6U9V | pdb_00006u9v

Cryo electron microscopy structure of the ATP-gated rat P2X7 ion channel in the apo, closed state

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	tRNA-synt_1e	e6u9vA01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: tRNA-synt_1e	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00864	ATP P2X receptor (P2X_receptor)	ATP P2X receptor	-	Family
A, B, C	PF20478	P2X purinoreceptor 7 intracellular domain (P2RX7_C)	P2X purinoreceptor 7 intracellular domain	This entry represents the intracellular domain found at the the C-terminus of P2X purinoreceptor 7 protein.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	P2X purinoceptor 7	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity protein binding signaling receptor binding lipid binding lipopolysaccharide binding scaffold protein binding cation binding magnesium ion binding metal ion binding monoatomic cation transmembrane transporter activity monoatomic ion channel activity sodium channel activity sodium ion transmembrane transporter activity monoatomic cation channel activity passive transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity transition metal ion binding copper ion binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity purinergic nucleotide receptor activity nucleotide receptor activity identical protein binding extracellularly ATP-gated monoatomic cation channel activity gated channel activity ATP-gated ion channel activity excitatory extracellular ligand-gated monoatomic ion channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity ligand-gated monoatomic cation channel activity potassium ion transmembrane transporter activity potassium channel activity zinc ion binding	response to stimulus response to chemical response to xenobiotic stimulus regulation of localization regulation of biological process regulation of cellular process transport regulation of transport regulation of monoatomic ion transport monoatomic ion transmembrane transport biological regulation positive regulation of biological process regulation of monoatomic ion transmembrane transport establishment of localization response to stimulus response to chemical response to xenobiotic stimulus regulation of localization regulation of biological process regulation of cellular process transport regulation of transport regulation of monoatomic ion transport monoatomic ion transmembrane transport biological regulation positive regulation of biological process regulation of monoatomic ion transmembrane transport establishment of localization transmembrane transport localization regulation of transmembrane transport positive regulation of transport positive regulation of monoatomic ion transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport cellular process positive regulation of cellular process catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process multicellular organismal process regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process multicellular organism development positive regulation of biomineral tissue development ossification anatomical structure development biomineral tissue development regulation of multicellular organismal process developmental process regulation of multicellular organismal development bone mineralization animal organ development tissue development positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification calcium ion transport metal ion transport monoatomic cation transmembrane transport monoatomic cation transport calcium ion transmembrane transport response to metal ion response to zinc ion anatomical structure morphogenesis cell morphogenesis skeletal system development skeletal system morphogenesis animal organ morphogenesis system development regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport cellular localization regulation of calcium ion transport into cytosol regulation of calcium ion transmembrane transport positive regulation of calcium ion transmembrane transport regulation of biological quality regulation of metal ion transport calcium ion transmembrane import into cytosol positive regulation of cytosolic calcium ion concentration positive regulation of calcium ion transport into cytosol regulation of cellular localization regulation of monoatomic cation transmembrane transport calcium ion transport into cytosol regulation of immune effector process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of myeloid leukocyte cytokine production involved in immune response cytokine production regulation of cytokine production regulation of immune system process positive regulation of immune effector process positive regulation of macromolecule metabolic process myeloid leukocyte cytokine production cytokine production involved in immune response positive regulation of immune system process production of molecular mediator of immune response regulation of biosynthetic process regulation of cytokine production involved in immune response immune response regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of gene expression biosynthetic process regulation of macrophage cytokine production positive regulation of gene expression immune system process positive regulation of cytokine production involved in immune response positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of macrophage cytokine production macrophage cytokine production regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process positive regulation of programmed cell death positive regulation of lymphocyte apoptotic process leukocyte apoptotic process regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process positive regulation of T cell apoptotic process lymphocyte apoptotic process regulation of T cell apoptotic process T cell apoptotic process apoptotic process programmed cell death positive regulation of leukocyte apoptotic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process regulation of generation of precursor metabolites and energy positive regulation of phosphate metabolic process nucleoside phosphate catabolic process organic acid metabolic process regulation of primary metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process regulation of purine nucleotide catabolic process positive regulation of nucleotide catabolic process regulation of small molecule metabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process