7N74 | pdb_00007n74

Cryo-EM structure of ATP13A2 D508N mutant in the E1-ATP-like state

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
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)
A	ABC_tran	e7n74A01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: ABC_tran	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	Isoform 3 of Polyamine-transporting ATPase 13A2	cation binding cupric ion binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding manganese ion binding monoatomic cation transmembrane transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity cation binding cupric ion binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding manganese ion binding monoatomic cation transmembrane transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity transmembrane transporter activity ATP-dependent activity ABC-type transporter activity polyamine transmembrane transporter activity ABC-type polyamine transporter activity 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 P-type ion transporter activity P-type transmembrane transporter activity phosphatidylinositol-3,5-bisphosphate binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding phosphatidic acid 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 zinc ion binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of biological process catabolic process regulation of cellular process autophagy intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of biological process catabolic process regulation of cellular process autophagy biological regulation regulation of catabolic process regulation of autophagy cellular process metabolic process regulation of autophagy of mitochondrion process utilizing autophagic mechanism regulation of metabolic process autophagy of mitochondrion regulation of protein metabolic process primary metabolic process protein catabolic process regulation of macromolecule metabolic process macromolecule catabolic process regulation of primary metabolic process chaperone-mediated autophagy regulation of chaperone-mediated autophagy protein metabolic process macromolecule metabolic process regulation of protein catabolic process membrane organization transport macroautophagy membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular component organization or biogenesis vesicle fusion transmembrane transport polyamine transmembrane transport spermine transmembrane transport nitrogen compound transport spermine transport polyamine transport regulation of macroautophagy regulation of biosynthetic process positive regulation of biological process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process intracellular calcium ion homeostasis calcium ion homeostasis regulation of localization establishment of protein localization cellular localization regulation of protein localization establishment of localization in cell intracellular protein localization regulation of intracellular transport regulation of transport regulation of establishment of protein localization intracellular transport regulation of protein transport protein transport regulation of cellular localization macromolecule localization regulation of intracellular protein transport intracellular protein transport cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress protein localization to organelle regulation of protein localization to nucleus protein localization to nucleus regulation of cellular component organization regulation of organelle organization regulation of mitochondrion organization mitochondrion organization regulation of protein catabolic process in the vacuole protein catabolic process in the vacuole lysosomal protein catabolic process regulation of lysosomal protein catabolic process negative regulation of biological process negative regulation of protein catabolic process in the vacuole negative regulation of protein catabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process negative regulation of metabolic process negative regulation of lysosomal protein catabolic process cellular component biogenesis extracellular vesicle biogenesis extracellular exosome biogenesis vacuole organization regulation of cellular component size autophagosome organization regulation of biological quality regulation of autophagosome size regulation of anatomical structure size lipid homeostasis neuron apoptotic process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process monoatomic ion transmembrane transport monoatomic ion transport cellular response to metal ion response to metal ion cellular response to manganese ion response to manganese ion intracellular zinc ion homeostasis positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport regulation of secretion by cell secretion by cell positive regulation of secretion secretion establishment of protein localization to extracellular region export from cell protein secretion positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport positive regulation of protein localization response to zinc ion cellular response to zinc ion vacuolar transport lysosomal transport protein localization to lysosome protein localization to vacuole exosomal secretion establishment of organelle localization positive regulation of exosomal secretion positive regulation of exocytosis organelle localization vesicle localization positive regulation of cellular component biogenesis regulation of exosomal secretion establishment of vesicle localization regulation of cellular component biogenesis regulation of vesicle-mediated transport exocytosis regulation of exocytosis	cellular anatomical structure membrane membrane-bounded organelle endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle cellular anatomical structure membrane membrane-bounded organelle endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle late endosome cytoplasm vesicle organelle membrane cell projection neuron projection plasma membrane bounded cell projection vacuole autophagosome vacuolar membrane autophagosome membrane lytic vacuole lytic vacuole membrane lysosomal membrane lysosome somatodendritic compartment cell body neuronal cell body multivesicular body membrane multivesicular body membrane-enclosed lumen vacuolar lumen lysosomal lumen intracellular organelle lumen organelle lumen transport vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001757	P-type ATPase	Family
A	IPR018303	P-type ATPase, phosphorylation site	PTM
A	IPR047819	P5B-type ATPase, N-terminal	Domain
A	IPR047821	P5B-type ATPase	Family
A	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
A	IPR006544	P-type ATPase, subfamily V	Family
A	IPR036412	HAD-like superfamily	Homologous Superfamily
A	IPR023299	P-type ATPase, cytoplasmic domain N	Homologous Superfamily
A	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
A	IPR059000	P-type ATPase, A domain	Domain
A	IPR023214	HAD superfamily	Homologous Superfamily
A	IPR008250	P-type ATPase, A domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NQ11	Parkinson disease neuronal ceroid lipofuscinosis Kufor-Rakeb syndrome secondary Parkinson disease autosomal recessive spastic paraplegia type 78 manganese poisoning Nerve Degeneration hereditary spastic paraplegia medulloblastoma adult neuronal ceroid lipofuscinosis glioblastoma infantile neuronal ceroid lipofuscinosis malignant glioma neuronal ceroid lipofuscinosis 4B autosomal recessive juvenile Parkinson disease 2 Parkinson disease neuronal ceroid lipofuscinosis Kufor-Rakeb syndrome secondary Parkinson disease autosomal recessive spastic paraplegia type 78 manganese poisoning Nerve Degeneration hereditary spastic paraplegia medulloblastoma adult neuronal ceroid lipofuscinosis glioblastoma infantile neuronal ceroid lipofuscinosis malignant glioma neuronal ceroid lipofuscinosis 4B autosomal recessive juvenile Parkinson disease 2 chronic obstructive pulmonary disease intellectual disability neurodegenerative disease paraplegia parkinsonian disorder rheumatoid arthritis inborn errors of metabolism juvenile neuronal ceroid lipofuscinosis lysosomal storage disease

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Transmembrane	Alpha-helical polytopic	P-type ATPase (P-ATPase)	P5-type ATPase cation transporter

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	P5B-ATPase ATP13A2, BeF-bound E2P-like state

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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