5XA8

Complete structure factors and an atomic model of the calcium pump (SERCA1A) and associated phospholipids in the E1-ALF4-ADP-2CA2+ crystals

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: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

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	Calcium ATPase, transduction domain A	8043666	3000975	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	HAD-like	8043668	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metal cation-transporting ATPase, ATP-binding domain N	8043669	3000981	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Calcium ATPase, transmembrane domain M	8043671	3000989	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	E1-E2_ATPase_N	e5xa8A2	A: beta sandwiches	X: jelly-roll	H: Calcium ATPase, transduction domain A (From Topology)	T: Calcium ATPase, transduction domain A	F: E1-E2_ATPase_N	ECOD (1.6)
A	Cation_ATPase_C	e5xa8A1	A: alpha bundles	X: Calcium ATPase transmembrane domain-related (From Homology)	H: Calcium ATPase transmembrane domain-related	T: Calcium ATPase transmembrane domain M	F: Cation_ATPase_C	ECOD (1.6)
A	Cation_ATPase	e5xa8A3	A: a+b complex topology	X: Metal cation-transporting ATPase, ATP-binding domain (From Topology)	H: Metal cation-transporting ATPase, ATP-binding domain (From Topology)	T: Metal cation-transporting ATPase, ATP-binding domain	F: Cation_ATPase	ECOD (1.6)
A	Hydrolase_3_1	e5xa8A4	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.150.10	Mainly Beta	Distorted Sandwich	Calcium-transporting ATPase, cytoplasmic transduction domain A	Calcium-transporting ATPase, cytoplasmic transduction domain A	CATH (4.3.0)
A	1.20.1110.10	Mainly Alpha	Up-down Bundle	Calcium-transporting ATPase, transmembrane domain	Calcium-transporting ATPase, transmembrane domain	CATH (4.3.0)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	3.40.1110.10	Alpha Beta	3-Layer(aba) Sandwich	Calcium-transporting ATPase, cytoplasmic domain N	Calcium-transporting ATPase, cytoplasmic domain N	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00689	Cation transporting ATPase, C-terminus (Cation_ATPase_C)	Cation transporting ATPase, C-terminus	-	Family
A	PF00702	haloacid dehalogenase-like hydrolase (Hydrolase)	haloacid dehalogenase-like hydrolase	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted fo ...	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain [1]. Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria [2].	Domain
A	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	PF00122	E1-E2 ATPase (E1-E2_ATPase)	E1-E2 ATPase	-	Family
A	PF13246	Cation transport ATPase (P-type) (Cation_ATPase)	Cation transport ATPase (P-type)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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 organic cyclic compound binding anion 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 organic cyclic compound 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 inorganic molecular entity transmembrane transporter activity inorganic cation 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 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 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 calcium ion transmembrane transporter activity regulation of ATP-dependent activity positive regulation of cation transmembrane transport positive regulation of ATP-dependent activity positive regulation of monoatomic ion transmembrane transport inorganic ion transmembrane transport inorganic cation transmembrane transport transmembrane transport regulation of molecular function regulation of transmembrane transport positive regulation of ATPase-coupled calcium transmembrane transporter activity monoatomic ion transmembrane transport regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport regulation of transporter activity monoatomic cation transmembrane transport regulation of calcium ion transmembrane transport positive regulation of molecular function positive regulation of calcium ion transmembrane transporter activity positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport regulation of monoatomic ion transmembrane transporter activity regulation of ATPase-coupled calcium transmembrane transporter activity positive regulation of transporter activity positive regulation of ion transmembrane transporter activity regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport	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	IPR004014	Cation-transporting P-type ATPase, N-terminal	Domain
A	IPR001757	P-type ATPase	Family
A	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
A	IPR006068	Cation-transporting P-type ATPase, C-terminal	Domain
A	IPR018303	P-type ATPase, phosphorylation site	PTM
A	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
A	IPR023214	HAD superfamily	Homologous Superfamily
A	IPR008250	P-type ATPase, A domain superfamily	Homologous Superfamily
A	IPR036412	HAD-like superfamily	Homologous Superfamily
A	IPR023299	P-type ATPase, cytoplasmic domain N	Homologous Superfamily
A	IPR005782	P-type ATPase, subfamily IIA, SERCA-type	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	P-type ATPase	Calcium ATPase and associated phospholipids in the E1-2Ca²⁺ crystals

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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.