3J8H | pdb_00003j8h

Structure of the rabbit ryanodine receptor RyR1 in complex with FKBP12 at 3.8 Angstrom resolution

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Rotamase-like	8098876	3000622	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Rotamase-like	8098876	3000622	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rotamase-like	8098876	3000622	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rotamase-like	8098876	3000622	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	e3j8hH1	A: Type III secretion system domain-like	X: Antibiotic binding domain of TipA-like multidrug resistance regulators	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Asparaginase_C	F:	ECOD (20:10:01)
F	e3j8hF1	A: Type III secretion system domain-like	X: Antibiotic binding domain of TipA-like multidrug resistance regulators	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Asparaginase_C	F:	ECOD (20:10:01)
D	e3j8hD1	A: Type III secretion system domain-like	X: Antibiotic binding domain of TipA-like multidrug resistance regulators	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Asparaginase_C	F:	ECOD (20:10:01)
B	e3j8hB1	A: Type III secretion system domain-like	X: Antibiotic binding domain of TipA-like multidrug resistance regulators	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Asparaginase_C	F:	ECOD (20:10:01)
G	e3j8hG1	A: Inserted helical domain in fatty acid synthase subunit beta	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: FAN1_HTH	F:	ECOD (20:10:01)
E	e3j8hE1	A: Inserted helical domain in fatty acid synthase subunit beta	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: FAN1_HTH	F:	ECOD (20:10:01)
C	e3j8hC1	A: Alpha-beta plaits	X: Pseudouridine synthase	H: Pseudouridine synthase	T: PilN	F:	ECOD (20:10:01)
A	e3j8hA1	A: Yeast killer toxin-like	X: Molybdenum cofactor biosynthesis proteins	H: Molybdenum cofactor biosynthesis proteins	T: EF-hand_7	F:	ECOD (20:10:01)
A	e3j8hA9	A: Yeast killer toxin-like	X: Molybdenum cofactor biosynthesis proteins	H: Molybdenum cofactor biosynthesis proteins	T: Ion_trans,RR_TM4-6	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF00254	FKBP-type peptidyl-prolyl cis-trans isomerase (FKBP_C)	FKBP-type peptidyl-prolyl cis-trans isomerase		Domain
A, C, E, G	PF00622	SPRY domain (SPRY)	SPRY domain	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of ...	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development [1,2,3,4]. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region [2]. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologues are domains in butyrophilin/ marenostrin/pyrin [1].	Domain
A, C, E, G	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, C, E, G	PF21119	Ryanodine receptor junctional solenoid repeat (RYDR_Jsol)	Ryanodine receptor junctional solenoid repeat	-	Repeat
A, C, E, G	PF01365	RIH domain (RYDR_ITPR)	RIH domain	-	Repeat
A, C, E, G	PF02026	RyR domain (RyR)	RyR domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Peptidyl-prolyl cis-trans isomerase FKBP1A	isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity	regulation of calcium ion transport regulation of localization regulation of cellular process transport monoatomic ion transmembrane transport regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport monoatomic cation transport regulation of calcium ion transport regulation of localization regulation of cellular process transport monoatomic ion transmembrane transport regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport monoatomic cation transport regulation of metal ion transport regulation of biological process calcium ion transmembrane import into cytosol regulation of transport regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport biological regulation establishment of localization transmembrane transport release of sequestered calcium ion into cytosol regulation of molecular function regulation of ryanodine-sensitive calcium-release channel activity regulation of transmembrane transport cellular process regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport sarcoplasmic reticulum calcium ion transport release of sequestered calcium ion into cytosol by sarcoplasmic reticulum release of sequestered calcium ion into cytosol by endoplasmic reticulum regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	cellular anatomical structure cytoplasmic side of membrane membrane side of membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular membrane-bounded organelle endomembrane system sarcoplasm intracellular organelle organelle endoplasmic reticulum cellular anatomical structure cytoplasmic side of membrane membrane side of membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular membrane-bounded organelle endomembrane system sarcoplasm intracellular organelle organelle endoplasmic reticulum sarcoplasmic reticulum organelle subcompartment endoplasmic reticulum subcompartment terminal cisterna protein-containing complex membrane protein complex ryanodine receptor complex transporter complex cell periphery bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane plasma membrane protein complex voltage-gated calcium channel complex plasma membrane cation channel complex transmembrane transporter complex sarcoplasmic reticulum membrane organelle membrane calcium channel complex monoatomic ion channel complex
