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Yorodumi- PDB-8tra: Cryo-EM structure of the rat P2X7 receptor in complex with the al... -
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-Basic information
Entry | Database: PDB / ID: 8tra | |||||||||
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Title | Cryo-EM structure of the rat P2X7 receptor in complex with the allosteric antagonist GSK1482160 | |||||||||
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 Platelet homeostasis / The NLRP3 inflammasome / regulation of presynaptic dense core granule exocytosis / 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 ...Platelet homeostasis / The NLRP3 inflammasome / regulation of presynaptic dense core granule exocytosis / 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 signaling pathway / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / lymphocyte apoptotic process / positive regulation of monoatomic ion transmembrane transport / gamma-aminobutyric acid secretion / pore complex assembly / positive regulation of interleukin-1 alpha production / plasma membrane organization / negative regulation of cell volume / positive regulation of gamma-aminobutyric acid secretion / ATP export / bleb / collagen metabolic process / plasma membrane phospholipid scrambling / response to fluid shear stress / T cell apoptotic process / positive regulation of prostaglandin secretion / bleb assembly / positive regulation of T cell apoptotic process / mitochondrial depolarization / vesicle budding from membrane / prostaglandin secretion / ceramide biosynthetic process / cellular response to dsRNA / programmed cell death / positive regulation of glutamate secretion / positive regulation of ossification / cell volume homeostasis / glutamate secretion / skeletal system morphogenesis / negative regulation of bone resorption / phospholipid translocation / positive regulation of macrophage cytokine production / positive regulation of calcium ion transport into cytosol / response to ATP / positive regulation of mitochondrial depolarization / response to zinc ion / T cell homeostasis / cellular response to organic cyclic compound / monoatomic cation transport / synaptic vesicle exocytosis / membrane depolarization / membrane protein ectodomain proteolysis / neuronal action potential / protein secretion / negative regulation of MAPK cascade / response to electrical stimulus / positive regulation of bone mineralization / response to mechanical stimulus / T cell proliferation / regulation of sodium ion transport / 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 / positive regulation of interleukin-1 beta production / mitochondrion organization / establishment of localization in cell / positive regulation of protein secretion / apoptotic signaling pathway / calcium ion transmembrane transport / lipopolysaccharide binding / response to bacterium / neuromuscular junction / cell morphogenesis / protein catabolic process / response to organic cyclic compound / terminal bouton / T cell mediated cytotoxicity / protein processing / positive regulation of interleukin-6 production / response to calcium ion / channel activity / positive regulation of T cell mediated cytotoxicity / calcium ion transport / MAPK cascade / cell-cell junction / nuclear envelope / signaling receptor activity / gene expression / scaffold protein binding / postsynapse / response to lipopolysaccharide / positive regulation of MAPK cascade / cell surface receptor signaling pathway / defense response to Gram-positive bacterium Similarity search - Function | |||||||||
Biological species | Rattus (rat) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.41 Å | |||||||||
Authors | Oken, A.C. / Ditter, I.A. / Lisi, N.E. / Krishnamurthy, I. / McCarthy, A.E. / Godsey, M.H. / Mansoor, S.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Adv / Year: 2024 Title: P2X receptors exhibit at least three modes of allosteric antagonism. Authors: Adam C Oken / Ismayn A Ditter / Nicolas E Lisi / Ipsita Krishnamurthy / Michael H Godsey / Steven E Mansoor / Abstract: P2X receptors are trimeric ion channels activated by adenosine triphosphate (ATP) that contribute to pathophysiological processes ranging from asthma to neuropathic pain and neurodegeneration. A ...P2X receptors are trimeric ion channels activated by adenosine triphosphate (ATP) that contribute to pathophysiological processes ranging from asthma to neuropathic pain and neurodegeneration. A number of small-molecule antagonists have been identified for these important pharmaceutical targets. However, the molecular pharmacology of P2X receptors is poorly understood because of the chemically disparate nature of antagonists and their differential actions on the seven constituent subtypes. Here, we report high-resolution cryo-electron microscopy structures of the homomeric rat P2X receptor bound to five previously known small-molecule allosteric antagonists and a sixth antagonist that we identify. Our structural, biophysical, and electrophysiological data define the molecular determinants of allosteric antagonism in this pharmacologically relevant receptor, revealing three distinct classes of antagonists that we call shallow, deep, and starfish. Starfish binders, exemplified by the previously unidentified antagonist methyl blue, represent a unique class of inhibitors with distinct functional properties that could be exploited to develop potent P2X ligands with substantial clinical impact. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tra.cif.gz | 567.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tra.ent.gz | 476.3 KB | Display | PDB format |
PDBx/mmJSON format | 8tra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tra_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8tra_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8tra_validation.xml.gz | 72.8 KB | Display | |
Data in CIF | 8tra_validation.cif.gz | 105.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/8tra ftp://data.pdbj.org/pub/pdb/validation_reports/tr/8tra | HTTPS FTP |
-Related structure data
Related structure data | 41575MC 8tr6C 8tr7C 8tr8C 8trbC 8trkC M: map data used to model this data C: citing same article (ref.) |
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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, 9 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: Rattus (rat) / References: UniProt: Q64663 #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 224 molecules
#2: Chemical | Mass: 334.721 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H14ClF3N2O2 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-PLM / #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
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-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: 1700 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8208 |
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: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 394113 / Symmetry type: POINT | ||||||||||||||||||||||||
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