3JAV

Structure of full-length IP3R1 channel in the apo-state determined by single particle cryo-EM

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
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	PF02815	e3javA2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF02815	ECOD (1.6)
A	PF08709	e3javA1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF08709	ECOD (1.6)
A	F_UNCLASSIFIED	e3javA7	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF01365	e3javA3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF01365	ECOD (1.6)
A	PF08454	e3javA4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF08454	ECOD (1.6)
A	PF00520	e3javA6	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520	ECOD (1.6)
B	PF02815	e3javB2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF02815	ECOD (1.6)
B	PF08709	e3javB5	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF08709	ECOD (1.6)
B	F_UNCLASSIFIED	e3javB7	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF01365	e3javB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF01365	ECOD (1.6)
B	PF08454	e3javB3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF08454	ECOD (1.6)
B	PF00520	e3javB6	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520	ECOD (1.6)
C	PF02815	e3javC2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF02815	ECOD (1.6)
C	PF08709	e3javC5	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF08709	ECOD (1.6)
C	F_UNCLASSIFIED	e3javC7	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF01365	e3javC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF01365	ECOD (1.6)
C	PF08454	e3javC3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF08454	ECOD (1.6)
C	PF00520	e3javC6	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520	ECOD (1.6)
D	PF02815	e3javD2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF02815	ECOD (1.6)
D	PF08709	e3javD5	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF08709	ECOD (1.6)
D	F_UNCLASSIFIED	e3javD7	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF01365	e3javD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF01365	ECOD (1.6)
D	PF08454	e3javD3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF08454	ECOD (1.6)
D	PF00520	e3javD6	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08454	RyR and IP3R Homology associated (RIH_assoc)	RyR and IP3R Homology associated	-	Repeat
A, B, C, D	PF02815	MIR domain (MIR)	MIR domain	The MIR (protein mannosyltransferase, IP3R and RyR) domain is a domain that may have a ligand transferase function [1].	Domain
A, B, C, D	PF08709	Inositol 1,4,5-trisphosphate/ryanodine receptor (Ins145_P3_rec)	Inositol 1,4,5-trisphosphate/ryanodine receptor	This domain corresponds to the ligand binding region on inositol 1,4,5-trisphosphate receptor, and the N terminal region of the ryanodine receptor. Both receptors are involved in Ca2+ release. They can couple to the activation of neurotransmitter-ga ...	This domain corresponds to the ligand binding region on inositol 1,4,5-trisphosphate receptor, and the N terminal region of the ryanodine receptor. Both receptors are involved in Ca2+ release. They can couple to the activation of neurotransmitter-gated receptors and voltage-gated Ca2+ channels on the plasma membrane, thus allowing the endoplasmic reticulum discriminate between different types of neuronal activity [1].	Domain
A, B, C, D	PF01365	RIH domain (RYDR_ITPR)	RIH domain	-	Repeat
A, B, C, D	PF00520	Ion transport protein (Ion_trans)	Ion transport protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Inositol 1,4,5-trisphosphate receptor type 1	binding phospholipid binding lipid binding phosphatidylinositol binding protein phosphatase binding phosphatase binding protein binding enzyme binding protein-containing complex binding calcium channel activity monoatomic cation transmembrane transporter activity intracellularly ligand-gated monoatomic ion channel activity gated channel activity monoatomic ion channel activity binding phospholipid binding lipid binding phosphatidylinositol binding protein phosphatase binding phosphatase binding protein binding enzyme binding protein-containing complex binding calcium channel activity monoatomic cation transmembrane transporter activity intracellularly ligand-gated monoatomic ion channel activity gated channel activity monoatomic ion channel activity inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels intracellularly gated calcium channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity monoatomic cation channel activity passive transmembrane transporter activity calcium ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity channel activity ligand-gated calcium channel activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity inositol 1,4,5-trisphosphate-gated calcium channel activity transporter activity metal ion transmembrane transporter activity ligand-gated monoatomic cation channel activity transmembrane transporter activity molecular function inhibitor activity channel regulator activity transporter inhibitor activity calcium channel inhibitor activity ion channel inhibitor activity ion channel regulator activity molecular function regulator activity calcium channel regulator activity transporter regulator activity channel inhibitor activity identical protein binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein domain specific binding transmembrane transporter binding alcohol binding inositol 1,4,5 trisphosphate binding anion binding	inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis endoplasmic reticulum calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis response to decreased oxygen levels cellular response to stimulus inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis endoplasmic reticulum calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus cellular process regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death positive regulation of cellular process regulation of neuron projection development multicellular organismal process regulation of cellular component organization positive regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization calcium ion transport metal ion transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport anatomical structure morphogenesis cell morphogenesis signaling cell communication G protein-coupled receptor signaling pathway signal