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Yorodumi- PDB-5svr: Crystal structure of the ATP-gated human P2X3 ion channel bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5svr | |||||||||
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Title | Crystal structure of the ATP-gated human P2X3 ion channel bound to competitive antagonist A-317491 | |||||||||
Components | P2X purinoceptor 3 | |||||||||
Keywords | MEMBRANE PROTEIN / Membrane protein Ion Channel Antagonist State | |||||||||
Function / homology | Function and homology information Platelet homeostasis / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / neuromuscular synaptic transmission / Elevation of cytosolic Ca2+ levels / peristalsis / urinary bladder smooth muscle contraction / response to carbohydrate / inorganic cation transmembrane transport / cellular response to ATP ...Platelet homeostasis / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / neuromuscular synaptic transmission / Elevation of cytosolic Ca2+ levels / peristalsis / urinary bladder smooth muscle contraction / response to carbohydrate / inorganic cation transmembrane transport / cellular response to ATP / positive regulation of calcium ion transport into cytosol / behavioral response to pain / protein homotrimerization / response to mechanical stimulus / positive regulation of calcium-mediated signaling / response to cold / hippocampal mossy fiber to CA3 synapse / establishment of localization in cell / calcium ion transmembrane transport / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / sensory perception of taste / response to heat / postsynapse / receptor complex / response to hypoxia / axon / signal transduction / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å | |||||||||
Authors | Mansoor, S.E. / Lu, W. / Oosterheert, W. / Shekhar, M. / Tajkhorshid, E. / Gouaux, E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2016 Title: X-ray structures define human P2X3 receptor gating cycle and antagonist action. Authors: Mansoor, S.E. / Lu, W. / Oosterheert, W. / Shekhar, M. / Tajkhorshid, E. / Gouaux, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5svr.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5svr.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 5svr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5svr_validation.pdf.gz | 737.1 KB | Display | wwPDB validaton report |
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Full document | 5svr_full_validation.pdf.gz | 747.3 KB | Display | |
Data in XML | 5svr_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5svr_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/5svr ftp://data.pdbj.org/pub/pdb/validation_reports/sv/5svr | HTTPS FTP |
-Related structure data
Related structure data | 5svjC 5svkC 5svlC 5svmC 5svpC 5svqC 5svsC 5svtC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 40745.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: P2RX3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P56373 |
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#2: Sugar |
-Non-polymers , 4 types, 5 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-71C / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.25 Å3/Da / Density % sol: 71.05 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 400, 100 mM Glycine, pH 8.5, 150 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.13→40 Å / Num. obs: 12308 / % possible obs: 98.3 % / Redundancy: 10.67 % / Net I/σ(I): 20.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.13→39.674 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 33.86 / 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: 3.13→39.674 Å
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Refine LS restraints |
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LS refinement shell |
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