6YSO | pdb_00006yso

Crystal structure of the (SR) Ca2+-ATPase solved by vanadium SAD phasing

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Calcium ATPase, transmembrane domain M	8043671	3000989	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metal cation-transporting ATPase, ATP-binding domain N	8043669	3000981	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8043668	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Calcium ATPase, transmembrane domain M	8043671	3000989	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8043668	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Calcium ATPase, transmembrane domain M	8043671	3000989	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Calcium ATPase, transduction domain A	8043666	3000975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metal cation-transporting ATPase, ATP-binding domain N	8043669	3000981	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Calcium ATPase, transduction domain A	8043666	3000975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Calcium ATPase, transmembrane domain M	8043671	3000989	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8043668	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Calcium ATPase, transmembrane domain M	8043671	3000989	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Calcium ATPase, transmembrane domain M	8043671	3000989	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8043668	3001890	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		e6ysoA1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T:	F:	ECOD (20:10:01)
B		e6ysoB1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1110.10	Alpha Beta	3-Layer(aba) Sandwich	Calcium-transporting ATPase, cytoplasmic domain N	Calcium-transporting ATPase, cytoplasmic domain N	CATH (utative)
B	3.40.1110.10	Alpha Beta	3-Layer(aba) Sandwich	Calcium-transporting ATPase, cytoplasmic domain N	Calcium-transporting ATPase, cytoplasmic domain N	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00689	Cation transporting ATPase, C-terminus (Cation_ATPase_C)	Cation transporting ATPase, C-terminus	-	Family
A, B	PF00690	Cation transporter/ATPase, N-terminus (Cation_ATPase_N)	Cation transporter/ATPase, N-terminus	Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport.	Domain
A, B	PF08282	haloacid dehalogenase-like hydrolase (Hydrolase_3)	haloacid dehalogenase-like hydrolase	This family contains haloacid dehalogenase-like hydrolase enzymes.	Domain
A, B	PF00122	P-type ATPase actuator domain (E1-E2_ATPase)	P-type ATPase actuator domain	This entry describes the actuator (A) domain found in P-type ATPases (also known as E1-E2 ATPases). The A domain serves as a built-in protein phosphatase that functions to dephosphorylate the phosphorylated P domain. The A domain is the smallest of t ...	This entry describes the actuator (A) domain found in P-type ATPases (also known as E1-E2 ATPases). The A domain serves as a built-in protein phosphatase that functions to dephosphorylate the phosphorylated P domain. The A domain is the smallest of the three cytoplasmic domains. It consists of a distorted jellyroll structure and two short helices [1-2].	Domain
A, B	PF13246	P-type ATPase, cytoplasmic domain N (Cation_ATPase)	P-type ATPase, cytoplasmic domain N	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity monoatomic cation transmembrane transporter activity P-type transmembrane transporter activity P-type calcium transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type ion transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity calcium ion transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity	multicellular organismal process system process regulation of biological process regulation of system process biological regulation negative regulation of biological process muscle contraction muscle system process regulation of muscle system process striated muscle contraction negative regulation of muscle contraction regulation of striated muscle contraction regulation of muscle contraction regulation of multicellular organismal process multicellular organismal process system process regulation of biological process regulation of system process biological regulation negative regulation of biological process muscle contraction muscle system process regulation of muscle system process striated muscle contraction negative regulation of muscle contraction regulation of striated muscle contraction regulation of muscle contraction regulation of multicellular organismal process negative regulation of multicellular organismal process negative regulation of striated muscle contraction positive regulation of biological process twitch skeletal muscle contraction multicellular organismal movement musculoskeletal movement positive regulation of fast-twitch skeletal muscle fiber contraction fast-twitch skeletal muscle fiber contraction regulation of twitch skeletal muscle contraction regulation of skeletal muscle contraction positive regulation of striated muscle contraction nervous system process neuromuscular process skeletal muscle contraction voluntary skeletal muscle contraction regulation of fast-twitch skeletal muscle fiber contraction positive regulation of muscle contraction positive regulation of multicellular organismal process heart process regulation of actin filament-based process regulation of cellular process regulation of heart contraction cardiac muscle contraction circulatory system process actin filament-based process positive regulation of actin filament-based movement blood circulation positive regulation of cellular process cardiac muscle cell contraction regulation of cardiac muscle contraction positive regulation of cardiac muscle cell contraction actin filament-based movement regulation of blood circulation regulation of actin filament-based movement cellular process regulation of cardiac muscle cell contraction actin-mediated cell contraction heart contraction regulation of localization regulation of calcium ion transport cellular localization positive regulation of calcium ion transport transport sarcoplasmic reticulum calcium ion transport calcium ion transport metal ion transport localization positive regulation of calcium ion import into sarcoplasmic reticulum establishment of localization in cell positive regulation of monoatomic ion transport monoatomic ion transport positive regulation of intracellular transport monoatomic cation transport regulation of metal ion transport regulation of intracellular transport regulation of transport regulation of monoatomic ion transport intracellular transport establishment of localization positive regulation of transport regulation of cellular localization regulation of calcium ion import into sarcoplasmic reticulum calcium ion import into sarcoplasmic reticulum regulation of ATP-dependent activity positive regulation of ATP-dependent activity monoatomic ion transmembrane transport regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport positive regulation of molecular function positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport transmembrane transport regulation of molecular function regulation of ATPase-coupled calcium transmembrane transporter activity regulation of transmembrane transport positive regulation of transporter activity positive regulation of ion transmembrane transporter activity positive regulation of ATPase-coupled calcium transmembrane transporter activity	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system sarcoplasm endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system sarcoplasm endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum sarcoplasmic reticulum sarcoplasmic reticulum membrane cytoplasm organelle membrane endoplasmic reticulum membrane perinuclear region of cytoplasm intracellular membraneless organelle H zone sarcomere membraneless organelle contractile muscle fiber A band supramolecular fiber myofibril supramolecular polymer supramolecular complex I band endoplasmic reticulum-Golgi intermediate compartment

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004014	Cation-transporting P-type ATPase, N-terminal	Domain
A, B	IPR001757	P-type ATPase	Family
A, B	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
A, B	IPR006068	Cation-transporting P-type ATPase, C-terminal	Domain
A, B	IPR018303	P-type ATPase, phosphorylation site	PTM
A, B	IPR059000	P-type ATPase, A domain	Domain
A, B	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
A, B	IPR023214	HAD superfamily	Homologous Superfamily
A, B	IPR008250	P-type ATPase, A domain superfamily	Homologous Superfamily
A, B	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B	IPR023299	P-type ATPase, cytoplasmic domain N	Homologous Superfamily
A, B	IPR005782	P-type ATPase, subfamily IIA, SERCA-type	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Alpha-helical polytopic	P-type ATPase (P-ATPase)	P-ATPase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	P-type ATPase	Sarcoplasmic reticulum Calcium ATPase, structure phased using vanadium

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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