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Yorodumi- PDB-6u9w: Cryo electron microscopy structure of the ATP-gated rat P2X7 ion ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u9w | |||||||||
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Title | Cryo electron microscopy structure of the ATP-gated rat P2X7 ion channel in the ATP-bound, open state | |||||||||
Components | P2X purinoceptor 7 | |||||||||
Keywords | MEMBRANE PROTEIN / Ion Channel Apoptosis | |||||||||
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 / 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 / ATP export / positive regulation of interleukin-1 alpha production / negative regulation of cell volume / cell death / plasma membrane organization / positive regulation of gamma-aminobutyric acid secretion / pore complex assembly / collagen metabolic process / bleb / : / plasma membrane phospholipid scrambling / 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 / programmed cell death / glutamate secretion / positive regulation of ossification / cellular response to dsRNA / cell volume homeostasis / positive regulation of glutamate secretion / negative regulation of bone resorption / skeletal system morphogenesis / positive regulation of macrophage cytokine production / phospholipid translocation / nuclear inner membrane / channel activity / positive regulation of mitochondrial depolarization / negative regulation of MAPK cascade / positive regulation of calcium ion transport into cytosol / response to ATP / response to zinc ion / positive regulation of catalytic activity / synaptic vesicle exocytosis / T cell homeostasis / membrane depolarization / monoatomic cation transport / membrane protein ectodomain proteolysis / cellular response to organic cyclic compound / protein secretion / neuronal action potential / positive regulation of bone mineralization / T cell proliferation / response to electrical stimulus / response to mechanical stimulus / extrinsic apoptotic signaling pathway / regulation of sodium ion transport / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / sensory perception of pain / reactive oxygen species metabolic process / positive regulation of glycolytic process / mitochondrion organization / protein serine/threonine kinase activator activity / : / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / establishment of localization in cell / positive regulation of protein secretion / apoptotic signaling pathway / lipopolysaccharide binding / response to bacterium / positive regulation of MAP kinase activity / protein catabolic process / neuromuscular junction / cell morphogenesis / response to organic cyclic compound / terminal bouton / T cell mediated cytotoxicity / protein processing / 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 / presynapse / signaling receptor activity Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Mansoor, S.E. / McCarthy, A.E. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2019 Title: Full-Length P2X Structures Reveal How Palmitoylation Prevents Channel Desensitization. Authors: Alanna E McCarthy / Craig Yoshioka / Steven E Mansoor / Abstract: P2X receptors are trimeric, non-selective cation channels activated by extracellular ATP. The P2X receptor subtype is a pharmacological target because of involvement in apoptotic, inflammatory, and ...P2X receptors are trimeric, non-selective cation channels activated by extracellular ATP. The P2X receptor subtype is a pharmacological target because of involvement in apoptotic, inflammatory, and tumor progression pathways. It is the most structurally and functionally distinct P2X subtype, containing a unique cytoplasmic domain critical for the receptor to initiate apoptosis and not undergo desensitization. However, lack of structural information about the cytoplasmic domain has hindered understanding of the molecular mechanisms underlying these processes. We report cryoelectron microscopy structures of full-length rat P2X receptor in apo and ATP-bound states. These structures reveal how one cytoplasmic element, the C-cys anchor, prevents desensitization by anchoring the pore-lining helix to the membrane with palmitoyl groups. They show a second cytoplasmic element with a unique fold, the cytoplasmic ballast, which unexpectedly contains a zinc ion complex and a guanosine nucleotide binding site. Our structures provide first insights into the architecture and function of a P2X receptor cytoplasmic domain. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6u9w.cif.gz | 566.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u9w.ent.gz | 484.3 KB | Display | PDB format |
PDBx/mmJSON format | 6u9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/6u9w ftp://data.pdbj.org/pub/pdb/validation_reports/u9/6u9w | HTTPS FTP |
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-Related structure data
Related structure data | 20703MC 6u9vC M: map data used to model this data 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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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 69904.016 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: P2rx7 / Production host: Homo sapiens (human) / References: UniProt: Q64663 |
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-Sugars , 2 types, 12 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 27 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | #6: Chemical | #7: Chemical | ChemComp-PLM / #8: Chemical | |
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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 |
-Sample preparation
Component | Name: P2X7 receptor ion channel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | 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 FIELDBright-field microscopy |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109570 / Symmetry type: POINT |