4DL0 | pdb_00004dl0

Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth K]	d4dl0k_	Coiled coil proteins	Parallel coiled-coil	V-type ATPase peripheral stalk subunit G coiled coil	V-type ATPase peripheral stalk subunit G coiled coil	automated matches	yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
E [auth G]	d4dl0g_	Coiled coil proteins	Parallel coiled-coil	V-type ATPase peripheral stalk subunit G coiled coil	V-type ATPase peripheral stalk subunit G coiled coil	automated matches	yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C [auth J]	d4dl0j2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	V-type ATPase subunit E-like	V-type ATPase subunit E C-terminal domain	V-type ATPase subunit E C-terminal domain	yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C [auth J]	d4dl0j1	Coiled coil proteins	Parallel coiled-coil	V-type ATPase peripheral stalk subunit E coiled coil	V-type ATPase peripheral stalk subunit E coiled coil	V-type ATPase peripheral stalk subunit E coiled coil	yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
F [auth E]	d4dl0e2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	V-type ATPase subunit E-like	V-type ATPase subunit E C-terminal domain	V-type ATPase subunit E C-terminal domain	yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
F [auth E]	d4dl0e1	Coiled coil proteins	Parallel coiled-coil	V-type ATPase peripheral stalk subunit E coiled coil	V-type ATPase peripheral stalk subunit E coiled coil	V-type ATPase peripheral stalk subunit E coiled coil	yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth I]		e4dl0I1	A: Globin-like	X: Nucleoside diphosphate kinases	H: Nucleoside diphosphate kinases	T: Aldo_ket_red	F:	ECOD (20:10:01)
D [auth C]		e4dl0C2	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T:	F:	ECOD (20:10:01)
B [auth K]		e4dl0K1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Phage tail protein-like	T: DUF4488	F:	ECOD (20:10:01)
E [auth G]		e4dl0G1	A: Glycosyl hydrolase domain-like	X: Hormone receptor domain (HRM, Pfam 02793)	H: Hormone receptor domain (HRM, Pfam 02793)	T: HRM	F:	ECOD (20:10:01)
C [auth J]		e4dl0J1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Med26	F:	ECOD (20:10:01)
F [auth E]		e4dl0E1	A: gp11/gp12 receptor-binding domain	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: VHP	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth I]	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D [auth C]	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B [auth K]	1.20.5.2950	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
E [auth G]	1.20.5.2950	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C [auth J]	3.30.2320.30	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold	ATP synthase, E subunit, C-terminal	CATH (4.3.0)
F [auth E]	3.30.2320.30	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold	ATP synthase, E subunit, C-terminal	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth I], D [auth C]	V-type proton ATPase subunit C	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 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 transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization homeostatic process biological regulation intracellular pH reduction Golgi lumen acidification 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 homeostatic process biological regulation intracellular pH reduction Golgi lumen acidification regulation of intracellular pH cellular homeostasis 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 vesicle organization cellular component organization organelle organization endosome organization cellular component organization or biogenesis endosomal lumen acidification endomembrane system organization vacuolar acidification	vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane fungal-type vacuole membrane ATPase dependent transmembrane transport complex protein-containing complex ATPase complex 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 proton-transporting two-sector ATPase complex proton-transporting two-sector ATPase complex, catalytic domain catalytic complex vacuolar proton-transporting V-type ATPase complex cation-transporting ATPase complex transmembrane transporter complex Golgi membrane Golgi apparatus endomembrane system
B [auth K], E [auth G]	V-type proton ATPase subunit G	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 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 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 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 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 transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization homeostatic process biological regulation intracellular pH reduction regulation of intracellular pH 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 homeostatic process biological regulation intracellular pH reduction regulation of intracellular pH vesicle organization cellular component organization organelle organization cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis endosome organization intracellular chemical homeostasis cellular component organization or biogenesis regulation of biological quality endosomal lumen acidification monoatomic cation homeostasis endomembrane system organization regulation of cellular pH intracellular monoatomic ion homeostasis Golgi lumen acidification vacuolar acidification	vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane fungal-type vacuole membrane ATPase dependent transmembrane transport complex protein-containing complex ATPase complex membrane protein complex proton-transporting V-type ATPase complex transporter complex proton-transporting two-sector ATPase complex catalytic complex vacuolar proton-transporting V-type ATPase complex cation-transporting ATPase complex transmembrane transporter complex proton-transporting V-type ATPase, V1 domain vacuolar proton-transporting V-type ATPase, V1 domain proton-transporting two-sector ATPase complex, catalytic domain Golgi membrane Golgi apparatus endomembrane system
C [auth J], F [auth E]	V-type proton ATPase subunit E	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 transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization homeostatic process biological regulation intracellular pH reduction Golgi lumen acidification 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 homeostatic process biological regulation intracellular pH reduction Golgi lumen acidification regulation of intracellular pH cellular homeostasis 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 vesicle organization cellular component organization organelle organization endosome organization cellular component organization or biogenesis endosomal lumen acidification endomembrane system organization vacuolar acidification	vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane fungal-type vacuole membrane ATPase dependent transmembrane transport complex protein-containing complex ATPase complex 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 proton-transporting two-sector ATPase complex proton-transporting two-sector ATPase complex, catalytic domain catalytic complex vacuolar proton-transporting V-type ATPase complex cation-transporting ATPase complex transmembrane transporter complex Golgi membrane Golgi apparatus endomembrane system membrane microdomain membrane raft

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth I], D [auth C]	IPR036132	Vacuolar ATP synthase subunit C superfamily	Homologous Superfamily
A [auth I], D [auth C]	IPR004907	ATPase, V1 complex, subunit C	Family
B [auth K], E [auth G]	IPR005124	Vacuolar (H+)-ATPase G subunit	Family
C [auth J], F [auth E]	IPR038495	V-type ATPase subunit E, C-terminal domain superfamily	Homologous Superfamily
C [auth J], F [auth E]	IPR002842	V-type ATPase subunit E	Family

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth I], B [auth K], C [auth J], D [auth C], E [auth G] A [auth I], B [auth K], C [auth J], D [auth C], E [auth G], F [auth E]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Vacuolar ATPase (V-ATPase)	Heterotrimeric EGChead Peripheral Stalk Complex

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.