6FOO | pdb_00006foo

Structure of Ryanodine Receptor 1 in nanodiscs in the presence of calcium and ATP

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	F_UNCLASSIFIED	e6fooD5	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: F_UNCLASSIFIED	ECOD (1.6)
D	SPRY	e6fooD10	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
D	Ins145_P3_rec	e6fooD9	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)
D	MIR	e6fooD11	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: MIR	ECOD (1.6)
D	EF-hand_8	e6fooD13	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_8	ECOD (1.6)
D	RyR	e6fooD6	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: RyR	ECOD (1.6)
D	RIH_assoc	e6fooD2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
D	KOG2243	e6fooD4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG2243	ECOD (1.6)
D	RYDR_ITPR_1	e6fooD8	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR_1	ECOD (1.6)
D	RYDR_ITPR	e6fooD3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR	ECOD (1.6)
D	RR_TM4-6	e6fooD1	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	F_UNCLASSIFIED	e6fooC5	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: F_UNCLASSIFIED	ECOD (1.6)
C	SPRY	e6fooC10	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	e6fooC9	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	e6fooC11	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	e6fooC13	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_8	ECOD (1.6)
C	RyR	e6fooC6	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	e6fooC2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
C	KOG2243	e6fooC4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG2243	ECOD (1.6)
C	RYDR_ITPR_1	e6fooC8	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	e6fooC3	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	e6fooC1	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	F_UNCLASSIFIED	e6fooB5	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: F_UNCLASSIFIED	ECOD (1.6)
B	SPRY	e6fooB10	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
B	Ins145_P3_rec	e6fooB9	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	e6fooB11	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	EF-hand_8	e6fooB13	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_8	ECOD (1.6)
B	RyR	e6fooB6	A: alpha duplicates or obligate multimers	X: RyR motifs (From Topology)	H: RyR motifs (From Topology)	T: RyR motifs	F: RyR	ECOD (1.6)
B	RIH_assoc	e6fooB2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
B	KOG2243	e6fooB4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG2243	ECOD (1.6)
B	RYDR_ITPR_1	e6fooB8	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	e6fooB3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RYDR_ITPR	ECOD (1.6)
B	RR_TM4-6	e6fooB1	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)
A	F_UNCLASSIFIED	e6fooA5	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: F_UNCLASSIFIED	ECOD (1.6)
A	SPRY	e6fooA10	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	e6fooA9	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	e6fooA11	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	e6fooA13	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_8	ECOD (1.6)
A	RyR	e6fooA6	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	e6fooA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RIH_assoc	ECOD (1.6)
A	KOG2243	e6fooA4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: KOG2243	ECOD (1.6)
A	RYDR_ITPR_1	e6fooA8	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	e6fooA3	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	e6fooA1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	PF08454	RyR and IP3R Homology associated (RIH_assoc)	RyR and IP3R Homology associated	-	Repeat
A, B, C, D	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, C, D	PF21119	Ryanodine receptor junctional solenoid repeat (RYDR_Jsol)	Ryanodine receptor junctional solenoid repeat	-	Repeat
A, B, C, D	PF01365	RIH domain (RYDR_ITPR)	RIH domain	-	Repeat
A, B, C, D	PF02026	RyR domain (RyR)	RyR domain	-	Family
A, B, C, D	PF00520	Ion transport protein (Ion_trans)	Ion transport protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	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 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

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Calcium Ion-Selective	RyR1 ryanodine receptor in lipid nanodiscs in presence of Ca²⁺ & ATP