4XD9
| Structure of Rpf2-Rrs1 complex involved in ribosome biogenesis | Descriptor: | Ribosome biogenesis protein (Rrs1), putative (AFU_orthologue AFUA_7G04430), Ribosome biogenesis protein, ... | Authors: | Asano, N, Kato, K, Yao, M. | Deposit date: | 2014-12-19 | Release date: | 2015-06-10 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis. Nucleic Acids Res., 43, 2015
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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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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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4XB3
| Structure of dextran glucosidase | Descriptor: | CALCIUM ION, Glucan 1,6-alpha-glucosidase, HEXAETHYLENE GLYCOL | Authors: | Kobayashi, M, Kato, K, Yao, M. | Deposit date: | 2014-12-16 | Release date: | 2015-08-26 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.093 Å) | Cite: | Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase Febs Lett., 589, 2015
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6KX1
| Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, Fab Fragment-SN-101-Heavy chain, Fab Fragment-SN-101-Light chain, ... | Authors: | Wakui, H, Tanaka, Y, Kato, K, Ose, T, Matsumoto, I, Min, Y, Tachibana, T, Nishimura, S.-I. | Deposit date: | 2019-09-09 | Release date: | 2020-07-29 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.773 Å) | Cite: | A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes Chem Sci, 11, 2020
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6L4T
| Structure of the peripheral FCPI from diatom | Descriptor: | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | Authors: | Nagao, R, Kato, K, Miyazaki, N, Akita, F, Shen, J.R. | Deposit date: | 2019-10-21 | Release date: | 2020-05-20 | Method: | ELECTRON MICROSCOPY (2.6 Å) | Cite: | Structure of photosystem I-light-harvesting supercomplex from a red-lineage diatom Nat Commun, 2020
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6L4U
| Structure of the PSI-FCPI supercomplex from diatom | Descriptor: | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | Authors: | Nagao, R, Kato, K, Miyazaki, N, Akita, F, Shen, J.R. | Deposit date: | 2019-10-21 | Release date: | 2020-05-20 | Method: | ELECTRON MICROSCOPY (2.4 Å) | Cite: | Structure of photosystem I-light-harvesting supercomplex from a red-lineage diatom Nat Commun, 2020
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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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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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3J7T
| Calcium atpase structure with two bound calcium ions determined by electron crystallography of thin 3D crystals | Descriptor: | CALCIUM ION, SODIUM ION, Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | Authors: | Yonekura, K, Kato, K, Ogasawara, M, Tomita, M, Toyoshima, C. | Deposit date: | 2014-08-07 | Release date: | 2015-02-18 | Last modified: | 2016-09-28 | Method: | ELECTRON CRYSTALLOGRAPHY (3.4 Å) | Cite: | Electron crystallography of ultrathin 3D protein crystals: atomic model with charges Proc.Natl.Acad.Sci.USA, 112, 2015
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4DBG
| Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative | Descriptor: | RING finger protein 31, RanBP-type and C3HC4-type zinc finger-containing protein 1 | Authors: | Yagi, H, Hiromoto, T, Mizushima, T, Kurimoto, E, Kato, K. | Deposit date: | 2012-01-15 | Release date: | 2012-04-04 | Last modified: | 2012-05-16 | Method: | X-RAY DIFFRACTION (2.71 Å) | Cite: | A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex Embo Rep., 13, 2012
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5JQP
| Crystal structure of ER glucosidase II heterodimeric complex consisting of catalytic subunit and the binding domain of regulatory subunit | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Alpha glucosidase-like protein, CALCIUM ION, ... | Authors: | Satoh, T, Toshimori, T, Noda, M, Uchiyama, S, Kato, K. | Deposit date: | 2016-05-05 | Release date: | 2016-09-14 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Interaction mode between catalytic and regulatory subunits in glucosidase II involved in ER glycoprotein quality control. Protein Sci., 25, 2016
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8F2R
