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)
A	SCOP2B Superfamily	MIR domain	8044061	3001569	SCOP2B (2022-06-29)
B	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)
A	Ins145_P3_rec	e5x9zA4	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	e5x9zA5	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	RIH_assoc	e5x9zA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
A	KOG3533	e5x9zA3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG3533	ECOD (1.6)
A	RYDR_ITPR_1	e5x9zA6	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	e5x9zA2	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	e5x9zB4	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	e5x9zB5	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	RIH_assoc	e5x9zB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
B	KOG3533	e5x9zB3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG3533	ECOD (1.6)
B	RYDR_ITPR_1	e5x9zB6	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	e5x9zB2	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	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	binding phospholipid binding lipid binding phosphatidylinositol 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 binding phospholipid binding lipid binding phosphatidylinositol 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 inorganic molecular entity transmembrane transporter activity channel activity ligand-gated calcium channel activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity ligand-gated monoatomic cation channel activity transmembrane transporter activity 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 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 cation binding metal ion binding protein binding protein domain specific binding identical protein 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 localization cellular localization transport monoatomic ion transmembrane transport negative regulation of biological process negative regulation of sequestering of calcium ion calcium ion transport metal ion transport maintenance of location in cell monoatomic cation transmembrane transport localization negative regulation of cellular process monoatomic ion transport monoatomic cation transport regulation of sequestering of calcium ion release of sequestered calcium ion into cytosol by endoplasmic reticulum calcium ion transmembrane import into cytosol sequestering of calcium ion inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol calcium ion transmembrane transport developmental process anatomical structure morphogenesis anatomical structure development 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 response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus mitochondrial calcium ion transmembrane transport calcium import into the mitochondrion voluntary musculoskeletal movement multicellular organismal movement musculoskeletal movement multicellular organismal process 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 protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis epithelial fluid transport transepithelial transport fluid 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 positive regulation of cell communication establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization positive regulation of insulin secretion intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels 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 regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion regulation of transport 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 positive regulation of transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion positive regulation of signaling multicellular organism development post-embryonic development ligand-gated ion channel signaling pathway	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system platelet dense granule membrane membrane intracellular vesicle cytoplasmic vesicle membrane membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system platelet dense granule membrane 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 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 endoplasmic reticulum sarcoplasmic reticulum transport vesicle transport vesicle membrane membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane synapse cell junction postsynaptic density postsynapse 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.