3WG7
 
 | | A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography | | 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: | Hirata, K, Shinzawa-Itoh, K, Yano, N, Takemura, S, Kato, K, Hatanaka, M, Muramoto, K, Kawahara, T, Tsukihara, T, Yamashita, E, Tono, K, Ueno, G, Hikima, T, Murakami, H, Inubushi, Y, Yabashi, M, Ishikawa, T, Yamamoto, M, Ogura, T, Sugimoto, H, Shen, J.R, Yoshikawa, S, Ago, H. | | Deposit date: | 2013-07-29 | | Release date: | 2014-04-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.
Nat.Methods, 11, 2014
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2Z5B
 | | Crystal Structure of a Novel Chaperone Complex for Yeast 20S Proteasome Assembly | | Descriptor: | Protein YPL144W, Uncharacterized protein YLR021W | | Authors: | Yashiroda, H, Mizushima, T, Okamoto, K, Kameyama, T, Hayashi, H, Kishimoto, T, Kasahara, M, Kurimoto, E, Sakata, E, Suzuki, A, Hirano, Y, Murata, S, Kato, K, Yamane, T, Tanaka, K. | | Deposit date: | 2007-07-03 | | Release date: | 2008-01-22 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.96 Å) | | Cite: | Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes
Nat.Struct.Mol.Biol., 15, 2008
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3A4U
 | | Crystal structure of MCFD2 in complex with carbohydrate recognition domain of ERGIC-53 | | Descriptor: | CALCIUM ION, GLYCEROL, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Nishio, M, Kamiya, Y, Mizushima, T, Wakatsuki, S, Sasakawa, H, Yamamoto, K, Uchiyama, S, Noda, M, McKay, A.R, Fukui, K, Hauri, H.P, Kato, K. | | Deposit date: | 2009-07-17 | | Release date: | 2010-01-05 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency.
Proc.Natl.Acad.Sci.USA, 107, 2010
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3VLE
 | | Crystal structure of yeast proteasome interacting protein | | Descriptor: | DNA mismatch repair protein HSM3 | | Authors: | Takagi, K, Kim, S, Kato, K, Tanaka, K, Saeki, Y, Mizushima, T. | | Deposit date: | 2011-12-01 | | Release date: | 2012-02-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.41 Å) | | Cite: | Structural basis for specific recognition of Rpt1, an ATPase subunit of the 26S proteasome, by a proteasome-dedicated chaperone Hsm3
J.Biol.Chem., 287, 2012
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3VLD
 | | Crystal structure of yeast proteasome interacting protein | | Descriptor: | DNA mismatch repair protein HSM3 | | Authors: | Takagi, K, Kim, S, Kato, K, Tanaka, K, Saeki, Y, Mizushima, T. | | Deposit date: | 2011-12-01 | | Release date: | 2012-02-22 | | Last modified: | 2012-04-18 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Structural basis for specific recognition of Rpt1, an ATPase subunit of the 26S proteasome, by a proteasome-dedicated chaperone Hsm3
J.Biol.Chem., 287, 2012
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3VLF
 | | Crystal structure of yeast proteasome interacting protein | | Descriptor: | 26S protease regulatory subunit 7 homolog, DNA mismatch repair protein HSM3 | | Authors: | Takagi, K, Kim, S, Kato, K, Tanaka, K, Saeki, Y, Mizushima, T. | | Deposit date: | 2011-12-01 | | Release date: | 2012-02-22 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (3.8 Å) | | Cite: | Structural basis for specific recognition of Rpt1, an ATPase subunit of the 26S proteasome, by a proteasome-dedicated chaperone Hsm3
J.Biol.Chem., 287, 2012
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3VR0
 | | Crystal structure of Pyrococcus furiosus PbaB, an archaeal proteasome activator | | Descriptor: | GOLD ION, Putative uncharacterized protein | | Authors: | Kumoi, K, Satoh, T, Hiromoto, T, Mizushima, T, Kamiya, Y, Noda, M, Uchiyama, S, Murata, K, Yagi, H, Kato, K. | | Deposit date: | 2012-04-02 | | Release date: | 2013-04-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | An archaeal homolog of proteasome assembly factor functions as a proteasome activator
Plos One, 8, 2013
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3VL1
 | | Crystal structure of yeast Rpn14 | | Descriptor: | 26S proteasome regulatory subunit RPN14 | | Authors: | Kim, S, Nishide, A, Saeki, Y, Takagi, K, Tanaka, K, Kato, K, Mizushima, T. | | Deposit date: | 2011-11-28 | | Release date: | 2012-05-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | New crystal structure of the proteasome-dedicated chaperone Rpn14 at 1.6 A resolution
Acta Crystallogr.,Sect.F, 68, 2012
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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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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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3A33
 | | UbcH5b~Ubiquitin Conjugate | | Descriptor: | GLYCEROL, Ubiquitin, Ubiquitin-conjugating enzyme E2 D2 | | Authors: | Sakata, E, Satoh, T, Yamamoto, S, Yamaguchi, Y, Yagi-Utsumi, M, Kurimoto, E, Wakatsuki, S, Kato, K. | | Deposit date: | 2009-06-08 | | Release date: | 2009-11-24 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal Structure of UbcH5b~Ubiquitin Intermediate: Insight into the Formation of the Self-Assembled E2~Ub Conjugates
Structure, 18, 2010
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3AY4
