5X9Z | pdb_00005x9z

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

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)
B	SCOP2B Superfamily	MIR domain	8044061	3001569	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MIR domain	8044061	3001569	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)
B	RyR	e5x9zB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RyR	ECOD (v294.1)
A	RyR	e5x9zA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RyR	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08454	RyR and IP3R Homology associated (RIH_assoc)	RyR and IP3R Homology associated	-	Repeat
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	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	ion binding binding anion binding phosphatidylinositol binding small molecule binding calcium channel activity monoatomic cation transmembrane transporter activity intracellularly ligand-gated monoatomic ion channel activity gated channel activity monoatomic ion channel activity intracellularly gated calcium channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity monoatomic cation channel activity ion binding binding anion binding phosphatidylinositol binding small molecule binding calcium channel activity monoatomic cation transmembrane transporter activity intracellularly ligand-gated monoatomic ion channel activity gated channel activity monoatomic ion channel activity 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 channel activity ligand-gated calcium channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity ligand-gated monoatomic cation channel activity transmembrane transporter activity protein phosphatase binding phosphatase binding protein binding enzyme binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding protein-containing complex binding inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels inositol 1,4,5-trisphosphate-gated calcium channel 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 calcium ion binding metal ion binding protein domain specific binding transmembrane transporter binding protein homodimerization activity protein dimerization activity alcohol binding inositol 1,4,5 trisphosphate 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 sexual reproduction reproductive process fertilization single fertilization regulation of cytosolic calcium ion concentration 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 release of sequestered calcium ion into cytosol by endoplasmic reticulum calcium ion transmembrane import into cytosol transport monoatomic ion transmembrane transport establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport release of sequestered calcium ion into cytosol localization intercellular transport monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport anatomical structure morphogenesis cell morphogenesis cellular response to stimulus response to stimulus signaling phospholipase C-activating G protein-coupled receptor signaling pathway cell communication G protein-coupled receptor signaling pathway signal transduction 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 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 mitochondrial calcium ion transmembrane transport calcium import into the mitochondrion voluntary musculoskeletal movement multicellular organismal movement musculoskeletal movement system process nervous system process neuromuscular process cellular response to nitrogen compound 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 protein-containing complex organization protein homotetramerization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization 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 organophosphorus response to purine-containing compound response to cAMP cellular response to cAMP regulation of hepatocyte proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation hepatocyte proliferation regulation of cell population proliferation positive regulation of hepatocyte proliferation regulation of epithelial cell proliferation epithelial cell proliferation 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 post-embryonic development	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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 intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen 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 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.