3NS4 | pdb_00003ns4

Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of GARP to a family of tethering complexes

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	SCOP2 Family	VPS53-like	8046251	4004984	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cullin repeat-like	8093175	3000059	SCOP2 (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	EF-hand_1	e3ns4A2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: EF-hand_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.357.110	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16854	Vacuolar protein sorting-associated protein 53 C-terminus (VPS53_C)	Vacuolar protein sorting-associated protein 53 C-terminus	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Vacuolar protein sorting-associated protein 53	-	cellular localization post-Golgi vesicle-mediated transport transport intracellular transport establishment of localization vesicle-mediated transport Golgi to vacuole transport localization intercellular transport establishment of localization in cell vacuolar transport cellular process Golgi vesicle transport establishment of protein localization cellular localization post-Golgi vesicle-mediated transport transport intracellular transport establishment of localization vesicle-mediated transport Golgi to vacuole transport localization intercellular transport establishment of localization in cell vacuolar transport cellular process Golgi vesicle transport establishment of protein localization protein targeting establishment of protein localization to vacuole protein localization to vacuole establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein localization protein targeting to vacuole intracellular protein transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi cellular homeostasis chemical homeostasis homeostatic process intracellular sphingolipid homeostasis intracellular chemical homeostasis lipid homeostasis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cytosol endosome membrane membrane endosome intracellular vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cytosol endosome membrane membrane endosome intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle organelle membrane protein-containing complex vesicle tethering complex GARP complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR031745	Vps53, C-terminal	Domain
A	IPR038260	Vps53, C-terminal domain superfamily	Homologous Superfamily
A	IPR007234	Vps53, N-terminal	Domain
A	IPR039766	Vacuolar protein sorting-associated protein 53	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.