3J8H

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)
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	PF00622	e3j8hA3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF00622	ECOD (1.6)
A	PF02815	e3j8hA2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF02815	ECOD (1.6)
A	PF08709	e3j8hA1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF08709	ECOD (1.6)
A	PF13499	e3j8hA8	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: PF13499	ECOD (1.6)
A	PF02026	e3j8hA6	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: PF02026	ECOD (1.6)
A	PF01365	e3j8hA10	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF01365	ECOD (1.6)
A	PF08454	e3j8hA13	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF08454	ECOD (1.6)
A	PF21119	e3j8hA11	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF21119	ECOD (1.6)
A	PF00520,PF06459	e3j8hA9	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520,PF06459	ECOD (1.6)
C	PF00622	e3j8hC12	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF00622	ECOD (1.6)
C	PF02815	e3j8hC10	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF02815	ECOD (1.6)
C	PF08709	e3j8hC11	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF08709	ECOD (1.6)
C	PF13499	e3j8hC13	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: PF13499	ECOD (1.6)
C	PF02026	e3j8hC9	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: PF02026	ECOD (1.6)
C	PF01365	e3j8hC6	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF01365	ECOD (1.6)
C	PF08454	e3j8hC3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF08454	ECOD (1.6)
C	PF21119	e3j8hC5	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF21119	ECOD (1.6)
C	PF00520,PF06459	e3j8hC1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520,PF06459	ECOD (1.6)
E	PF00622	e3j8hE9	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF00622	ECOD (1.6)
E	PF02815	e3j8hE10	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF02815	ECOD (1.6)
E	PF08709	e3j8hE11	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF08709	ECOD (1.6)
E	PF13499	e3j8hE13	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: PF13499	ECOD (1.6)
E	PF02026	e3j8hE8	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: PF02026	ECOD (1.6)
E	PF01365	e3j8hE5	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF01365	ECOD (1.6)
E	PF08454	e3j8hE3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF08454	ECOD (1.6)
E	PF21119	e3j8hE6	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF21119	ECOD (1.6)
E	PF00520,PF06459	e3j8hE1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520,PF06459	ECOD (1.6)
G	PF00622	e3j8hG9	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF00622	ECOD (1.6)
G	PF02815	e3j8hG10	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF02815	ECOD (1.6)
G	PF08709	e3j8hG11	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF08709	ECOD (1.6)
G	PF13499	e3j8hG13	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: PF13499	ECOD (1.6)
G	PF02026	e3j8hG8	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: PF02026	ECOD (1.6)
G	PF01365	e3j8hG5	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF01365	ECOD (1.6)
G	PF08454	e3j8hG3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF08454	ECOD (1.6)
G	PF21119	e3j8hG6	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF21119	ECOD (1.6)
G	PF00520,PF06459	e3j8hG1	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: PF00520,PF06459	ECOD (1.6)
B	PF00254	e3j8hB1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: PF00254	ECOD (1.6)
D	PF00254	e3j8hD1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: PF00254	ECOD (1.6)
F	PF00254	e3j8hF1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: PF00254	ECOD (1.6)
H	PF00254	e3j8hH1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: PF00254	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	-	Family
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	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, C, E, G	PF21119	Ryanodine receptor junctional solenoid repeat (RYDR_Jsol)	Ryanodine receptor junctional solenoid repeat	This entry represents a region of the Ryanodine receptor composed of alpha helical ARM repeats [1]. This region has been termed the Junctional solenoid region (Jsol) [1].	Domain
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	binding toxic substance binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding binding toxic substance binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding calcium-induced calcium release activity calcium channel activity monoatomic cation transmembrane transporter activity intracellularly ligand-gated monoatomic ion channel activity gated channel activity monoatomic ion channel activity ryanodine-sensitive calcium-release 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 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	cellular response to stimulus cellular response to nitrogen compound response to organic substance response to stimulus response to organonitrogen compound response to endogenous stimulus cellular response to caffeine cellular response to organic cyclic compound response to nitrogen compound response to purine-containing compound response to alkaloid cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to organonitrogen compound response to chemical cellular response to stimulus cellular response to nitrogen compound response to organic substance response to stimulus response to organonitrogen compound response to endogenous stimulus cellular response to caffeine cellular response to organic cyclic compound response to nitrogen compound response to purine-containing compound response to alkaloid cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to organonitrogen compound response to chemical cellular process cellular response to organic substance cellular response to alkaloid cellular response to purine-containing compound response to organic cyclic 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 inorganic substance cellular response to metal ion response to inorganic substance 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 multicellular organismal process system process muscle contraction muscle system process 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 muscle structure development skeletal muscle organ 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 cellular anatomical entity intracellular membrane-bounded organelle endomembrane system sarcoplasm intracellular organelle endoplasmic reticulum subcompartment terminal cisterna organelle endoplasmic reticulum sarcoplasmic reticulum cytoplasm membrane-bounded organelle intracellular anatomical structure organelle subcompartment cellular anatomical entity intracellular membrane-bounded organelle endomembrane system sarcoplasm intracellular organelle endoplasmic reticulum subcompartment terminal cisterna organelle endoplasmic reticulum sarcoplasmic reticulum cytoplasm membrane 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 cell periphery endoplasmic reticulum protein-containing complex plasma membrane protein complex voltage-gated calcium channel complex plasma membrane 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 catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity	regulation of calcium ion transmembrane transporter activity regulation of calcium ion transport regulation of localization regulation of cellular process intracellular calcium ion homeostasis negative regulation of biological process calcium ion transport localization monoatomic cation homeostasis monoatomic cation transport intracellular monoatomic ion homeostasis regulation of biological process regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport regulation of calcium ion transmembrane transporter activity regulation of calcium ion transport regulation of localization regulation of cellular process intracellular calcium ion homeostasis negative regulation of biological process calcium ion transport localization monoatomic cation homeostasis monoatomic cation transport intracellular monoatomic ion homeostasis 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 regulation of cation channel activity inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol regulation of molecular function regulation of transmembrane transport chemical homeostasis cellular localization inorganic ion homeostasis transport homeostatic process monoatomic ion transmembrane transport regulation of transmembrane transporter activity 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 transporter activity 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 regulation of monoatomic ion transmembrane transporter activity calcium ion transmembrane import into cytosol regulation of transport sequestering of calcium ion biological regulation regulation of ryanodine-sensitive calcium-release channel activity cellular homeostasis 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	cytoplasmic side of membrane membrane cellular anatomical entity side of membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular membrane-bounded organelle endomembrane system sarcoplasm intracellular organelle organelle endoplasmic reticulum cytoplasmic side of membrane membrane cellular anatomical entity 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

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	IPR001179	FKBP-type peptidyl-prolyl cis-trans isomerase domain	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