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- EMDB-41570: Cryo-EM structure of the rat P2X7 receptor in the apo closed state -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of the rat P2X7 receptor in the apo closed state | |||||||||
![]() | Sharpened volume of the apo closed state of | |||||||||
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![]() | 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 | single particle reconstruction / cryo EM / Resolution: 2.53 Å | |||||||||
![]() | Oken AC / Lisi NE / Krishnamurthy I / McCarthy AE / Godsey MH / Glasfeld A / Mansoor SE | |||||||||
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 AC / Lisi NE / Krishnamurthy I / McCarthy AE / Godsey MH / Glasfeld A / Mansoor SE | |||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
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Header (meta data) | ![]() | |||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tr5MC ![]() 41581 ![]() 42976 ![]() 8trjC ![]() 8v4sC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Sharpened volume of the apo closed state of | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.648 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Membrane protein
Entire | Name: Membrane protein |
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Components |
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-Supramolecule #1: Membrane protein
Supramolecule | Name: Membrane protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: P2X purinoceptor 7
Macromolecule | Name: P2X purinoceptor 7 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 68.472461 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MPACCSWNDV FQYETNKVTR IQSVNYGTIK WILHMTVFSY VSFALMSDKL YQRKEPLISS VHTKVKGVAE VTENVTEGGV TKLVHGIFD TADYTLPLQG NSFFVMTNYL KSEGQEQKLC PEYPSRGKQC HSDQGCIKGW MDPQSKGIQT GRCIPYDQKR K TCEIFAWC ...String: MPACCSWNDV FQYETNKVTR IQSVNYGTIK WILHMTVFSY VSFALMSDKL YQRKEPLISS VHTKVKGVAE VTENVTEGGV TKLVHGIFD TADYTLPLQG NSFFVMTNYL KSEGQEQKLC PEYPSRGKQC HSDQGCIKGW MDPQSKGIQT GRCIPYDQKR K TCEIFAWC PAEEGKEAPR PALLRSAENF TVLIKNNIDF PGHNYTTRNI LPGMNISCTF HKTWNPQCPI FRLGDIFQEI GE NFTEVAV QGGIMGIEIY WDCNLDSWSH RCQPKYSFRR LDDKYTNESL FPGYNFRYAK YYKENGMEKR TLIKAFGVRF DIL VFGTGG KFDIIQLVVY IGSTLSYFGL ATVCIDLIIN TYASTCCRSR VYPSCKCCEP CAVNEYYYRK KCEPIVEPKP TLKY VSFVD EPHIWMVDQQ LLGKSLQDVK GQEVPRPQTD FLELSRLSLS LHHSPPIPGQ PEEMQLLQIE AVPRSRDSPD WCQCG NCLP SQLPENRRAL EELCCRRKPG QCITTSELFS KIVLSREALQ LLLLYQEPLL ALEGEAINSK LRHCAYRSYA TWRFVS QDM ADFAILPSCC RWKIRKEFPK TQGQYSGFKY PY UniProtKB: P2X purinoceptor 7 |
-Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 3 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ![]() ChemComp-GDP: |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #5: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 15 / Formula: PLM |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-Macromolecule #6: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 6 / Number of copies: 1 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 204 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 8580 / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 263974 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |