8W83
 
 | | HLA-DQ2.5-alpha1 gliadin peptide in complex with DQN0344AE02 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, DQN0344AE02 Fab heavy chain, DQN0344AE02 Fab light chain, ... | | Authors: | Irie, M, Tsushima, T, Teranishi-Ikawa, Y, Takahashi, N, Ishii, S, Okura, Y, Fukami, T.A, Torizawa, T. | | Deposit date: | 2023-08-31 | | Release date: | 2023-11-08 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (2.818 Å) | | Cite: | Characterizations of a neutralizing antibody broadly reactive to multiple gluten peptide:HLA-DQ2.5 complexes in the context of celiac disease.
Nat Commun, 14, 2023
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2RQZ
 | | Structure of sugar modified epidermal growth factor-like repeat 12 of mouse Notch-1 receptor | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose, Neurogenic locus notch homolog protein 1 | | Authors: | Shimizu, K, Fujitani, N, Hosoguchi, K, Nishimura, S. | | Deposit date: | 2010-02-26 | | Release date: | 2010-10-13 | | Last modified: | 2020-07-29 | | Method: | SOLUTION NMR | | Cite: | Chemical Synthesis, Folding, and Structural Insights into O-Fucosylated Epidermal Growth Factor-like Repeat 12 of Mouse Notch-1 Receptor
J.Am.Chem.Soc., 132, 2010
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6G3B
 | | AvaII restriction endonuclease in complex with an RNA/DNA hybrid | | Descriptor: | DNA (5'-D(*CP*CP*AP*TP*GP*GP*TP*CP*CP*TP*A)-3'), RNA (5'-R(P*GP*UP*AP*GP*GP*AP*CP*CP*AP*UP*G)-3'), Type II site-specific deoxyribonuclease | | Authors: | Kisiala, M, Kowalska, M, Czapinska, H, Bochtler, M. | | Deposit date: | 2018-03-24 | | Release date: | 2019-04-10 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation
Nucleic Acids Res., 2020
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2RR2
 | | Structure of O-fucosylated epidermal growth factor-like repeat 12 of mouse Notch-1 receptor | | Descriptor: | Neurogenic locus notch homolog protein 1, alpha-L-fucopyranose | | Authors: | Hosoguchi, K, Shimizu, K, Fujitani, N, Nishimura, S. | | Deposit date: | 2010-02-26 | | Release date: | 2010-10-13 | | Last modified: | 2020-07-29 | | Method: | SOLUTION NMR | | Cite: | Chemical Synthesis, Folding, and Structural Insights into O-Fucosylated Epidermal Growth Factor-like Repeat 12 of Mouse Notch-1 Receptor
J.Am.Chem.Soc., 132, 2010
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2RR0
 | | Structure of epidermal growth factor-like repeat 12 of mouse Notch-1 receptor | | Descriptor: | Neurogenic locus notch homolog protein 1 | | Authors: | Hosoguchi, K, Shimizu, K, Fujitani, N, Nishimura, S. | | Deposit date: | 2010-02-26 | | Release date: | 2010-10-13 | | Last modified: | 2011-07-13 | | Method: | SOLUTION NMR | | Cite: | Chemical Synthesis, Folding, and Structural Insights into O-Fucosylated Epidermal Growth Factor-like Repeat 12 of Mouse Notch-1 Receptor
J.Am.Chem.Soc., 132, 2010
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3VJH
 | | Human PPAR GAMMA ligand binding domain in complex with JKPL35 | | Descriptor: | (2S)-2-[4-methoxy-3-({[4-(trifluoromethyl)benzoyl]amino}methyl)benzyl]pentanoic acid, Peroxisome proliferator-activated receptor gamma | | Authors: | Tomioka, D, Kuwabara, N, Hashimoto, H, Sato, M, Shimizu, T. | | Deposit date: | 2011-10-20 | | Release date: | 2012-08-29 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.22 Å) | | Cite: | Peroxisome proliferator-activated receptors (PPARs) have multiple binding points that accommodate ligands in various conformations: phenylpropanoic acid-type PPAR ligands bind to PPAR in different conformations, depending on the subtype.
