5GKZ | pdb_00005gkz

Structure of RyR1 in a closed state (C3 conformer)

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Rotamase-like	8098876	3000622	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rotamase-like	8098876	3000622	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Rotamase-like	8098876	3000622	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Rotamase-like	8098876	3000622	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	SPRY	e5gkzA6	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
A	Ins145_P3_rec	e5gkzA11	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	e5gkzA2	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	EF-hand_8	e5gkzA1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_8	ECOD (1.6)
A	RyR	e5gkzA10	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: RyR	ECOD (1.6)
A	RIH_assoc	e5gkzA9	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
A	KOG2243	e5gkzA12	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG2243	ECOD (1.6)
A	RYDR_ITPR_1	e5gkzA4	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	e5gkzA8	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR	ECOD (1.6)
A	RR_TM4-6	e5gkzA5	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: RR_TM4-6	ECOD (1.6)
C	SPRY	e5gkzC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
C	Ins145_P3_rec	e5gkzC12	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)
C	MIR	e5gkzC5	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: MIR	ECOD (1.6)
C	EF-hand_8	e5gkzC4	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_8	ECOD (1.6)
C	RyR	e5gkzC8	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: RyR	ECOD (1.6)
C	RIH_assoc	e5gkzC3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
C	KOG2243	e5gkzC10	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG2243	ECOD (1.6)
C	RYDR_ITPR_1	e5gkzC7	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR_1	ECOD (1.6)
C	RYDR_ITPR	e5gkzC11	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR	ECOD (1.6)
C	RR_TM4-6	e5gkzC2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: RR_TM4-6	ECOD (1.6)
E	SPRY	e5gkzE3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
E	Ins145_P3_rec	e5gkzE7	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)
E	MIR	e5gkzE12	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: MIR	ECOD (1.6)
E	EF-hand_8	e5gkzE9	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_8	ECOD (1.6)
E	RyR	e5gkzE11	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: RyR	ECOD (1.6)
E	RIH_assoc	e5gkzE6	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
E	KOG2243	e5gkzE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG2243	ECOD (1.6)
E	RYDR_ITPR_1	e5gkzE5	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR_1	ECOD (1.6)
E	RYDR_ITPR	e5gkzE2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR	ECOD (1.6)
E	RR_TM4-6	e5gkzE13	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: RR_TM4-6	ECOD (1.6)
G	SPRY	e5gkzG8	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
G	Ins145_P3_rec	e5gkzG2	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)
G	MIR	e5gkzG12	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: MIR	ECOD (1.6)
G	EF-hand_8	e5gkzG10	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_8	ECOD (1.6)
G	RyR	e5gkzG13	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: RyR	ECOD (1.6)
G	RIH_assoc	e5gkzG11	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
G	KOG2243	e5gkzG5	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG2243	ECOD (1.6)
G	RYDR_ITPR_1	e5gkzG4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR_1	ECOD (1.6)
G	RYDR_ITPR	e5gkzG9	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR	ECOD (1.6)
G	RR_TM4-6	e5gkzG1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: RR_TM4-6	ECOD (1.6)
B	FKBP_C	e5gkzB1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: FKBP_C	ECOD (1.6)
D	FKBP_C	e5gkzD1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: FKBP_C	ECOD (1.6)
F	FKBP_C	e5gkzF1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: FKBP_C	ECOD (1.6)
H	FKBP_C	e5gkzH1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: FKBP_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
B, D, F, H	PF00254	FKBP-type peptidyl-prolyl cis-trans isomerase (FKBP_C)	FKBP-type peptidyl-prolyl cis-trans isomerase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 inorganic molecular entity transmembrane transporter activity channel activity ligand-gated calcium channel activity inorganic cation transmembrane 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 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 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 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 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 regulation of localization cellular localization regulation of cellular process negative regulation of biological process negative regulation of sequestering of calcium ion maintenance of location in cell negative regulation of cellular process regulation of sequestering of calcium ion regulation of biological process calcium ion transmembrane import into cytosol sequestering of calcium ion biological regulation maintenance of location release of sequestered calcium ion into cytosol 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 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
B, D, F, H	Peptidyl-prolyl cis-trans isomerase FKBP1A	isomerase activity RNA polymerase II CTD heptapeptide repeat modifying activity catalytic activity, acting on a protein RNA polymerase II CTD heptapeptide repeat peptidyl-prolyl isomerase activity RNA polymerase II CTD heptapeptide repeat P6 isomerase activity peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity RNA polymerase II CTD heptapeptide repeat P3 isomerase activity	regulation of calcium ion transport regulation of localization regulation of cellular process intracellular calcium ion homeostasis negative regulation of biological process sarcoplasmic reticulum calcium ion transport release of sequestered calcium ion into cytosol by sarcoplasmic reticulum calcium ion transport localization monoatomic cation homeostasis monoatomic cation transport intracellular monoatomic ion homeostasis release of sequestered calcium ion into cytosol by endoplasmic reticulum regulation of biological process regulation of calcium ion transport regulation of localization regulation of cellular process intracellular calcium ion homeostasis negative regulation of biological process sarcoplasmic reticulum calcium ion transport release of sequestered calcium ion into cytosol by sarcoplasmic reticulum calcium ion transport localization monoatomic cation homeostasis monoatomic cation transport intracellular monoatomic ion homeostasis release of sequestered calcium ion into cytosol by endoplasmic reticulum regulation of biological process regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport chemical homeostasis cellular localization inorganic ion homeostasis transport homeostatic process monoatomic ion transmembrane transport calcium ion homeostasis regulation of monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion metal ion transport maintenance of location in cell regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport intracellular monoatomic cation homeostasis monoatomic ion homeostasis negative regulation of cellular process monoatomic ion transport intracellular chemical homeostasis regulation of metal ion transport regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol regulation of transport sequestering of calcium ion biological regulation cellular homeostasis cellular process regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum regulation of calcium ion transmembrane transporter activity regulation of cation channel activity regulation of molecular function regulation of transmembrane transporter activity regulation of transporter activity regulation of monoatomic ion transmembrane transporter activity regulation of ryanodine-sensitive calcium-release channel activity	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 cytoplasmic side of membrane membrane side of membrane cytosol 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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