9YG4 | pdb_00009yg4

VPS13A/Nt-CaM

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth C]	SCOP2B Superfamily	EF-hand	8033438	3001983	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C]	PF13499	EF-hand domain pair (EF-hand_7)	EF-hand domain pair		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Intermembrane lipid transfer protein VPS13A	-	localization transport macromolecule localization lipid localization lipid transport establishment of localization catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism establishment of protein localization cellular localization protein targeting localization transport macromolecule localization lipid localization lipid transport establishment of localization catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism establishment of protein localization cellular localization protein targeting establishment of protein localization to vacuole intracellular transport protein localization to vacuole establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle vacuolar transport intracellular protein localization protein targeting to vacuole intracellular protein transport protein catabolic process in the vacuole lysosomal protein catabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process maintenance of protein location protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell protein retention in Golgi apparatus Golgi to endosome transport post-Golgi vesicle-mediated transport vesicle-mediated transport intercellular transport cytosolic transport Golgi vesicle transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen endomembrane system membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen endomembrane system intracellular organelle lumen cytoplasmic vesicle neuronal dense core vesicle lumen vesicle neuronal dense core vesicle vesicle lumen dense core granule secretory granule lumen organelle lumen secretory granule dense core granule lumen secretory vesicle mitochondrial membrane membrane organelle envelope mitochondrial envelope organelle membrane cytosol cell projection sperm midpiece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane neuron projection vacuolar membrane lytic vacuole vacuole lytic vacuole membrane bounding membrane of organelle lysosomal membrane lysosome Golgi apparatus lipid droplet membraneless organelle intracellular membraneless organelle endosome membrane endosome cytoplasmic vesicle membrane vesicle membrane organelle outer membrane mitochondrial outer membrane outer membrane somatodendritic compartment cell body neuronal cell body
A [auth C]	Calmodulin-1	cytoskeletal protein binding titin binding protein binding binding enzyme regulator activity protein phosphatase activator activity enzyme activator activity phosphatase activator activity molecular function activator activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity channel regulator activity ion channel regulator activity cytoskeletal protein binding titin binding protein binding binding enzyme regulator activity protein phosphatase activator activity enzyme activator activity phosphatase activator activity molecular function activator activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity channel regulator activity ion channel regulator activity calcium channel regulator activity transporter regulator activity molecular function inhibitor activity transporter inhibitor activity calcium channel inhibitor activity ion channel inhibitor activity channel inhibitor activity cyclase regulator activity cyclase activator activity adenylate cyclase regulator activity adenylate cyclase activator activity protein serine/threonine kinase activator activity kinase activator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity cation binding ion binding calcium ion binding metal ion binding small molecule binding transmembrane transporter binding kinase binding enzyme binding protein kinase binding calcium-dependent protein binding	organelle localization by membrane tethering localization organelle localization cellular process membrane docking heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation organelle localization by membrane tethering localization organelle localization cellular process membrane docking heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process regulation of biological quality heart contraction blood circulation regulation of heart rate regulation of localization regulation of calcium ion transport negative regulation of ion transmembrane transporter activity regulation of cellular process negative regulation of calcium ion transmembrane transporter activity transport negative regulation of monoatomic ion transport monoatomic ion transmembrane transport negative regulation of biological process negative regulation of ryanodine-sensitive calcium-release channel activity regulation of transmembrane transporter activity negative regulation of transport regulation of monoatomic ion transmembrane transport negative regulation of transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport intercellular transport negative regulation of monoatomic ion transmembrane transport negative regulation of release of sequestered calcium ion into cytosol negative regulation of cellular process monoatomic ion transport negative regulation of cation transmembrane transport monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport negative regulation of transporter activity negative regulation of molecular function establishment of localization negative regulation of calcium ion transport transmembrane transport regulation of molecular function release of sequestered calcium ion into cytosol regulation of transmembrane transport regulation of ryanodine-sensitive calcium-release channel activity regulation of monoatomic cation transmembrane transport negative regulation of calcium ion transmembrane transport calcium ion transmembrane transport response to stimulus response to metal ion response to chemical response to calcium ion 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 negative regulation of voltage-gated calcium channel activity regulation of voltage-gated calcium channel activity negative regulation of high voltage-gated calcium channel activity cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation autophagosome membrane docking metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism cellular response to interferon-beta response to peptide response to interferon-beta response to cytokine cellular response to cytokine stimulus regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell division cell cycle regulation of cell cycle cell cycle process cellular response to stimulus cardiac muscle contraction intracellular signal transduction cell communication intracellular