3VOC
 
 | | Crystal structure of the catalytic domain of beta-amylase from paenibacillus polymyxa | | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Beta/alpha-amylase, ... | | Authors: | Nishimura, S, Fujioka, T, Nakaniwa, T, Tada, T. | | Deposit date: | 2012-01-21 | | Release date: | 2013-02-20 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structural analysis by X-ray crystallography and small-angle scattering of the multi-domain beta-amylase from Paenibacillus polymyxa
To be Published
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2LAA
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5OWP
 | | Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3 | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-alpha-D-galactopyranose, 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE, ... | | Authors: | Bermejo, I.A, Albuquerque, I.S, Somovilla, V.J, Martinez-Saez, N, Castro-Lopez, J, Garcia-Martin, F, Hinou, H, Nishimura, S, Jimenez-Barbero, J, Asensio, J.L, Avenoza, A, Busto, J.H, Hurtado-Guerrero, R, Peregrina, J.M, Bernardes, G.J, Corzana, F. | | Deposit date: | 2017-09-02 | | Release date: | 2017-12-13 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | The Use of Fluoroproline in MUC1 Antigen Enables Efficient Detection of Antibodies in Patients with Prostate Cancer.
J. Am. Chem. Soc., 139, 2017
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5X7Y
 | | Crystal Structure of the Dog Lipocalin Allergen Can f 6 | | Descriptor: | DI(HYDROXYETHYL)ETHER, Lipocalin-Can f 6 allergen | | Authors: | Yamamoto, K, Otani, T, Sugiura, K, Nakatsuji, M, Nishimura, S, Inui, T. | | Deposit date: | 2017-02-28 | | Release date: | 2018-04-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Crystal structure of the dog allergen Can f 6 and structure-based implications of its cross-reactivity with the cat allergen Fel d 4.
Sci Rep, 9, 2019
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1BQT
 | | THREE-DIMENSIONAL STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR-I (IGF-I) DETERMINED BY 1H-NMR AND DISTANCE GEOMETRY, 6 STRUCTURES | | Descriptor: | INSULIN-LIKE GROWTH FACTOR-I | | Authors: | Sato, A, Nishimura, S, Ohkubo, T, Kyogoku, Y, Koyama, S, Kobayashi, M, Yasuda, T, Kobayashi, Y. | | Deposit date: | 1998-08-18 | | Release date: | 1999-05-18 | | Last modified: | 2022-02-16 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional structure of human insulin-like growth factor-I (IGF-I) determined by 1H-NMR and distance geometry.
Int.J.Pept.Protein Res., 41, 1993
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5XQG
 | | Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose | | Descriptor: | 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose, CALCIUM ION, Pcrglx protein | | Authors: | Kunishige, Y, Iwai, M, Tada, T, Nishimura, S, Sakamoto, T. | | Deposit date: | 2017-06-07 | | Release date: | 2018-03-21 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.74 Å) | | Cite: | Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26
FEBS Lett., 592, 2018
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6DJP
 | | Integrin alpha-v beta-8 in complex with the Fabs 8B8 and 68 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 68 heavy chain Fab, ... | | Authors: | Cormier, A, Campbell, M.G, Nishimura, S.L, Cheng, Y. | | Deposit date: | 2018-05-25 | | Release date: | 2018-07-25 | | Last modified: | 2020-07-29 | | Method: | ELECTRON MICROSCOPY (4.8 Å) | | Cite: | Cryo-EM structure of the alpha v beta 8 integrin reveals a mechanism for stabilizing integrin extension.
Nat. Struct. Mol. Biol., 25, 2018
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5XQO
 | | Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with tetrameric substrate | | Descriptor: | 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose, 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose, CALCIUM ION, ... | | Authors: | Kunishige, Y, Iwai, M, Tada, T, Nishimura, S, Sakamoto, T. | | Deposit date: | 2017-06-07 | | Release date: | 2018-03-21 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26
FEBS Lett., 592, 2018
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8HRH
 | | SN-131/1B2 anti-MUC1 antibody with a glycopeptide | | Descriptor: | 1-ACETYL-L-PROLINE, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ALANINE, ... | | Authors: | Wakui, H, Horidome, C, Yao, M, Ose, T, Nishimura, S.-I. | | Deposit date: | 2022-12-15 | | Release date: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Structural and molecular insight into antibody recognition of dynamic neoepitopes in membrane tethered MUC1 of pancreatic cancer cells and secreted exosomes.
Rsc Chem Biol, 4, 2023
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1AA9
 | | HUMAN C-HA-RAS(1-171)(DOT)GDP, NMR, MINIMIZED AVERAGE STRUCTURE | | Descriptor: | C-HA-RAS, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION | | Authors: | Ito, Y, Yamasaki, Y, Muto, Y, Kawai, G, Nishimura, S, Miyazawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1997-01-27 | | Release date: | 1997-07-29 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein.
Biochemistry, 36, 1997
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8VSD
 | | avb8/L-TGF-b1/GARP | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Jin, M, Cheng, Y, Nishimura, S.L. | | Deposit date: | 2024-01-23 | | Release date: | 2024-09-11 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Dynamic allostery drives autocrine and paracrine TGF-beta signaling
Cell(Cambridge,Mass.), 2024
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2LAB
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6TGG
 | | scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar | | Descriptor: | 1,2-ETHANEDIOL, Mucin-1, ScFv_SM3, ... | | Authors: | Bermejo, I.A, Navo, C.D, Castro-Lopez, J, Samchez-Fernandez, E.M, Guerreiro, A, Avenoza, A, Busto, J.H, Garcia-Martin, F, Nishimura, S.I, Garcia-Fernandez, J.M, Ortiz-Mellet, C, Bernardes, G.J.L, Hurtado-Guerrero, R, Peregrina, J.M, Corzana, F. | | Deposit date: | 2019-11-15 | | Release date: | 2020-04-08 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Synthesis, conformational analysis and in vivo assays of an anti-cancer vaccine that features an unnatural antigen based on an sp 2 -iminosugar fragment.
Chem Sci, 11, 2020
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8VSC
 | | L-TGF-b1/GARP | | Descriptor: | Transforming growth factor beta activator LRRC32, Transforming growth factor beta-1 proprotein | | Authors: | Jin, M, Cheng, Y, Nishimura, S.L. | | Deposit date: | 2024-01-23 | | Release date: | 2024-09-11 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Dynamic allostery drives autocrine and paracrine TGF-beta signaling
Cell(Cambridge,Mass.), 2024
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8VSB
 | | L-TGF-b3/GARP | | Descriptor: | Transforming growth factor beta activator LRRC32, Transforming growth factor beta-3 proprotein | | Authors: | Jin, M, Cheng, Y, Nishimura, S.L. | | Deposit date: | 2024-01-23 | | Release date: | 2024-09-11 | | Method: | ELECTRON MICROSCOPY (2.93 Å) | | Cite: | Dynamic allostery drives autocrine and paracrine TGF-beta signaling
Cell(Cambridge,Mass.), 2024
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8VS6
 | | L-TGF-b3/avb8 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Jin, M, Cheng, Y, Nishimura, S.L. | | Deposit date: | 2024-01-23 | | Release date: | 2024-09-11 | | Method: | ELECTRON MICROSCOPY (2.73 Å) | | Cite: | Dynamic allostery drives autocrine and paracrine TGF-beta signaling
Cell(Cambridge,Mass.), 2024
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6UJA
 | | Integrin alpha-v beta-8 in complex with pro-TGF-beta1 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Campbell, M.G, Cormier, A, Cheng, Y, Nishimura, S.L. | | Deposit date: | 2019-10-02 | | Release date: | 2020-02-05 | | Last modified: | 2020-07-29 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Cryo-EM Reveals Integrin-Mediated TGF-beta Activation without Release from Latent TGF-beta.
Cell, 180, 2020
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6UJB
 | | Integrin alpha-v beta-8 in complex with the Fabs C6D4 and 11D12v2 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C6D4 heavy chain Fab, ... | | Authors: | Campbell, M.G, Cormier, A, Cheng, Y, Nishimura, S.L. | | Deposit date: | 2019-10-02 | | Release date: | 2020-02-05 | | Last modified: | 2020-07-29 | | Method: | ELECTRON MICROSCOPY (3.51 Å) | | Cite: | Cryo-EM Reveals Integrin-Mediated TGF-beta Activation without Release from Latent TGF-beta.
Cell, 180, 2020
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6UJC
 | | Integrin alpha-v beta-8 in complex with the Fabs C6-RGD3 and 11D12v2 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C6-RGD3 heavy chain Fab, ... | | Authors: | Campbell, M.G, Cormier, A, Cheng, Y, Nishimura, S.L. | | Deposit date: | 2019-10-02 | | Release date: | 2020-02-05 | | Last modified: | 2020-07-29 | | Method: | ELECTRON MICROSCOPY (3.56 Å) | | Cite: | Cryo-EM Reveals Integrin-Mediated TGF-beta Activation without Release from Latent TGF-beta.
Cell, 180, 2020
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7DRU
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5XQJ
 | | Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose | | Descriptor: | 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-[beta-D-galactopyranose-(1-4)]alpha-L-rhamnopyranose, 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose, CALCIUM ION, ... | | Authors: | Kunishige, Y, Iwai, M, Tada, T, Nishimura, S, Sakamoto, T. | | Deposit date: | 2017-06-07 | | Release date: | 2018-04-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26
FEBS Lett., 592, 2018
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1VBN
 | | Escherichia coli tyrosyl-tRNA synthetase mutant complexed with Tyr-AMS | | Descriptor: | 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE, Tyrosyl-tRNA synthetase | | Authors: | Kobayashi, T, Sakamoto, K, Takimura, T, Kamata, K, Sekine, R, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-02-27 | | Release date: | 2005-01-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102, 2005
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1VBM
 | | Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS | | Descriptor: | 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE, SULFATE ION, Tyrosyl-tRNA synthetase | | Authors: | Kobayashi, T, Sakamoto, K, Takimura, T, Kamata, K, Sekine, R, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-02-27 | | Release date: | 2005-01-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.
J.Mol.Biol., 346, 2005
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1WQ3
 | | Escherichia coli tyrosyl-tRNA synthetase mutant complexed with 3-iodo-L-tyrosine | | Descriptor: | 3-IODO-TYROSINE, Tyrosyl-tRNA synthetase | | Authors: | Kobayashi, T, Sakamoto, K, Nureki, O, Takimura, T, Kamata, K, Sekine, R, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-09-20 | | Release date: | 2005-01-25 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102, 2005
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1WQ4
 | | Escherichia coli tyrosyl-tRNA synthetase mutant complexed with L-tyrosine | | Descriptor: | TYROSINE, Tyrosyl-tRNA synthetase | | Authors: | Kobayashi, T, Sakamoto, K, Nureki, O, Takimura, T, Kamata, K, Sekine, R, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-09-20 | | Release date: | 2005-01-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102, 2005
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