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Yorodumi- PDB-5x2m: Crystal structure of the medaka fish taste receptor T1r2a-T1r3 li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x2m | ||||||
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Title | Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-glutamine | ||||||
Components |
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Keywords | SIGNALING PROTEIN/IMMUNE SYSTEM / receptor / ligand binding / amino acid / venus-flytrap domain / SIGNALING PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information sweet taste receptor activity / sensory perception of umami taste / G protein-coupled receptor activity / plasma membrane Similarity search - Function | ||||||
Biological species | Oryzias latipes (Japanese medaka) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 Å | ||||||
Authors | Nuemket, N. / Yasui, N. / Atsumi, N. / Yamashita, A. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structural basis for perception of diverse chemical substances by T1r taste receptors Authors: Nuemket, N. / Yasui, N. / Kusakabe, Y. / Nomura, Y. / Atsumi, N. / Akiyama, S. / Nango, E. / Kato, Y. / Kaneko, M.K. / Takagi, J. / Hosotani, M. / Yamashita, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x2m.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5x2m.ent.gz | 866.4 KB | Display | PDB format |
PDBx/mmJSON format | 5x2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x2m_validation.pdf.gz | 546.7 KB | Display | wwPDB validaton report |
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Full document | 5x2m_full_validation.pdf.gz | 578.5 KB | Display | |
Data in XML | 5x2m_validation.xml.gz | 97.8 KB | Display | |
Data in CIF | 5x2m_validation.cif.gz | 137.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/5x2m ftp://data.pdbj.org/pub/pdb/validation_reports/x2/5x2m | HTTPS FTP |
-Related structure data
Related structure data | 5x2nC 5x2oC 5x2pC 5x2qC 1a6tS 2e4uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Taste receptor, type 1, member ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 51471.105 Da / Num. of mol.: 2 / Fragment: UNP residues 12-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryzias latipes (Japanese medaka) / Gene: TAS1R2a / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A173M0G2 #2: Protein | Mass: 53131.977 Da / Num. of mol.: 2 / Fragment: UNP residues 12-483 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryzias latipes (Japanese medaka) / Gene: TAS1R3 / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A173M094 |
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-Antibody , 2 types, 4 molecules HJLK
#3: Antibody | Mass: 24182.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) #4: Antibody | Mass: 23899.240 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
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-Sugars , 1 types, 27 molecules
#5: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 785 molecules
#6: Chemical | ChemComp-GLN / #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-CA / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 12~13% (w/v) PEG 1500, 3% (v/v) PEG400, 0.1 M MES, 5 mM Glutamine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 142788 / % possible obs: 97.1 % / Redundancy: 3.3 % / Rsym value: 0.078 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7093 / Rsym value: 0.705 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E4U, 1A6T Resolution: 2.206→49.891 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.206→49.891 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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