Utsumi, M, Itoh, S.G, Okumura, H, Yanagisawa, K, Kato, K, Nishimura, K. | | Deposit date: | 2022-06-24 | | Release date: | 2023-07-05 | | Last modified: | 2024-05-15 | | Method: | SOLID-STATE NMR | | Cite: | The Double-Layered Structure of Amyloid-beta Assemblage on GM1-Containing Membranes Catalytically Promotes Fibrillization.
Acs Chem Neurosci, 14, 2023
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7EDA
 | | Structure of monomeric photosystem II | | Descriptor: | (3R)-beta,beta-caroten-3-ol, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | | Authors: | Yu, H, Hamaguchi, T, Nakajima, Y, Kato, K, kawakami, K, Akita, F, Yonekura, K, Shen, J.R. | | Deposit date: | 2021-03-15 | | Release date: | 2021-07-07 | | Last modified: | 2021-08-04 | | Method: | ELECTRON MICROSCOPY (2.78 Å) | | Cite: | Cryo-EM structure of monomeric photosystem II at 2.78 angstrom resolution reveals factors important for the formation of dimer.
Biochim Biophys Acta Bioenerg, 1862, 2021
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3AVE
 | | Crystal Structure of the Fucosylated Fc Fragment from Human Immunoglobulin G1 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Ig gamma-1 chain C region, ZINC ION | | Authors: | Matsumiya, S, Yamaguchi, Y, Saito, J, Nagano, M, Sasakawa, H, Otaki, S, Satoh, M, Shitara, K, Kato, K. | | Deposit date: | 2011-03-04 | | Release date: | 2011-04-06 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Corrigendum to "Structural Comparison of Fucosylated and Nonfucosylated Fc Fragments of Human Immunoglobulin G1" [J. Mol. Biol. 386/3 (2007) 767-779]
J.Mol.Biol., 408, 2011
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7Y3F
 | | Structure of the Anabaena PSI-monomer-IsiA supercomplex | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Nagao, R, Kato, K, Hamaguchi, T, Kawakami, K, Yonekura, K, Shen, J.R. | | Deposit date: | 2022-06-10 | | Release date: | 2023-03-01 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (2.62 Å) | | Cite: | Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120.
Nat Commun, 14, 2023
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7DBT
 | | Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase (AMNP) from Ramazzottius varieornatus (Mn2+-bound form) | | Descriptor: | AMNP/g12777, MANGANESE (II) ION | | Authors: | Yoshida, Y, Satoh, T, Ota, C, Tanaka, S, Horikawa, D.D, Tomita, M, Kato, K, Arakawa, K. | | Deposit date: | 2020-10-21 | | Release date: | 2021-10-06 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades.
Bmc Genomics, 23, 2022
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7DBU
 | | Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase (AMNP) from Ramazzottius varieornatus (Zn2+-bound form) | | Descriptor: | AMNP/g12777, ZINC ION | | Authors: | Yoshida, Y, Satoh, T, Ota, C, Tanaka, S, Horikawa, D.D, Tomita, M, Kato, K, Arakawa, K. | | Deposit date: | 2020-10-21 | | Release date: | 2021-10-06 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades.
Bmc Genomics, 23, 2022
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