signaling cassette signal transduction regulation of cardiac muscle contraction muscle contraction regulation of striated muscle contraction calcium-mediated signaling regulation of muscle contraction signaling regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion striated muscle contraction regulation of cardiac muscle contraction by calcium ion signaling muscle system process regulation of muscle system process import into cell cellular localization presynaptic endocytosis vesicle-mediated transport vesicle-mediated transport in synapse establishment of localization in cell endocytosis cell communication by electrical coupling involved in cardiac conduction cell communication by electrical coupling regulation of cell communication by electrical coupling involved in cardiac conduction cardiac conduction regulation of cell communication cell communication involved in cardiac conduction regulation of cell communication by electrical coupling export across plasma membrane negative regulation of calcium ion export across plasma membrane regulation of calcium ion export across plasma membrane calcium ion export across plasma membrane export from cell biological process involved in interspecies interaction between organisms immune response response to other organism defense response response to type II interferon defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus calcineurin-mediated signaling developmental process head development animal organ development brain development nervous system development substantia nigra development multicellular organism development central nervous system development midbrain development anatomical structure development animal gross anatomical part developmental process neural nucleus development system development positive regulation of cell communication cell surface receptor signaling pathway via STAT positive regulation of signal transduction positive regulation of biological process positive regulation of receptor signaling pathway via STAT regulation of signal transduction positive regulation of receptor signaling pathway via JAK-STAT positive regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway regulation of response to stimulus regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT positive regulation of signaling regulation of action potential regulation of cardiac muscle cell action potential action potential cardiac muscle cell action potential regulation of membrane potential G protein-coupled receptor signaling pathway modulation of chemical synaptic transmission long-term synaptic potentiation synaptic signaling regulation of synaptic plasticity trans-synaptic signaling cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling detection of stimulus detection of chemical stimulus detection of calcium ion	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle cell projection intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle cell projection sperm midpiece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection protein-containing complex transmembrane transporter complex membrane membrane protein complex cation channel complex transporter complex calcium channel complex monoatomic ion channel complex axon synapse neuron projection axon terminus presynapse distal axon calyx of Held cell junction neuron projection terminus sarcomere contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex myelin sheath vesicle centrosome microtubule organizing center presynaptic cytosol cell periphery plasma membrane catalytic complex nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen voltage-gated potassium channel complex plasma membrane protein complex potassium channel complex extracellular region polymeric cytoskeletal fiber spindle microtubule microtubule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR056748	Intermembrane lipid transfer protein VPS13-like, C-terminal	Domain
B	IPR026854	Vacuolar protein sorting-associated protein 13, N-terminal domain	Domain
B	IPR056747	VPS13-like, middle region	Domain
B	IPR026847	Vacuolar protein sorting-associated protein 13	Family
B	IPR009543	Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain	Domain
A [auth C]	IPR002048	EF-hand domain	Domain
A [auth C]	IPR050230	Calmodulin/Myosin light chain/Troponin C-like	Family
A [auth C]	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
A [auth C]	IPR011992	EF-hand domain pair	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	: Q96RL7	chorea-acanthocytosis neuroacanthocytosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor astrocytic tumor Chorea Acanthocytosis Syndrome Cohen syndrome glioblastoma malignant ependymoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma Parkinson disease ulcerative colitis atypical teratoid rhabdoid tumor chorea-acanthocytosis neuroacanthocytosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor astrocytic tumor Chorea Acanthocytosis Syndrome Cohen syndrome glioblastoma malignant ependymoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma Parkinson disease ulcerative colitis atypical teratoid rhabdoid tumor colorectal cancer invasive ductal breast carcinoma malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma breast cancer choreatic disease epilepsy large cell medulloblastoma medulloblastoma neurodegenerative disease
A [auth C]	: P0DP23	long QT syndrome catecholaminergic polymorphic ventricular tachycardia Alzheimer disease long QT syndrome 14 cocaine abuse Weight Gain cannabis dependence cocaine dependence phencyclidine abuse catecholaminergic polymorphic ventricular tachycardia 4 rheumatoid arthritis subependymal giant cell astrocytoma glioblastoma large cell medulloblastoma lung adenocarcinoma long QT syndrome catecholaminergic polymorphic ventricular tachycardia Alzheimer disease long QT syndrome 14 cocaine abuse Weight Gain cannabis dependence cocaine dependence phencyclidine abuse catecholaminergic polymorphic ventricular tachycardia 4 rheumatoid arthritis subependymal giant cell astrocytoma glioblastoma large cell medulloblastoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm myopathy astrocytic tumor osteosarcoma pituitary cancer primitive neuroectodermal tumor Crohn disease schizophrenia familial long QT syndrome lung cancer malignant ependymoma nasopharyngeal carcinoma atypical teratoid rhabdoid tumor ovarian cancer Pick disease catecholaminergic polymorphic ventricular tachycardia 2 plasma cell myeloma psoriasis exocrine pancreatic carcinoma sinusitis hepatocellular carcinoma ulcerative colitis lymphoplasmacytic lymphoma malignant glioma medulloblastoma amyotrophic lateral sclerosis oligodendroglioma breast cancer pilocytic astrocytoma

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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.