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- PDB-8v4s: Cryo-EM structure of the rat P2X7 receptor in the apo closed stat... -
+Open data
-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 | |||||||||
Components | P2X purinoceptor 7 | |||||||||
Keywords | MEMBRANE PROTEIN / Ion Channel / Ligand-gate Ion Channel / P2X Receptor / Allosteric Antagonist / High-Affinity Agonist | |||||||||
Function / homology | Function and homology information 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 / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / lymphocyte apoptotic process / purinergic nucleotide receptor signaling pathway / positive regulation of monoatomic ion transmembrane transport / gamma-aminobutyric acid secretion / pore complex assembly / positive regulation of interleukin-1 alpha production / plasma membrane organization / positive regulation of gamma-aminobutyric acid secretion / negative regulation of cell volume / bleb / collagen metabolic process / plasma membrane phospholipid scrambling / ATP export / response to fluid shear stress / T cell apoptotic process / positive regulation of prostaglandin secretion / bleb assembly / mitochondrial depolarization / vesicle budding from membrane / ceramide biosynthetic process / positive regulation of T cell apoptotic process / programmed cell death / prostaglandin secretion / positive regulation of ossification / cellular response to dsRNA / cell volume homeostasis / glutamate secretion / positive regulation of glutamate secretion / negative regulation of bone resorption / skeletal system morphogenesis / phospholipid translocation / positive regulation of macrophage cytokine production / response to ATP / response to zinc ion / positive regulation of mitochondrial depolarization / positive regulation of calcium ion transport into cytosol / T cell homeostasis / synaptic vesicle exocytosis / monoatomic cation transport / membrane depolarization / membrane protein ectodomain proteolysis / : / protein secretion / negative regulation of MAPK cascade / neuronal action potential / positive regulation of bone mineralization / response to electrical stimulus / response to mechanical stimulus / regulation of sodium ion transport / T cell proliferation / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / sensory perception of pain / protein serine/threonine kinase activator activity / reactive oxygen species metabolic process / positive regulation of glycolytic process / positive regulation of interleukin-1 beta production / apoptotic signaling pathway / mitochondrion organization / positive regulation of protein secretion / establishment of localization in cell / response to bacterium / lipopolysaccharide binding / protein catabolic process / neuromuscular junction / T cell mediated cytotoxicity / terminal bouton / cell morphogenesis / : / protein processing / calcium ion transmembrane transport / response to calcium ion / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / calcium ion transport / MAPK cascade / cell-cell junction / nuclear envelope / channel activity / signaling receptor activity / scaffold protein binding / gene expression / response to lipopolysaccharide / positive regulation of MAPK cascade / cell surface receptor signaling pathway / postsynapse / defense response to Gram-positive bacterium Similarity search - Function | |||||||||
Biological species | Rattus (rat) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||
Authors | Oken, A.C. / Lisi, N.E. / Krishnamurthy, I. / McCarthy, A.E. / Godsey, M.H. / Glasfeld, A. / Mansoor, S.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: High-affinity agonism at the P2X receptor is mediated by three residues outside the orthosteric pocket. Authors: Adam C Oken / Nicolas E Lisi / Ipsita Krishnamurthy / Alanna E McCarthy / Michael H Godsey / Arthur Glasfeld / Steven E Mansoor / Abstract: P2X receptors are trimeric ATP-gated ion channels that activate diverse signaling cascades. Due to its role in apoptotic pathways, selective activation of P2X is a potential experimental tool and ...P2X receptors are trimeric ATP-gated ion channels that activate diverse signaling cascades. Due to its role in apoptotic pathways, selective activation of P2X is a potential experimental tool and therapeutic approach in cancer biology. However, mechanisms of high-affinity P2X activation have not been defined. We report high-resolution cryo-EM structures of wild-type rat P2X bound to the high-affinity agonist BzATP as well as significantly improved apo receptor structures in the presence and absence of sodium. Apo structures define molecular details of pore architecture and reveal how a partially hydrated Na ion interacts with the conductance pathway in the closed state. Structural, electrophysiological, and direct binding data of BzATP reveal that three residues just outside the orthosteric ATP-binding site are responsible for its high-affinity agonism. This work provides insights into high-affinity agonism for any P2X receptor and lays the groundwork for development of subtype-specific agonists applicable to cancer therapeutics. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v4s.cif.gz | 349.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v4s.ent.gz | 283.4 KB | Display | PDB format |
PDBx/mmJSON format | 8v4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/8v4s ftp://data.pdbj.org/pub/pdb/validation_reports/v4/8v4s | HTTPS FTP |
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-Related structure data
Related structure data | 42976MC 8tr5C 8trjC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein / Sugars , 2 types, 12 molecules ABC
#1: Protein | Mass: 68472.461 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus (rat) / Gene: P2rx7 / Cell line (production host): HEK293 GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q64663 |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 255 molecules
#2: Chemical | |
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#3: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-PLM / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Membrane protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Rattus (rat) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 GNTI- |
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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 |
-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 |