Annotations: 7YTJ

Cryo-EM structure of VTC complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2B Superfamily	CYTH-like phosphatases	8052394	3001426	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 D]	Proton_antipo_M,Proton_antipo_N	e7ytjD01	A: beta barrels	X: Fe-binding domain in prismane-like proteins	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Proton_antipo_M,Proton_antipo_N	ECOD (v294.2)
E	Proton_antipo_M,Proton_antipo_N	e7ytjE01	A: beta barrels	X: Fe-binding domain in prismane-like proteins	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Proton_antipo_M,Proton_antipo_N	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D]	PF09359	VTC domain (VTC)	VTC domain	This presumed domain is found in the yeast vacuolar transport chaperone proteins VTC2, VTC3 and VTC4. This domain is also found in a variety of bacterial proteins.	Domain
A [auth D]	PF02656	Domain of unknown function (DUF202) (DUF202)	Domain of unknown function (DUF202)	-	Family
B [auth A], C [auth B], D [auth C]	PF02656	Domain of unknown function (DUF202) (DUF202)	Domain of unknown function (DUF202)	-	Family
E	PF09359	VTC domain (VTC)	VTC domain	This presumed domain is found in the yeast vacuolar transport chaperone proteins VTC2, VTC3 and VTC4. This domain is also found in a variety of bacterial proteins.	Domain
E	PF02656	Domain of unknown function (DUF202) (DUF202)	Domain of unknown function (DUF202)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D]	Vacuolar transporter chaperone 4	kinase activity transferase activity polyphosphate kinase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups protein binding binding calmodulin binding ion binding inositol hexakisphosphate binding alcohol binding anion binding small molecule binding	localization cellular localization transport establishment of localization in cell vacuolar transport intracellular transport cellular process establishment of localization catabolic process autophagy microautophagy metabolic process process utilizing autophagic mechanism membrane organization localization cellular localization transport establishment of localization in cell vacuolar transport intracellular transport cellular process establishment of localization catabolic process autophagy microautophagy metabolic process process utilizing autophagic mechanism membrane organization engulfment of target by autophagosome autophagosome assembly organelle assembly vacuole organization macroautophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly membrane invagination cellular component organization or biogenesis biosynthetic process polyphosphate biosynthetic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process phosphorus metabolic process polyphosphate metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuolar membrane storage vacuole membrane lytic vacuole membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuolar membrane storage vacuole membrane lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane bounding membrane of organelle organelle membrane fungal-type vacuole membrane autophagosome membrane autophagosome cell periphery cell cortex protein-containing complex vacuolar transporter chaperone complex membrane protein complex intracellular protein-containing complex endoplasmic reticulum endomembrane system organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane
B [auth A], C [auth B], D [auth C]	Vacuolar transporter chaperone 1	RNA binding binding nucleic acid binding mRNA binding	localization cellular localization transport establishment of localization in cell vacuolar transport intracellular transport cellular process establishment of localization catabolic process autophagy microautophagy metabolic process process utilizing autophagic mechanism organelle fusion localization cellular localization transport establishment of localization in cell vacuolar transport intracellular transport cellular process establishment of localization catabolic process autophagy microautophagy metabolic process process utilizing autophagic mechanism organelle fusion cellular component organization vacuole fusion organelle organization vacuole organization vacuole fusion, non-autophagic cellular component organization or biogenesis membrane organization engulfment of target by autophagosome autophagosome assembly organelle assembly macroautophagy autophagosome organization cellular component biogenesis cellular component assembly membrane invagination biosynthetic process polyphosphate biosynthetic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process phosphorus metabolic process polyphosphate metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuolar membrane storage vacuole membrane lytic vacuole membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuolar membrane storage vacuole membrane lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane bounding membrane of organelle organelle membrane fungal-type vacuole membrane autophagosome membrane autophagosome cell periphery cell cortex nuclear membrane nucleus endomembrane system organelle envelope nuclear envelope protein-containing complex vacuolar transporter chaperone complex membrane protein complex intracellular protein-containing complex endoplasmic reticulum organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane
E	Vacuolar transporter chaperone 3	protein binding binding calmodulin binding ion binding inositol hexakisphosphate binding alcohol binding anion binding small molecule binding	phosphate ion homeostasis intracellular phosphate ion homeostasis cellular homeostasis inorganic ion homeostasis chemical homeostasis homeostatic process intracellular chemical homeostasis localization cellular localization transport establishment of localization in cell vacuolar transport intracellular transport cellular process phosphate ion homeostasis intracellular phosphate ion homeostasis cellular homeostasis inorganic ion homeostasis chemical homeostasis homeostatic process intracellular chemical homeostasis localization cellular localization transport establishment of localization in cell vacuolar transport intracellular transport cellular process establishment of localization catabolic process autophagy microautophagy metabolic process process utilizing autophagic mechanism organelle fusion cellular component organization vacuole fusion organelle organization vacuole organization vacuole fusion, non-autophagic cellular component organization or biogenesis membrane organization engulfment of target by autophagosome autophagosome assembly organelle assembly macroautophagy autophagosome organization cellular component biogenesis cellular component assembly membrane invagination biosynthetic process polyphosphate biosynthetic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process phosphorus metabolic process polyphosphate metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuolar membrane storage vacuole membrane lytic vacuole membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuolar membrane storage vacuole membrane lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane bounding membrane of organelle organelle membrane fungal-type vacuole membrane autophagosome membrane autophagosome cell periphery cell cortex protein-containing complex vacuolar transporter chaperone complex membrane protein complex intracellular protein-containing complex endoplasmic reticulum endomembrane system organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D]	IPR042267	VTC domain superfamily	Homologous Superfamily
A [auth D]	IPR003807	Domain of unknown function DUF202	Domain
A [auth D]	IPR004331	SPX domain	Domain
A [auth D]	IPR018966	VTC domain	Domain
A [auth D]	IPR051572	Vacuolar Transporter Chaperone Complex Subunit	Family
B [auth A], C [auth B], D [auth C]	IPR003807	Domain of unknown function DUF202	Domain
B [auth A], C [auth B], D [auth C]	IPR051572	Vacuolar Transporter Chaperone Complex Subunit	Family
E	IPR042267	VTC domain superfamily	Homologous Superfamily
E	IPR003807	Domain of unknown function DUF202	Domain
E	IPR004331	SPX domain	Domain
E	IPR018966	VTC domain	Domain
E	IPR051572	Vacuolar Transporter Chaperone Complex Subunit	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth D], B [auth A], C [auth B], D [auth C], E	OPM	Transmembrane	Alpha-helical polytopic	Polyphosphate polymerase	Vacuolar polyphosphate polymerase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth D], B [auth A], C [auth B], D [auth C], E	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth D], B [auth A], C [auth B], D [auth C], E	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth D], B [auth A], C [auth B], D [auth C], E	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Vacuolar Transporter Chaperone (VTC) Complex Family	Vacuolar transporter chaperone VTC1-VTC3-VTC4 complex

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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.