5XA1

Crystal structure of inositol 1,4,5-trisphosphate receptor cytosolic domain with inositol 1,4,5-trisphosphate

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	IP3 receptor type 1 binding core domain 2	8044060	3000619	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	IP3 receptor type 1 binding core domain 2	8044060	3000619	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Ins145_P3_rec	e5xa1A5	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Ins145_P3_rec	ECOD (1.6)
A	MIR	e5xa1A1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: MIR	ECOD (1.6)
A	KOG3533	e5xa1A3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG3533	ECOD (1.6)
A	RYDR_ITPR_1	e5xa1A4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR_1	ECOD (1.6)
A	RYDR_ITPR_2	e5xa1A2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR_2	ECOD (1.6)
B	Ins145_P3_rec	e5xa1B5	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Ins145_P3_rec	ECOD (1.6)
B	MIR	e5xa1B2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: MIR	ECOD (1.6)
B	KOG3533	e5xa1B3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG3533	ECOD (1.6)
B	RYDR_ITPR_1	e5xa1B4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR_1	ECOD (1.6)
B	RYDR_ITPR_2	e5xa1B1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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	PF01365	RIH domain (RYDR_ITPR)	RIH domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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 regulation of biological process positive regulation of programmed cell death 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 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 cellular 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 anatomical structure morphogenesis cell morphogenesis cellular response to stimulus response to stimulus 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 transport regulation of transport regulation of monoatomic ion transport establishment of localization calcium ion transport metal ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus 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 cellular response to chemical stimulus G protein-coupled acetylcholine receptor signaling pathway response to chemical response to acetylcholine negative regulation of programmed cell death negative regulation of biological process negative regulation of apoptotic process negative regulation of cellular process epithelial fluid transport transepithelial transport fluid transport gland development animal organ development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration 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 cellular localization monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion maintenance of location in cell monoatomic cation transmembrane transport regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol sequestering of calcium ion inorganic ion transmembrane transport inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol calcium ion transmembrane transport intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress intracellular signal transduction apoptotic signaling pathway cellular response to stress 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 intracellular signaling cassette 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 calcium-mediated signaling 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	IPR036300	Mir domain superfamily	Homologous Superfamily
A, B	IPR000699	RIH domain	Domain
A, B	IPR013662	RyR/IP3R Homology associated domain	Domain
A, B	IPR016093	MIR motif	Domain
A, B	IPR015925	Ryanodine/Inositol 1,4,5-trisphosphate receptor	Family
A, B	IPR035910	RyR/IP3 receptor binding core, RIH domain superfamily	Homologous Superfamily
A, B	IPR014821	Inositol 1,4,5-trisphosphate/ryanodine receptor	Domain
A, B	IPR000493	Inositol 1,4,5-trisphosphate receptor	Family
A, B	IPR005821	Ion transport domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.