J.Med.Chem., 55, 2012
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3VJI
 | | Human PPAR gamma ligand binding domain in complex with JKPL53 | | Descriptor: | (2S)-2-{4-butoxy-3-[({4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]benzoyl}amino)methyl]benzyl}butanoic acid, Peroxisome proliferator-activated receptor gamma | | Authors: | Tomioka, D, Kuwabara, N, Hashimoto, H, Sato, M, Shimizu, T. | | Deposit date: | 2011-10-20 | | Release date: | 2012-08-29 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.61 Å) | | Cite: | Peroxisome proliferator-activated receptors (PPARs) have multiple binding points that accommodate ligands in various conformations: phenylpropanoic acid-type PPAR ligands bind to PPAR in different conformations, depending on the subtype.
J.Med.Chem., 55, 2012
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8RKI
 | | Molecular basis of ZP3/ZP1 heteropolymerization: crystal structure of a native vertebrate egg coat filament fragment | | Descriptor: | Choriogenin H, YTTERBIUM (III) ION, Zona pellucida sperm-binding protein 3, ... | | Authors: | Wiseman, B, Zamora-Caballero, S, de Sanctis, D, Yasumasu, S, Jovine, L. | | Deposit date: | 2023-12-25 | | Release date: | 2024-03-13 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (4.2 Å) | | Cite: | ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat.
Cell, 187, 2024
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8BQU
 | | Molecular basis of ZP3/ZP1 heteropolymerization: crystal structure of a native vertebrate egg coat filament | | Descriptor: | Choriogenin H, Zona pellucida sperm-binding protein 3, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | | Authors: | Bokhove, M, de Sanctis, D, Yasumasu, S, Jovine, L. | | Deposit date: | 2022-11-21 | | Release date: | 2024-03-13 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat.
Cell, 187, 2024
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8YEK
 | | Cryo-EM structure of the channelrhodopsin GtCCR2 | | Descriptor: | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE, GtCCR2, RETINAL | | Authors: | Tanaka, T, Iida, W, Sano, F.K, Oda, K, Shihoya, W, Nureki, O. | | Deposit date: | 2024-02-22 | | Release date: | 2024-09-04 | | Method: | ELECTRON MICROSCOPY (2.73 Å) | | Cite: | The high-light-sensitivity mechanism and optogenetic properties of the bacteriorhodopsin-like channelrhodopsin GtCCR4
Mol.Cell, 2024
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8YEL
 | | Cryo-EM structure of the channelrhodopsin GtCCR4 | | Descriptor: | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE, Cation channel rhodopsin 4, RETINAL | | Authors: | Tanaka, T, Iida, W, Sano, F.K, Oda, K, Shihoya, W, Nureki, O. | | Deposit date: | 2024-02-22 | | Release date: | 2024-09-04 | | Method: | ELECTRON MICROSCOPY (2.71 Å) | | Cite: | The high-light-sensitivity mechanism and optogenetic properties of the bacteriorhodopsin-like channelrhodopsin GtCCR4
Mol.Cell, 2024
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8YEJ
 | | Cryo-EM structure of the channelrhodopsin GtCCR2 focused on the monomer | | Descriptor: | GtCCR2, RETINAL | | Authors: | Tanaka, T, Iida, W, Sano, F.K, Oda, K, Shihoya, W, Nureki, O. | | Deposit date: | 2024-02-22 | | Release date: | 2024-09-04 | | Method: | ELECTRON MICROSCOPY (2.86 Å) | | Cite: | The high-light-sensitivity mechanism and optogenetic properties of the bacteriorhodopsin-like channelrhodopsin GtCCR4
Mol.Cell, 2024
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6A86
 | | Pholiota squarrosa lectin | | Descriptor: | (3R)-butane-1,3-diol, lectin | | Authors: | Yamasaki, K, Yamasaki, T, Kubota, T. | | Deposit date: | 2018-07-06 | | Release date: | 2019-04-10 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL).
Glycobiology, 29, 2019
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6A87
 | | Pholiota squarrosa lectin (PhoSL) in complex with fucose(alpha1-6)GlcNAc | | Descriptor: | METHANETHIOL, alpha-L-fucopyranose, alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Yamasaki, K, Yamasaki, T, Kubota, T. | | Deposit date: | 2018-07-06 | | Release date: | 2019-04-10 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.41 Å) | | Cite: | Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL).
