6VQJ | pdb_00006vqj

Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth G]	SCOP2B Superfamily	Vacuolar ATP synthase subunit C	8099588	3001744	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 [auth G]	PX	e6vqjG1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: PX	ECOD (develop294)
D [auth K]	7tm_2	e6vqjK1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: 7tm_2	ECOD (develop294)
C [auth J]	7tm_2	e6vqjJ1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: 7tm_2	ECOD (develop294)
B [auth I]	7tm_2	e6vqjI1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: 7tm_2	ECOD (develop294)
G [auth O]	CBS	e6vqjO1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: CBS	ECOD (develop294)
F [auth N]	CBS	e6vqjN1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: CBS	ECOD (develop294)
E [auth M]	CBS	e6vqjM1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: CBS	ECOD (develop294)
H [auth a]	CBS	e6vqja1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: CBS	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G]	PF03223	V-ATPase subunit C (V-ATPase_C)	V-ATPase subunit C	-	Family
B [auth I], C [auth J], D [auth K]	PF01991	ATP synthase (E/31 kDa) subunit (vATP-synt_E)	ATP synthase (E/31 kDa) subunit	-	Family
E [auth M], F [auth N], G [auth O]	PF03179	Vacuolar (H+)-ATPase G subunit (V-ATPase_G)	Vacuolar (H+)-ATPase G subunit	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G]	V-type proton ATPase subunit C 1	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	synaptic vesicle maturation cellular localization homeostatic process transport monoatomic ion transmembrane transport synaptic vesicle cycle vesicle-mediated transport vesicle-mediated transport in synapse monoatomic cation transmembrane transport vesicle organization cellular component organization localization establishment of localization in cell monoatomic ion transport synaptic vesicle maturation cellular localization homeostatic process transport monoatomic ion transmembrane transport synaptic vesicle cycle vesicle-mediated transport vesicle-mediated transport in synapse monoatomic cation transmembrane transport vesicle organization cellular component organization localization establishment of localization in cell monoatomic ion transport cellular component organization or biogenesis synaptic vesicle lumen acidification monoatomic cation transport developmental process proton transmembrane transport developmental maturation establishment of localization transmembrane transport organelle organization cellular homeostasis neuron cellular homeostasis cellular process	ATPase dependent transmembrane transport complex protein-containing complex ATPase complex catalytic complex membrane membrane protein complex proton-transporting V-type ATPase, V1 domain proton-transporting V-type ATPase complex transporter complex cation-transporting ATPase complex cellular anatomical structure proton-transporting two-sector ATPase complex proton-transporting two-sector ATPase complex, catalytic domain transmembrane transporter complex ATPase dependent transmembrane transport complex protein-containing complex ATPase complex catalytic complex membrane membrane protein complex proton-transporting V-type ATPase, V1 domain proton-transporting V-type ATPase complex transporter complex cation-transporting ATPase complex cellular anatomical structure proton-transporting two-sector ATPase complex proton-transporting two-sector ATPase complex, catalytic domain transmembrane transporter complex cell periphery plasma membrane membrane-bounded organelle intracellular anatomical structure vacuolar proton-transporting V-type ATPase, V1 domain intracellular organelle bounding membrane of organelle vacuolar membrane vacuole intracellular membrane-bounded organelle vacuolar proton-transporting V-type ATPase complex organelle cytoplasm organelle membrane apical part of cell extrinsic component of synaptic vesicle membrane synapse intracellular vesicle transport vesicle membrane extrinsic component of organelle membrane endomembrane system presynapse cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane cell junction vesicle transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle extrinsic component of membrane exocytic vesicle coated vesicle membrane clathrin-coated vesicle coated vesicle clathrin-coated vesicle membrane
B [auth I], C [auth J], D [auth K]	V-type proton ATPase subunit E 1	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity ATPase binding protein binding binding enzyme binding	monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization synaptic vesicle maturation cellular localization homeostatic process synaptic vesicle cycle monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization synaptic vesicle maturation cellular localization homeostatic process synaptic vesicle cycle vesicle-mediated transport vesicle-mediated transport in synapse vesicle organization cellular component organization establishment of localization in cell cellular component organization or biogenesis synaptic vesicle lumen acidification developmental process developmental maturation organelle organization cellular homeostasis neuron cellular homeostasis	ATPase dependent transmembrane transport complex membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure membrane protein complex proton-transporting V-type ATPase complex proton-transporting V-type ATPase, V1 domain transporter complex vacuolar proton-transporting V-type ATPase, V1 domain intracellular organelle cellular anatomical structure bounding membrane of organelle proton-transporting two-sector ATPase complex ATPase dependent transmembrane transport complex membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure membrane protein complex proton-transporting V-type ATPase complex proton-transporting V-type ATPase, V1 domain transporter complex vacuolar proton-transporting V-type ATPase, V1 domain intracellular organelle cellular anatomical structure bounding membrane of organelle proton-transporting two-sector ATPase complex proton-transporting two-sector ATPase complex, catalytic domain vacuolar membrane catalytic complex membrane vacuole intracellular membrane-bounded organelle vacuolar proton-transporting V-type ATPase complex cation-transporting ATPase complex transmembrane transporter complex organelle cytoplasm organelle membrane cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle vesicle cytosol cell projection actin-based cell projection microvillus plasma membrane bounded cell projection extrinsic component of synaptic vesicle membrane synapse transport vesicle membrane extrinsic component of organelle membrane presynapse vesicle membrane synaptic vesicle synaptic vesicle membrane cell junction transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle extrinsic component of membrane exocytic vesicle coated vesicle membrane clathrin-coated vesicle coated vesicle clathrin-coated vesicle membrane