transduction ion channel modulating, G protein-coupled receptor signaling pathway phospholipase C-activating G protein-coupled receptor signaling pathway regulation of localization regulation of calcium ion transport positive regulation of calcium ion transport regulation of transport regulation of monoatomic ion transport positive regulation of transport positive regulation of monoatomic ion transport regulation of metal ion transport positive regulation of cytosolic calcium ion concentration regulation of biological quality voluntary musculoskeletal movement multicellular organismal movement musculoskeletal movement system process nervous system process neuromuscular process cellular response to nitrogen compound response to organic substance synaptic signaling phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway cellular response to acetylcholine response to oxygen-containing compound cell-cell signaling response to nitrogen compound acetylcholine receptor signaling pathway postsynaptic signal transduction cellular response to oxygen-containing compound G protein-coupled acetylcholine receptor signaling pathway response to acetylcholine negative regulation of programmed cell death negative regulation of biological process negative regulation of apoptotic process negative regulation of cellular process regulation of postsynaptic cytosolic calcium ion concentration regulation of cytosolic calcium ion concentration epithelial fluid transport transepithelial transport fluid transport gland development animal organ development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration intracellular signal transduction calcium-mediated signaling intracellular signaling cassette response to organonitrogen compound response to endogenous stimulus response to organophosphorus cellular response to organic cyclic compound response to purine-containing compound response to cAMP cellular response to endogenous stimulus cellular response to organonitrogen compound cellular response to cAMP cellular response to organic substance response to organic cyclic compound regulation of hepatocyte proliferation positive regulation of cell population proliferation gland morphogenesis animal organ morphogenesis epithelial cell proliferation liver morphogenesis cell population proliferation positive regulation of epithelial cell proliferation epithelial cell proliferation involved in liver morphogenesis hepatocyte proliferation regulation of cell population proliferation positive regulation of hepatocyte proliferation regulation of epithelial cell proliferation dendrite development cellular localization negative regulation of sequestering of calcium ion maintenance of location in cell regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol sequestering of calcium ion maintenance of location release of sequestered calcium ion into cytosol intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress apoptotic signaling pathway intrinsic apoptotic signaling pathway response to endoplasmic reticulum stress negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction negative regulation of cell communication regulation of intracellular signal transduction regulation of calcium-mediated signaling regulation of signaling negative regulation of response to stimulus negative regulation of calcium-mediated signaling negative regulation of signal transduction regulation of response to stimulus regulation of cell communication protein localization positive regulation of cell communication establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization cellular macromolecule localization positive regulation of insulin secretion regulation of peptide hormone secretion regulation of hormone levels organic substance transport positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion positive regulation of protein localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion secretion by cell regulation of secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion secretion regulation of peptide transport regulation of establishment of protein localization export from cell regulation of protein transport positive regulation of protein secretion peptide transport protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion positive regulation of signaling post-embryonic development ligand-gated ion channel signaling pathway	membrane cellular anatomical entity membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system platelet dense granule membrane intracellular vesicle cytoplasmic vesicle membrane membrane cellular anatomical entity membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system platelet dense granule membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle platelet dense granule secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection smooth endoplasmic reticulum membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum smooth endoplasmic reticulum endoplasmic reticulum membrane phosphatase complex protein-containing complex catalytic complex calcineurin complex protein serine/threonine phosphatase complex intracellular protein-containing complex perinuclear region of cytoplasm organelle inner membrane nuclear membrane nuclear inner membrane sarcoplasm sarcoplasmic reticulum cell body neuronal cell body postsynapse synapse cell junction transport vesicle transport vesicle membrane membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cell periphery plasma membrane plasma membrane region synaptic membrane presynapse GABA-ergic synapse postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse Schaffer collateral - CA1 synapse platelet dense tubular network

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036300	Mir domain superfamily	Homologous Superfamily
A, B, C, D	IPR000699	RIH domain	Domain
A, B, C, D	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B, C, D	IPR013662	RyR/IP3R Homology associated domain	Domain
A, B, C, D	IPR016093	MIR motif	Domain
A, B, C, D	IPR015925	Ryanodine/Inositol 1,4,5-trisphosphate receptor	Family
A, B, C, D	IPR035910	RyR/IP3 receptor binding core, RIH domain superfamily	Homologous Superfamily
A, B, C, D	IPR014821	Inositol 1,4,5-trisphosphate/ryanodine receptor	Domain
A, B, C, D	IPR000493	Inositol 1,4,5-trisphosphate receptor	Family
A, B, C, D	IPR005821	Ion transport domain	Domain