 | | Crystal structure of nonfucosylated Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa | | 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, Low affinity immunoglobulin gamma Fc region receptor III-A, ... | | Authors: | Mizushima, T, Takemoto, E, Yagi, H, Shibata-Koyama, M, Isoda, Y, Iida, S, Satoh, M, Kato, K. | | Deposit date: | 2011-04-28 | | Release date: | 2011-08-03 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural basis for improved efficacy of therapeutic antibodies on defucosylation of their Fc glycans
Genes Cells, 16, 2011
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3WHJ
 | | Crystal structure of Nas2 N-terminal domain | | Descriptor: | CADMIUM ION, Probable 26S proteasome regulatory subunit p27, SULFATE ION | | Authors: | Satoh, T, Saeki, Y, Hiromoto, T, Wang, Y.-H, Uekusa, Y, Yagi, H, Yoshihara, H, Yagi-Utsumi, M, Mizushima, T, Tanaka, K, Kato, K. | | Deposit date: | 2013-08-26 | | Release date: | 2014-03-26 | | Last modified: | 2022-08-24 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Structure, 22, 2014
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3WHK
 | | Crystal structure of PAN-Rpt5C chimera | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A | | Authors: | Satoh, T, Saeki, Y, Hiromoto, T, Wang, Y.-H, Uekusa, Y, Yagi, H, Yoshihara, H, Yagi-Utsumi, M, Mizushima, T, Tanaka, K, Kato, K. | | Deposit date: | 2013-08-26 | | Release date: | 2014-03-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Structure, 22, 2014
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3WHU
 | | Crystal structure of ERGIC-53/MCFD2, Calcium/Man2-bound form | | Descriptor: | CALCIUM ION, GLYCEROL, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Satoh, T, Suzuki, K, Kato, K. | | Deposit date: | 2013-08-30 | | Release date: | 2014-01-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural Basis for Disparate Sugar-Binding Specificities in the Homologous Cargo Receptors ERGIC-53 and VIP36
Plos One, 9, 2014
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3WT1
 | | Crystal structure of the b'-a' domain of thermophilic fungal protein disulfide isomerase (reduced form) | | Descriptor: | GLYCEROL, Protein disulfide-isomerase | | Authors: | Inagaki, K, Satoh, T, Itoh, S.G, Okumura, H, Kato, K. | | Deposit date: | 2014-04-02 | | Release date: | 2014-11-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Redox-dependent conformational transition of catalytic domain of protein disulfide isomerase indicated by crystal structure-based molecular dynamics simulation
Chem.Phys.Lett., 618, 2015
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3WHT
 | | Crystal structure of ERGIC-53/MCFD2, Calcium-free form | | Descriptor: | CALCIUM ION, CHLORIDE ION, GLYCEROL, ... | | Authors: | Satoh, T, Suzuki, K, Kato, K. | | Deposit date: | 2013-08-30 | | Release date: | 2014-01-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural Basis for Disparate Sugar-Binding Specificities in the Homologous Cargo Receptors ERGIC-53 and VIP36
Plos One, 9, 2014
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3WHL
 | | Crystal structure of Nas2 N-terminal domain complexed with PAN-Rpt5C chimera | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Probable 26S proteasome regulatory subunit p27, Proteasome-activating nucleotidase, ... | | Authors: | Satoh, T, Saeki, Y, Hiromoto, T, Wang, Y.-H, Uekusa, Y, Yagi, H, Yoshihara, H, Yagi-Utsumi, M, Mizushima, T, Tanaka, K, Kato, K. | | Deposit date: | 2013-08-26 | | Release date: | 2014-03-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (4 Å) | | Cite: | Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Structure, 22, 2014
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3WT2
 | | Crystal structure of the b'-a' domain of thermophilic fungal protein disulfide isomerase (oxidized form) | | Descriptor: | Protein disulfide-isomerase | | Authors: | Inagaki, K, Satoh, T, Itoh, S.G, Okumura, H, Kato, K. | | Deposit date: | 2014-04-02 | | Release date: | 2014-11-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Redox-dependent conformational transition of catalytic domain of protein disulfide isomerase indicated by crystal structure-based molecular dynamics simulation
Chem.Phys.Lett., 618, 2015
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3WNX
 | | Crystal structure of ERGIC-53/MCFD2, Calcium/Man3-bound form | | Descriptor: | CALCIUM ION, Multiple coagulation factor deficiency protein 2, Protein ERGIC-53, ... | | Authors: | Satoh, T, Suzuki, K, Yamaguchi, T, Kato, K. | | Deposit date: | 2013-12-18 | | Release date: | 2014-01-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Structural Basis for Disparate Sugar-Binding Specificities in the Homologous Cargo Receptors ERGIC-53 and VIP36
Plos One, 9, 2014
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2D5U
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2DPF
 | | Crystal Structure of curculin1 homodimer | | Descriptor: | Curculin, SULFATE ION | | Authors: | Kurimoto, E, Suzuki, M, Amemiya, E, Yamaguchi, Y, Nirasawa, S, Shimba, N, Xu, N, Kashiwagi, T, Kawai, M, Suzuki, E, Kato, K. | | Deposit date: | 2006-05-11 | | Release date: | 2007-05-15 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Curculin Exhibits Sweet-tasting and Taste-modifying Activities through Its Distinct Molecular Surfaces.
J.Biol.Chem., 282, 2007
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