positive regulation of phosphorus metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process positive regulation of ATP metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of phosphorus metabolic process regulation of nucleotide catabolic process positive regulation of carbohydrate metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process energy derivation by oxidation of organic compounds positive regulation of nucleotide metabolic process positive regulation of purine nucleotide catabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process carbohydrate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process positive regulation of glycolytic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy regulation of catabolic process regulation of glycolytic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of catabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process positive regulation of small molecule metabolic process purine ribonucleoside diphosphate catabolic process regulation of cellular component organization positive regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly positive regulation of bleb assembly cellular component biogenesis cellular component organization cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of bleb assembly regulation of plasma membrane bounded cell projection assembly bleb assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly establishment of localization in cell cellular response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction regulation of response to stimulus MAPK cascade regulation of cell communication negative regulation of MAPK cascade positive regulation of cell communication positive regulation of response to biotic stimulus positive regulation of signal transduction pattern recognition receptor signaling pathway regulation of NLRP3 inflammasome complex assembly positive regulation of NLRP3 inflammasome complex assembly response to biotic stimulus immune response-activating signaling pathway inflammasome-mediated signaling pathway positive regulation of immune response canonical inflammasome complex assembly innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway response to other organism regulation of innate immune response response to external stimulus positive regulation of intracellular signal transduction positive regulation of inflammasome-mediated signaling pathway regulation of inflammasome-mediated signaling pathway defense response to other organism regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly positive regulation of defense response activation of innate immune response regulation of immune response inflammatory response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway regulation of cytoplasmic pattern recognition receptor signaling pathway positive regulation of response to stimulus regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response protein-containing complex assembly response to external biotic stimulus positive regulation of innate immune response defense response protein-containing complex organization defense response to symbiont positive regulation of signaling cell surface receptor signaling pathway establishment of organelle localization regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport vesicle-mediated transport in synapse secretory granule localization calcium ion-regulated exocytosis of neurotransmitter trans-synaptic signaling neurotransmitter secretion regulation of synaptic vesicle exocytosis dense core granule exocytosis neurotransmitter transport presynaptic modulation of chemical synaptic transmission regulation of secretion signal release from synapse exocytosis regulation of trans-synaptic signaling regulation of presynaptic dense core granule exocytosis regulation of dense core granule exocytosis regulation of calcium ion-dependent exocytosis of neurotransmitter regulation of calcium ion-dependent exocytosis modulation of chemical synaptic transmission regulation of regulated secretory pathway synaptic signaling dense core granule localization secretion by cell regulation of secretion by cell organelle localization signal release presynaptic dense core vesicle exocytosis calcium-ion regulated exocytosis vesicle localization secretion establishment of vesicle localization regulation of neurotransmitter transport neuronal dense core vesicle exocytosis export from cell cell-cell signaling regulation of vesicle-mediated transport chemical synaptic transmission regulation of neurotransmitter secretion regulation of exocytosis anterograde trans-synaptic signaling collagen metabolic process release of sequestered calcium ion into cytosol intercellular transport apoptotic signaling pathway nitrogen compound transport positive regulation of amine transport positive regulation of secretion gamma-aminobutyric acid transport regulation of amino acid transport organic anion transport gamma-aminobutyric acid secretion carboxylic acid transport regulation of gamma-aminobutyric acid secretion positive regulation of gamma-aminobutyric acid secretion acid secretion positive regulation of organic acid transport organic acid transport amino acid transport amine transport positive regulation of amino acid transport regulation of organic acid transport regulation of amine transport regulation of prostaglandin secretion monocarboxylic acid transport fatty acid transport prostaglandin secretion positive regulation of icosanoid secretion lipid transport regulation of fatty acid transport positive regulation of lipid transport lipid export from cell prostaglandin transport regulation of lipid transport positive regulation of secretion by cell icosanoid transport regulation of icosanoid secretion positive regulation of prostaglandin secretion icosanoid secretion lipid localization positive regulation of lipid localization regulation of lipid localization macromolecule localization positive regulation of fatty acid transport system process sensory perception nervous system process sensory perception of pain regulation of glutamate secretion glutamate secretion positive regulation of glutamate secretion acidic amino acid transport dicarboxylic acid transport regulation of sodium ion transport sodium ion transport response to lipid response to oxygen-containing compound response to