Glycobiology, 29, 2019
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7VU9
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3AM2
 | | Clostridium perfringens enterotoxin | | Descriptor: | GLYCEROL, Heat-labile enterotoxin B chain, UNKNOWN ATOM OR ION | | Authors: | Kitadokoro, K, Nishimura, K, Kamitani, S, Kimura, J, Fukui, A, Abe, H, Horiguchi, Y. | | Deposit date: | 2010-08-12 | | Release date: | 2011-04-13 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.51 Å) | | Cite: | Crystal Structure of Clostridium perfringens Enterotoxin Displays Features of {beta}-Pore-forming Toxins
J.Biol.Chem., 286, 2011
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3L85
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7WDT
 | | 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with GlcNAc-6S | | Descriptor: | 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose, 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose, Beta-N-acetylhexosaminidase, ... | | Authors: | Yamada, C, Kashima, T, Fushinobu, S, Katoh, T, Katayama, T. | | Deposit date: | 2021-12-22 | | Release date: | 2022-12-28 | | Last modified: | 2023-06-14 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
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7WDU
 | | 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with PUGNAc-6S | | Descriptor: | Beta-N-acetylhexosaminidase, CALCIUM ION, [[(3R,4R,5S,6R)-3-acetamido-4,5-bis(oxidanyl)-6-(sulfooxymethyl)oxan-2-ylidene]amino] N-phenylcarbamate | | Authors: | Kashima, T, Yamada, C, Fushinobu, S, Katoh, T, Katayama, T. | | Deposit date: | 2021-12-22 | | Release date: | 2022-12-28 | | Last modified: | 2023-06-14 | | Method: | X-RAY DIFFRACTION (2.23 Å) | | Cite: | A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
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2ZFU
 | | Structure of the methyltransferase-like domain of nucleomethylin | | Descriptor: | Cerebral protein 1, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Minami, H, Hashimoto, H, Murayama, A, Yanagisawa, J, Sato, M, Shimizu, T. | | Deposit date: | 2008-01-14 | | Release date: | 2008-12-02 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Epigenetic control of rDNA loci in response to intracellular energy status
Cell(Cambridge,Mass.), 133, 2008
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2P6L
 | | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, diphthine synthase | | Authors: | Yamamoto, H, Matsuura, Y, Ono, N, Shimada, H, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-19 | | Release date: | 2007-09-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of PH0725 from Pyrococcus horikoshii OT3
To be Published
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2P6I
 | | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, diphthine synthase | | Authors: | Yamamoto, H, Matsuura, Y, Morikawa, Y, Shimada, H, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-18 | | Release date: | 2007-09-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of PH0725 from Pyrococcus horikoshii OT3
To be Published
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2PCK
 | | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, diphthine synthase | | Authors: | Yamamoto, H, Morikawa, Y, Matsuura, Y, Shimada, H, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-30 | | Release date: | 2007-10-02 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal structure of PH0725 from Pyrococcus horikoshii OT3
To be Published
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4WR5
 | | Crystal Structure of GST Mutated with Halogenated Tyrosine (7cGST-1) | | Descriptor: | GLUTATHIONE, Glutathione S-transferase class-mu 26 kDa isozyme, SULFATE ION | | Authors: | Akasaka, R, Kawazoe, M, Tomabechi, Y, Ohtake, K, Itagaki, T, Takemoto, C, Shirouzu, M, Yokoyama, S, Sakamoto, K. | | Deposit date: | 2014-10-23 | | Release date: | 2015-08-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Protein stabilization utilizing a redefined codon
Sci Rep, 5, 2015
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4WR4
 | | Crystal Structure of GST Mutated with Halogenated Tyrosine (7bGST-1) | | Descriptor: | GLUTATHIONE, Glutathione S-transferase class-mu 26 kDa isozyme, SULFATE ION | | Authors: | Akasaka, R, Kawazoe, M, Tomabechi, Y, Ohtake, K, Itagaki, T, Takemoto, C, Shirouzu, M, Yokoyama, S, Sakamoto, K. | | Deposit date: | 2014-10-23 | | Release date: | 2015-08-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Protein stabilization utilizing a redefined codon
Sci Rep, 5, 2015
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