4X42
 
 | | Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3 | | Descriptor: | Envelope protein E, SULFATE ION | | Authors: | Kulkarni, M.R, Islam, M.M, Numoto, N, Elahi, M.M, Ito, N, Kuroda, Y. | | Deposit date: | 2014-12-02 | | Release date: | 2015-09-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.78 Å) | | Cite: | Structural and biophysical analysis of sero-specific immune responses using epitope grafted Dengue ED3 mutants.
Biochim.Biophys.Acta, 1854, 2015
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8JT7
 | | Structure of arginine oxidase from Pseudomonas sp. TRU 7192 | | Descriptor: | Amine oxidoreductase, FLAVIN-ADENINE DINUCLEOTIDE | | Authors: | Yamaguchi, H, Numoto, N, Suzuki, H, Nishikawa, K, Kamegawa, A, Takahashi, K, Sugiki, M, Fujiyoshi, Y. | | Deposit date: | 2023-06-21 | | Release date: | 2024-06-26 | | Method: | ELECTRON MICROSCOPY (2.34 Å) | | Cite: | Structural basis of arginine oxidase from Pseudomonas sp. TRU 7192
To Be Published
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8YTN
 | | Single-chain Fv antibody of E11 | | Descriptor: | GLYCEROL, Single-chain Fv antibody of E11 | | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | | Deposit date: | 2024-03-26 | | Release date: | 2024-07-03 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.72 Å) | | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758, 2024
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8YTO
 | | Single-chain Fv antibody of E11 complex with NP-glycine | | Descriptor: | 2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, GLYCEROL, ... | | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | | Deposit date: | 2024-03-26 | | Release date: | 2024-07-03 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.04 Å) | | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758, 2024
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8YTP
 | | Single-chain Fv antibody of E11 complex with NP-glycine under reducing conditions | | Descriptor: | 2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid, Single-chain Fv antibody of E11 | | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | | Deposit date: | 2024-03-26 | | Release date: | 2024-07-03 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (1.36 Å) | | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758, 2024
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6L6K
 | | Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1 | | Descriptor: | 1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)benzotriazole-5-carboxylic acid, CALCIUM ION, Nuclear receptor coactivator 1, ... | | Authors: | Shimizu, K, Numoto, N, Nakano, S, Makishima, M, Kakuta, H, Ito, N. | | Deposit date: | 2019-10-29 | | Release date: | 2020-11-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of dimeric RXRalpha-LBD complexed with partial agonist CBt-PMN and SRC1
To Be Published
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6LB4
 | | Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator | | Descriptor: | 1,2-ETHANEDIOL, 6-[ethyl-[3-(2-methoxyethoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid, Nuclear receptor coactivator 2, ... | | Authors: | Imai, D, Numoto, N, Nakano, S, Kakuta, H, Ito, N. | | Deposit date: | 2019-11-13 | | Release date: | 2020-11-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator
To Be Published
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6LB6
 | | Crystal structure of dimeric RXR-LBD complexed with partial agonist NEt-4IB and TIF2 co-activator | | Descriptor: | 6-[ethyl-[4-(2-methylpropoxy)-3-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid, Nuclear receptor coactivator 2, Retinoic acid receptor RXR-alpha | | Authors: | Imai, D, Numoto, N, Nakano, S, Kakuta, H, Ito, N. | | Deposit date: | 2019-11-13 | | Release date: | 2020-11-18 | | Last modified: | 2024-10-02 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for the full and partial agonist activities of retinoid X receptor alpha ligands with an iso-butoxy and an isopropyl group
Biochem.Biophys.Res.Commun., 734, 2024
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6LCA
 | | Crystal structure of human Dishevelled1 PDZ domain homotrimer | | Descriptor: | SULFATE ION, Segment polarity protein dishevelled homolog DVL-1 | | Authors: | Yasukochi, S, Numoto, N, Tenno, N, Tenno, T, Ito, N, Hiroaki, H. | | Deposit date: | 2019-11-18 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of human Dishevelled1 PDZ domain homotrimer
To Be Published
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8IBL
 | | MES bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Alpha/beta hydrolase family protein, CALCIUM ION, ... | | Authors: | Emori, M, Numoto, N, Kamiya, N, Oda, M. | | Deposit date: | 2023-02-10 | | Release date: | 2023-03-15 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism.
Biorxiv, 2023
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8IBM
 | | Sulfate bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, SULFATE ION | | Authors: | Emori, M, Numoto, N, Kamiya, N, Oda, M. | | Deposit date: | 2023-02-10 | | Release date: | 2023-03-15 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism.
Biorxiv, 2023
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5GJI
 | | PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex | | Descriptor: | GLYCEROL, Phosphatidylinositol 3-kinase regulatory subunit alpha, SULFATE ION, ... | | Authors: | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2016-06-30 | | Release date: | 2016-12-14 | | Last modified: | 2017-05-10 | | Method: | X-RAY DIFFRACTION (0.9 Å) | | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
J. Biol. Chem., 292, 2017
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5GJH
 | | Gads SH2 domain/CD28-derived peptide complex | | Descriptor: | GRB2-related adapter protein 2, T-cell-specific surface glycoprotein CD28 | | Authors: | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2016-06-30 | | Release date: | 2016-12-14 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
J. Biol. Chem., 292, 2017
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5B1C
 | | Crystal structure of DEN4 ED3 mutant with L387I | | Descriptor: | Envelope protein E, SULFATE ION | | Authors: | Kulkarni, M.R, Numoto, N, Ito, N, Kuroda, Y. | | Deposit date: | 2015-12-02 | | Release date: | 2016-02-24 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.003 Å) | | Cite: | Modeling and experimental assessment of a buried Leu-Ile mutation in dengue envelope domain III
Biochem.Biophys.Res.Commun., 471, 2016
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5AUL
 | | PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex | | Descriptor: | GLYCEROL, Phosphatidylinositol 3-kinase regulatory subunit alpha, T-cell-specific surface glycoprotein CD28 | | Authors: | Inaba, S, Numoto, N, Morii, H, Ikura, T, Oda, M, Ito, N. | | Deposit date: | 2015-04-28 | | Release date: | 2016-05-25 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
J. Biol. Chem., 292, 2017
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5B1R
 | | Crystal structure of mouse CD72a CTLD | | Descriptor: | ACETATE ION, B-cell differentiation antigen CD72, GLYCEROL | | Authors: | Shinagawa, K, Numoto, N, Tsubata, T, Ito, N. | | Deposit date: | 2015-12-15 | | Release date: | 2016-10-19 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | CD72 negatively regulates B lymphocyte responses to the lupus-related endogenous toll-like receptor 7 ligand Sm/RNP
J.Exp.Med., 213, 2016
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2E0I
 | | Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 432aa long hypothetical deoxyribodipyrimidine photolyase, FLAVIN-ADENINE DINUCLEOTIDE | | Authors: | Fujihashi, M, Numoto, N, Kobayashi, Y, Mizushima, A, Tsujimura, M, Nakamura, A, Kawarabayashi, Y, Miki, K. | | Deposit date: | 2006-10-10 | | Release date: | 2006-11-28 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal Structure of Archaeal Photolyase from Sulfolobus tokodaii with Two FAD Molecules: Implication of a Novel Light-harvesting Cofactor
J.Mol.Biol., 365, 2007
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8GCL
 | | Cryo-EM structure of hAQP2 in DDM | | Descriptor: | Aquaporin-2 | | Authors: | Kamegawa, A, Suzuki, S, Nishikawa, K, Numoto, N, Suzuki, H, Fujiyoshi, Y. | | Deposit date: | 2023-03-02 | | Release date: | 2023-06-21 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (2.89 Å) | | Cite: | Structural analysis of the water channel AQP2 by single-particle cryo-EM.
J.Struct.Biol., 215, 2023
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6ICG
 | | Grb2 SH2 domain in phosphopeptide free form | | Descriptor: | GLYCEROL, Growth factor receptor-bound protein 2, SULFATE ION | | Authors: | Hosoe, Y, Numoto, N, Inaba, S, Ogawa, S, Morii, H, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2018-09-06 | | Release date: | 2019-07-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.15 Å) | | Cite: | Structural and functional properties of Grb2 SH2 dimer in CD28 binding.
Biophys Physicobio., 16, 2019
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8IF4
 | | Structure of human alpha-2/delta-1 without mirogabalin | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Voltage-dependent calcium channel subunit alpha-2/delta-1 | | Authors: | Kozai, D, Numoto, N, Fujiyoshi, Y. | | Deposit date: | 2023-02-17 | | Release date: | 2023-04-05 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (3.23 Å) | | Cite: | Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human alpha 2 delta 1, a Voltage-Gated Calcium Channel Subunit.
J.Mol.Biol., 435, 2023
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8IF3
 | | Structure of human alpha-2/delta-1 with mirogabalin | | Descriptor: | 2-[(1R,5S,6S)-6-(aminomethyl)-3-ethyl-6-bicyclo[3.2.0]hept-3-enyl]acetic 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: | Kozai, D, Numoto, N, Fujiyoshi, Y. | | Deposit date: | 2023-02-17 | | Release date: | 2023-04-05 | | Last modified: | 2023-04-12 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human alpha 2 delta 1, a Voltage-Gated Calcium Channel Subunit.
J.Mol.Biol., 435, 2023
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7VQP
 | | Vitamin D receptor complexed with a lithocholic acid derivative | | Descriptor: | 3-((R)-4-((3R,5R,8R,9S,10S,13R,14S,17R)-3-(2-hydroxy-2-methylpropyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-17-yl)pentanamido)propanoic acid, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Kato, K, Numoto, N, Kagechika, H, Tanatani, A, Ito, N. | | Deposit date: | 2021-10-20 | | Release date: | 2022-03-09 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists.
Biomolecules, 12, 2022
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6K4Z
 | | Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID | | Descriptor: | 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID, GLYCEROL, SULFATE ION, ... | | Authors: | Nishiguchi, A, Numoto, N, Ito, N, Azuma, T, Oda, M. | | Deposit date: | 2019-05-27 | | Release date: | 2019-09-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain.
Mol.Immunol., 114, 2019
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6LB5
 | | Crystal structure of dimeric RXR-LBD complexed with full agonist NEt-3IB and TIF2 co-activator | | Descriptor: | 6-[ethyl-[3-(2-methylpropoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid, Nuclear receptor coactivator 2, Retinoic acid receptor RXR-alpha | | Authors: | Imai, D, Numoto, N, Nakano, S, Kakuta, H, Ito, N. | | Deposit date: | 2019-11-13 | | Release date: | 2020-11-18 | | Last modified: | 2024-10-02 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for the full and partial agonist activities of retinoid X receptor alpha ligands with an iso-butoxy and an isopropyl group
Biochem.Biophys.Res.Commun., 734, 2024
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6ICH
 | | Grb2 SH2 domain in domain swapped dimer form | | Descriptor: | Growth factor receptor-bound protein 2 | | Authors: | Hosoe, Y, Numoto, N, Inaba, S, Ogawa, S, Morii, H, Abe, R, Ito, N, Oda, M. | | Deposit date: | 2018-09-06 | | Release date: | 2019-07-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural and functional properties of Grb2 SH2 dimer in CD28 binding.
Biophys Physicobio., 16, 2019
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