lipopolysaccharide response to bacterium response to molecule of bacterial origin proteolysis membrane protein proteolysis membrane protein ectodomain proteolysis cellular response to nitrogen compound cellular response to chemical stimulus cellular response to dsRNA response to dsRNA response to nitrogen compound multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells membrane organization plasma membrane organization endomembrane system organization interleukin-1 production positive regulation of interleukin-1 alpha production positive regulation of interleukin-1 production regulation of interleukin-1 production regulation of interleukin-1 alpha production interleukin-1 alpha production response to calcium ion import into cell vacuole organization organelle assembly lytic vacuole organization phagosome maturation vesicle organization lysosome organization organelle organization phagolysosome assembly phagocytosis endocytosis regulation of mitochondrial depolarization positive regulation of membrane depolarization positive regulation of mitochondrial depolarization mitochondrial depolarization regulation of membrane depolarization regulation of mitochondrial membrane potential membrane depolarization regulation of membrane potential extrinsic apoptotic signaling pathway pore complex assembly phospholipid translocation phospholipid transport lipid translocation regulation of membrane lipid distribution plasma membrane phospholipid scrambling organophosphate ester transport regulation of cellular component size cell volume homeostasis negative regulation of cell volume cellular homeostasis regulation of cell size regulation of anatomical structure size regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production interleukin-1 beta production response to electrical stimulus response to abiotic stimulus vesicle budding from membrane cell population proliferation cell activation lymphocyte activation leukocyte proliferation leukocyte activation mononuclear cell proliferation T cell activation lymphocyte proliferation T cell proliferation negative regulation of tissue remodeling negative regulation of bone remodeling regulation of bone remodeling regulation of tissue remodeling regulation of bone resorption bone resorption negative regulation of bone resorption tissue remodeling bone remodeling negative regulation of multicellular organismal process protein trimerization protein homotrimerization protein complex oligomerization protein homooligomerization adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of leukocyte mediated cytotoxicity leukocyte mediated immunity positive regulation of adaptive immune response regulation of T cell mediated immunity T cell mediated cytotoxicity positive regulation of T cell mediated cytotoxicity regulation of adaptive immune response regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity adaptive immune response regulation of leukocyte mediated immunity regulation of T cell mediated cytotoxicity regulation of lymphocyte mediated immunity positive regulation of T cell mediated immunity regulation of cell killing positive regulation of cell killing cell killing ATP transport nucleotide transport purine ribonucleotide transport carbohydrate derivative transport purine nucleotide transport adenine nucleotide transport ATP export nucleobase-containing compound transport purinergic nucleotide receptor signaling pathway response to fluid shear stress phospholipid transfer to membrane reactive oxygen species metabolic process NAD transport interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production ceramide metabolic process sphingolipid biosynthetic process ceramide biosynthetic process lipid biosynthetic process sphingolipid metabolic process lipid metabolic process leukocyte homeostasis T cell homeostasis lymphocyte homeostasis protein maturation protein processing positive regulation of organelle organization regulation of cytoskeleton organization positive regulation of cytoskeleton organization regulation of organelle organization cytoskeleton organization action potential transmission of nerve impulse neuronal action potential positive regulation of MAPK cascade establishment of protein localization regulation of protein localization positive regulation of establishment of protein localization protein localization to extracellular region positive regulation of protein transport intracellular protein localization regulation of establishment of protein localization establishment of protein localization to extracellular region regulation of protein transport protein secretion positive regulation of protein secretion regulation of protein secretion protein transport positive regulation of protein localization response to mechanical stimulus response to organophosphorus response to ATP response to purine-containing compound mitochondrion organization defense response to Gram-positive bacterium defense response to bacterium	cell-cell junction cellular anatomical structure anchoring junction cell junction membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system neuromuscular junction cell-cell junction cellular anatomical structure anchoring junction cell junction membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system neuromuscular junction synapse cell periphery plasma membrane membrane protein-containing complex cell surface external side of plasma membrane side of membrane cytoplasm somatodendritic compartment cell body neuronal cell body postsynapse axon neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon terminal bouton neuron projection terminus bleb

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR059116	ATP P2X receptor-like	Family
A, B, C	IPR001429	P2X purinoreceptor	Family
A, B, C	IPR046815	P2X purinoreceptor 7, intracellular domain	Domain
A, B, C	IPR027309	P2X purinoreceptor extracellular domain superfamily	Homologous Superfamily
A, B, C	IPR053792	ATP P2X receptor, conserved site	Conserved Site
A, B, C	IPR003050	P2X7 purinoceptor	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Transmembrane	Alpha-helical polytopic	ENaC/P2X	ATP-gated cation channel

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	ATP-gated P2X₇ ion channel, apo protein in closed state

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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