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Yorodumi- PDB-5u2h: Crystal structure of the ATP-gated P2X7 ion channel bound to ATP ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u2h | |||||||||
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Title | Crystal structure of the ATP-gated P2X7 ion channel bound to ATP and allosteric antagonist A804598 | |||||||||
Components | P2X purinoceptor | |||||||||
Keywords | MEMBRANE PROTEIN / membrane protein: ATP-gated ion channel: agonist and allosteric antagonist bound: closed state | |||||||||
Function / homology | Function and homology information NAD transport / phagolysosome assembly / phospholipid transfer to membrane / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / gamma-aminobutyric acid secretion / positive regulation of interleukin-1 alpha production / negative regulation of cell volume / plasma membrane organization / positive regulation of gamma-aminobutyric acid secretion ...NAD transport / phagolysosome assembly / phospholipid transfer to membrane / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / gamma-aminobutyric acid secretion / positive regulation of interleukin-1 alpha production / negative regulation of cell volume / plasma membrane organization / positive regulation of gamma-aminobutyric acid secretion / pore complex assembly / collagen metabolic process / : / response to fluid shear stress / positive regulation of prostaglandin secretion / T cell apoptotic process / ceramide biosynthetic process / bleb assembly / mitochondrial depolarization / vesicle budding from membrane / positive regulation of T cell apoptotic process / prostaglandin secretion / glutamate secretion / cellular response to dsRNA / positive regulation of glutamate secretion / negative regulation of bone resorption / skeletal system morphogenesis / positive regulation of macrophage cytokine production / phospholipid translocation / positive regulation of mitochondrial depolarization / negative regulation of MAPK cascade / response to ATP / response to zinc ion / synaptic vesicle exocytosis / T cell homeostasis / membrane protein ectodomain proteolysis / protein secretion / positive regulation of bone mineralization / T cell proliferation / response to electrical stimulus / response to mechanical stimulus / extrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / sensory perception of pain / reactive oxygen species metabolic process / mitochondrion organization / positive regulation of interleukin-1 beta production / positive regulation of protein secretion / lipopolysaccharide binding / protein catabolic process / neuromuscular junction / cell morphogenesis / T cell mediated cytotoxicity / protein processing / positive regulation of T cell mediated cytotoxicity / response to calcium ion / positive regulation of interleukin-6 production / MAPK cascade / cell-cell junction / presynapse / postsynapse / response to lipopolysaccharide / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / response to xenobiotic stimulus / inflammatory response / positive regulation of protein phosphorylation / external side of plasma membrane / neuronal cell body / mitochondrion / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Ailuropoda melanoleuca (giant panda) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.903 Å | |||||||||
Authors | Karasawa, A. / Kawate, T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2016 Title: Structural basis for subtype-specific inhibition of the P2X7 receptor. Authors: Karasawa, A. / Kawate, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u2h.cif.gz | 128.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u2h.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 5u2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/5u2h ftp://data.pdbj.org/pub/pdb/validation_reports/u2/5u2h | HTTPS FTP |
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-Related structure data
Related structure data | 5u1lC 5u1uC 5u1vC 5u1wC 5u1xC 5u1yC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38716.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The N- and C-termini, and several other loop regions are disordered and the electron density was not well-defined. Source: (gene. exp.) Ailuropoda melanoleuca (giant panda) / Gene: P2RX7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G1M6C4 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Sugar | ChemComp-NAG / | #5: Chemical | ChemComp-ATP / | |
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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: 5.06 Å3/Da / Density % sol: 75.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 33% PEG 400, 100 mM MES (pH 6.5), 100 mM NaCl, 5% Glycerol, and 1 mM A804598 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 14, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3.9→48.39 Å / Num. obs: 14545 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 157.97 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.039 / Rrim(I) all: 0.122 / Net I/σ(I): 15.4 / Num. measured all: 145035 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A804598 bound P2X7 Resolution: 3.903→48.387 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.69 / 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: 3.903→48.387 Å
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Refine LS restraints |
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LS refinement shell |
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