| Human CCC complex | Descriptor: | COMM domain-containing protein 1, COMM domain-containing protein 10, COMM domain-containing protein 2, ... | Authors: | Healy, M.D, McNally, K.E, Butkovic, R, Chilton, M, Kato, K, Sacharz, J, McConville, C, Moody, E.R.R, Shaw, S, Planelles-Herrero, V.J, Kadapalakere, S.Y, Ross, J, Borucu, U, Palmer, C.S, Chen, K, Croll, T.I, Hall, R.J, Caruana, N.J, Ghai, R, Nguyen, T.H.D, Heesom, K.J, Saitoh, S, Berger, I, Berger-Schaffitzel, C, Williams, T.A, Stroud, D.A, Derivery, E, Collins, B.M, Cullen, P.J. | Deposit date: | 2022-11-08 | Release date: | 2023-05-24 | Method: | ELECTRON MICROSCOPY (3.12 Å) | Cite: | Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Cell, 186, 2023
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8F2U
| Human CCC complex | Descriptor: | COMM domain-containing protein 1, COMM domain-containing protein 10, COMM domain-containing protein 2, ... | Authors: | Healy, M.D, McNally, K.E, Butkovic, R, Chilton, M, Kato, K, Sacharz, J, McConville, C, Moody, E.R.R, Shaw, S, Planelles-Herrero, V.J, Kadapalakere, S.Y, Ross, J, Borucu, U, Palmer, C.S, Chen, K, Croll, T.I, Hall, R.J, Caruana, N.J, Ghai, R, Nguyen, T.H.D, Heesom, K.J, Saitoh, S, Berger, I, Berger-Schaffitzel, C, Williams, T.A, Stroud, D.A, Derivery, E, Collins, B.M, Cullen, P.J. | Deposit date: | 2022-11-08 | Release date: | 2023-05-24 | Method: | ELECTRON MICROSCOPY (3.53 Å) | Cite: | Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Cell, 186, 2023
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4WJ3
| Crystal structure of the asparagine transamidosome from Pseudomonas aeruginosa | Descriptor: | 76mer-tRNA, Aspartate--tRNA(Asp/Asn) ligase, Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, ... | Authors: | Suzuki, T, Nakamura, A, Kato, K, Tanaka, I, Yao, M. | Deposit date: | 2014-09-29 | Release date: | 2014-12-31 | Last modified: | 2020-02-05 | Method: | X-RAY DIFFRACTION (3.705 Å) | Cite: | Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis Proc.Natl.Acad.Sci.USA, 112, 2015
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4WJ4
| Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid | Descriptor: | 76mer-tRNA, ASPARTIC ACID, Aspartate--tRNA(Asp/Asn) ligase | Authors: | Suzuki, T, Nakamura, A, Kato, K, Tanaka, I, Yao, M. | Deposit date: | 2014-09-29 | Release date: | 2014-12-31 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (3.294 Å) | Cite: | Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis Proc.Natl.Acad.Sci.USA, 112, 2015
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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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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: | 2023-11-22 | 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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5X6B
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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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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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1WR6
| Crystal structure of GGA3 GAT domain in complex with ubiquitin | Descriptor: | ADP-ribosylation factor binding protein GGA3, ubiquitin | Authors: | Kawasaki, M, Shiba, T, Shiba, Y, Yamaguchi, Y, Matsugaki, N, Igarashi, N, Suzuki, M, Kato, R, Kato, K, Nakayama, K, Wakatsuki, S. | Deposit date: | 2004-10-12 | Release date: | 2005-06-28 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Molecular mechanism of ubiquitin recognition by GGA3 GAT domain. Genes Cells, 10, 2005
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1WRD
| Crystal structure of Tom1 GAT domain in complex with ubiquitin | Descriptor: | Target of Myb protein 1, Ubiquitin | Authors: | Akutsu, M, Kawasaki, M, Katoh, Y, Shiba, T, Yamaguchi, Y, Kato, R, Kato, K, Nakayama, K, Wakatsuki, S. | Deposit date: | 2004-10-14 | Release date: | 2005-10-11 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain. Febs Lett., 579, 2005
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5WTQ
| Crystal structure of human proteasome-assembling chaperone PAC4 | Descriptor: | CHLORIDE ION, NICKEL (II) ION, Proteasome assembly chaperone 4 | Authors: | Kurimoto, E, Satoh, T, Ito, Y, Ishihara, E, Tanaka, K, Kato, K. | Deposit date: | 2016-12-13 | Release date: | 2017-03-22 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation Protein Sci., 26, 2017
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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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