A, C, E, G	Ryanodine receptor 1	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 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 binding toxic substance 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 calcium-induced calcium release activity ryanodine-sensitive calcium-release channel activity protein binding calmodulin binding identical protein binding cation binding calcium ion binding metal ion binding ATP-gated ion channel activity voltage-gated calcium channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity voltage-gated monoatomic cation channel activity transmembrane transporter binding disordered domain specific binding protein domain specific binding	multicellular organismal process system process muscle contraction muscle system process striated muscle contraction cellular response to nitrogen compound cellular response to stimulus response to stimulus cellular response to caffeine response to nitrogen compound response to purine-containing compound response to alkaloid cellular response to chemical stimulus response to chemical multicellular organismal process system process muscle contraction muscle system process striated muscle contraction cellular response to nitrogen compound cellular response to stimulus response to stimulus cellular response to caffeine response to nitrogen compound response to purine-containing compound response to alkaloid cellular response to chemical stimulus response to chemical cellular process cellular response to alkaloid cellular response to purine-containing compound response to caffeine inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cellular response to metal ion response to metal ion cellular response to calcium ion response to calcium ion transport monoatomic ion transmembrane transport establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport localization monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport developmental process myotube cell development skeletal muscle fiber development cellular developmental process skeletal muscle tissue development animal organ development cell development tissue development muscle cell differentiation myotube differentiation striated muscle tissue development muscle structure development skeletal muscle organ development striated muscle cell development muscle cell development cell differentiation anatomical structure development muscle tissue development muscle organ development striated muscle cell differentiation skin development 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 bone maturation developmental maturation multicellular organism development skeletal system development ossification anatomical structure maturation ossification involved in bone maturation animal organ maturation bone development system development calcium ion transmembrane import into cytosol release of sequestered calcium ion into cytosol release of sequestered calcium ion into cytosol by endoplasmic reticulum sarcoplasmic reticulum calcium ion transport release of sequestered calcium ion into cytosol by sarcoplasmic reticulum heart development heart morphogenesis circulatory system development anatomical structure morphogenesis outflow tract morphogenesis animal organ morphogenesis	membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system sarcoplasm intracellular organelle endoplasmic reticulum subcompartment terminal cisterna cellular anatomical structure organelle endoplasmic reticulum sarcoplasmic reticulum cytoplasm membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system sarcoplasm intracellular organelle endoplasmic reticulum subcompartment terminal cisterna cellular anatomical structure organelle endoplasmic reticulum sarcoplasmic reticulum cytoplasm membrane intracellular membraneless organelle Z disc sarcomere I band membraneless organelle contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex cell periphery sarcolemma plasma membrane smooth endoplasmic reticulum organelle membrane bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network sarcoplasmic reticulum membrane endoplasmic reticulum membrane protein-containing complex membrane protein complex ryanodine receptor complex transporter complex endoplasmic reticulum protein-containing complex plasma membrane protein complex voltage-gated calcium channel complex cation channel complex transmembrane transporter complex calcium channel complex monoatomic ion channel complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR046357	Peptidyl-prolyl cis-trans isomerase domain superfamily	Homologous Superfamily
B, D, F, H	IPR050689	FKBP-type Peptidyl-prolyl cis-trans Isomerase	Family
B, D, F, H	IPR001179	FKBP-type peptidyl-prolyl cis-trans isomerase domain	Domain
A, C, E, G	IPR036300	Mir domain superfamily	Homologous Superfamily
A, C, E, G	IPR000699	RIH domain	Domain
A, C, E, G	IPR013662	RyR/IP3R Homology associated domain	Domain
A, C, E, G	IPR016093	MIR motif	Domain
A, C, E, G	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, C, E, G	IPR003877	SPRY domain	Domain
A, C, E, G	IPR001870	B30.2/SPRY domain	Domain
A, C, E, G	IPR009460	Ryanodine Receptor TM 4-6	Domain
A, C, E, G	IPR015925	Ryanodine/Inositol 1,4,5-trisphosphate receptor	Family
A, C, E, G	IPR048581	Ryanodine receptor, junctional solenoid domain	Domain
A, C, E, G	IPR035910	RyR/IP3 receptor binding core, RIH domain superfamily	Homologous Superfamily
A, C, E, G	IPR003032	Ryanodine receptor Ryr	Domain
A, C, E, G	IPR035761	Ryanodine receptor, SPRY domain 1	Domain
A, C, E, G	IPR014821	Inositol 1,4,5-trisphosphate/ryanodine receptor	Domain
A, C, E, G	IPR035764	Ryanodine receptor, SPRY domain 2	Domain
A, C, E, G	IPR013333	Ryanodine receptor	Family
A, C, E, G	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
A, C, E, G	IPR011992	EF-hand domain pair	Homologous Superfamily
A, C, E, G	IPR005821	Ion transport domain	Domain
A, C, E, G	IPR035762	Ryanodine receptor, SPRY domain 3	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H	OPM	Transmembrane	Alpha-helical polytopic	Ion channel (VIC) superfamily	Ryanodine receptor

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Calcium Ion-Selective	RyR1 ryanodine receptor, closed state in complex with FKBP12. Cryo-EM structure