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- PDB-8v4s: Cryo-EM structure of the rat P2X7 receptor in the apo closed stat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8v4s | |||||||||
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Title | Cryo-EM structure of the rat P2X7 receptor in the apo closed state purified in the absence of sodium | |||||||||
![]() | P2X purinoceptor 7 | |||||||||
![]() | MEMBRANE PROTEIN / Ion Channel / Ligand-gate Ion Channel / P2X Receptor / Allosteric Antagonist / High-Affinity Agonist | |||||||||
Function / homology | ![]() The NLRP3 inflammasome / regulation of presynaptic dense core granule exocytosis / Platelet homeostasis / positive regulation of lymphocyte apoptotic process / positive regulation of bleb assembly / NAD transport / phagolysosome assembly / Elevation of cytosolic Ca2+ levels / phospholipid transfer to membrane / positive regulation of cytoskeleton organization ...The NLRP3 inflammasome / regulation of presynaptic dense core granule exocytosis / Platelet homeostasis / positive regulation of lymphocyte apoptotic process / positive regulation of bleb assembly / NAD transport / phagolysosome assembly / Elevation of cytosolic Ca2+ levels / phospholipid transfer to membrane / positive regulation of cytoskeleton organization / organic cation transport / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / lymphocyte apoptotic process / purinergic nucleotide receptor signaling pathway / gamma-aminobutyric acid secretion / positive regulation of monoatomic ion transmembrane transport / pore complex assembly / ATP export / positive regulation of interleukin-1 alpha production / negative regulation of cell volume / plasma membrane organization / cell death / positive regulation of gamma-aminobutyric acid secretion / : / collagen metabolic process / bleb / plasma membrane phospholipid scrambling / response to fluid shear stress / positive regulation of prostaglandin secretion / T cell apoptotic process / bleb assembly / ceramide biosynthetic process / mitochondrial depolarization / vesicle budding from membrane / programmed cell death / positive regulation of T cell apoptotic process / prostaglandin secretion / positive regulation of ossification / cellular response to dsRNA / glutamate secretion / cell volume homeostasis / positive regulation of glutamate secretion / negative regulation of bone resorption / positive regulation of macrophage cytokine production / skeletal system morphogenesis / phospholipid translocation / channel activity / nuclear inner membrane / negative regulation of MAPK cascade / response to ATP / positive regulation of catalytic activity / positive regulation of calcium ion transport into cytosol / positive regulation of mitochondrial depolarization / response to zinc ion / T cell homeostasis / synaptic vesicle exocytosis / monoatomic cation transport / membrane depolarization / membrane protein ectodomain proteolysis / cellular response to organic cyclic compound / neuronal action potential / protein secretion / positive regulation of bone mineralization / T cell proliferation / response to electrical stimulus / regulation of sodium ion transport / 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 / positive regulation of glycolytic process / reactive oxygen species metabolic process / protein serine/threonine kinase activator activity / : / mitochondrion organization / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / establishment of localization in cell / positive regulation of protein secretion / lipopolysaccharide binding / apoptotic signaling pathway / response to bacterium / positive regulation of MAP kinase activity / neuromuscular junction / protein catabolic process / cell morphogenesis / terminal bouton / response to organic cyclic compound / T cell mediated cytotoxicity / protein processing / response to calcium ion / positive regulation of interleukin-6 production / positive regulation of T cell mediated cytotoxicity / calcium ion transport / MAPK cascade / cell-cell junction / presynapse / signaling receptor activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||
![]() | Oken, A.C. / Lisi, N.E. / Krishnamurthy, I. / McCarthy, A.E. / Godsey, M.H. / Glasfeld, A. / Mansoor, S.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: High-affinity agonism at the P2X7 receptor is mediated by three residues outside the orthosteric pocket Authors: Oken, A.C. / Lisi, N.E. / Krishnamurthy, I. / McCarthy, A.E. / Godsey, M.H. / Glasfeld, A. / Mansoor, S.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 349.2 KB | Display | ![]() |
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PDB format | ![]() | 283.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 42976 ![]() 41570 ![]() 41581 ![]() 8tr5C ![]() 8trjC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein / Sugars , 2 types, 12 molecules ABC![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 68472.461 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 255 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-PLM / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Membrane protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 11353 |
EM imaging optics | Energyfilter slit width: 20 eV |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 273076 / Symmetry type: POINT |