E [auth M], F [auth N], G [auth O]	V-type proton ATPase subunit G	monoatomic cation transmembrane transporter activity P-type transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type proton-exporting transporter activity ATP-dependent activity P-type ion transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity P-type transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type proton-exporting transporter activity ATP-dependent activity P-type ion transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity 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 proton-transporting ATPase activity, rotational mechanism ATPase-coupled ion transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism	monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization synaptic vesicle maturation cellular localization homeostatic process synaptic vesicle cycle monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization synaptic vesicle maturation cellular localization homeostatic process synaptic vesicle cycle vesicle-mediated transport vesicle-mediated transport in synapse vesicle organization cellular component organization establishment of localization in cell cellular component organization or biogenesis synaptic vesicle lumen acidification developmental process developmental maturation organelle organization cellular homeostasis neuron cellular homeostasis	ATPase dependent transmembrane transport complex membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure membrane protein complex proton-transporting V-type ATPase complex transporter complex intracellular organelle cellular anatomical structure bounding membrane of organelle proton-transporting two-sector ATPase complex vacuolar membrane catalytic complex ATPase dependent transmembrane transport complex membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure membrane protein complex proton-transporting V-type ATPase complex transporter complex intracellular organelle cellular anatomical structure bounding membrane of organelle proton-transporting two-sector ATPase complex vacuolar membrane catalytic complex membrane vacuole intracellular membrane-bounded organelle vacuolar proton-transporting V-type ATPase complex cation-transporting ATPase complex transmembrane transporter complex organelle cytoplasm organelle membrane synapse intracellular vesicle transport vesicle membrane endomembrane system presynapse cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane cell junction vesicle transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle exocytic vesicle proton-transporting V-type ATPase, V1 domain vacuolar proton-transporting V-type ATPase, V1 domain proton-transporting two-sector ATPase complex, catalytic domain extrinsic component of synaptic vesicle membrane extrinsic component of organelle membrane extrinsic component of membrane
H [auth a]	V-type proton ATPase 116 kDa subunit a isoform 1	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity ATPase binding protein binding binding enzyme binding	regulation of biological process catabolic process regulation of cellular process macroautophagy autophagy biological regulation regulation of catabolic process regulation of autophagy regulation of macroautophagy cellular process metabolic process process utilizing autophagic mechanism regulation of metabolic process synaptic vesicle maturation regulation of biological process catabolic process regulation of cellular process macroautophagy autophagy biological regulation regulation of catabolic process regulation of autophagy regulation of macroautophagy cellular process metabolic process process utilizing autophagic mechanism regulation of metabolic process synaptic vesicle maturation cellular localization homeostatic process transport monoatomic ion transmembrane transport synaptic vesicle cycle vesicle-mediated transport vesicle-mediated transport in synapse monoatomic cation transmembrane transport vesicle organization cellular component organization localization establishment of localization in cell monoatomic ion transport cellular component organization or biogenesis synaptic vesicle lumen acidification monoatomic cation transport developmental process proton transmembrane transport developmental maturation establishment of localization transmembrane transport organelle organization cellular homeostasis neuron cellular homeostasis intracellular pH reduction regulation of intracellular pH vacuolar acidification chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis regulation of biological quality monoatomic cation homeostasis regulation of cellular pH intracellular monoatomic ion homeostasis	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle Golgi apparatus cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle Golgi apparatus endomembrane system nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen axon synapse neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon terminal bouton cell junction neuron projection terminus ATPase dependent transmembrane transport complex protein-containing complex ATPase complex vacuolar proton-transporting V-type ATPase, V0 domain membrane protein complex proton-transporting V-type ATPase complex transporter complex bounding membrane of organelle proton-transporting two-sector ATPase complex proton-transporting V-type ATPase, V0 domain vacuolar membrane catalytic complex vacuole proton-transporting two-sector ATPase complex, proton-transporting domain vacuolar proton-transporting V-type ATPase complex cation-transporting ATPase complex transmembrane transporter complex organelle membrane cytosol perinuclear region of cytoplasm cell periphery plasma membrane transport vesicle membrane vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle exocytic vesicle coated vesicle membrane clathrin-coated vesicle coated vesicle clathrin-coated vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G]	IPR004907	ATPase, V1 complex, subunit C	Family
A [auth G]	IPR036132	Vacuolar ATP synthase subunit C superfamily	Homologous Superfamily
B [auth I], C [auth J], D [auth K]	IPR038495	V-type ATPase subunit E, C-terminal domain superfamily	Homologous Superfamily
B [auth I], C [auth J], D [auth K]	IPR002842	V-type ATPase subunit E	Family
E [auth M], F [auth N], G [auth O]	IPR005124	Vacuolar (H+)-ATPase G subunit	Family
H [auth a]	IPR026028	ATPase, V0 complex, subunit 116kDa, eukaryotic	Family
H [auth a]	IPR002490	V-type ATPase, V0 complex, 116kDa subunit family	Family

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.