4TU3 | pdb_00004tu3

Crystal structure of yeast Sac1/Vps74 complex

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)
B [auth A]	SCOP2B Superfamily	Winged helix DNA-binding domain	8106700	3000034	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)
B [auth A]	GntR	e4tu3A1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: GntR	ECOD (v294.1)
A [auth X]	GntR	e4tu3X1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: GntR	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	1.10.3630.10	Mainly Alpha	Orthogonal Bundle	yeast vps74-n-term truncation variant fold	yeast vps74-n-term truncation variant domain like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF05719	Golgi phosphoprotein 3 (GPP34) (GPP34)	Golgi phosphoprotein 3 (GPP34)	-	Family
A [auth X]	PF02383	SacI homology domain (Syja_N)	SacI homology domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	Vacuolar protein sorting-associated protein 74	binding ion binding anion binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol-4-phosphate binding small molecule binding protein binding enzyme binding	carbohydrate derivative biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein N-linked glycosylation macromolecule biosynthetic process biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process Golgi to plasma membrane transport establishment of protein localization carbohydrate derivative biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein N-linked glycosylation macromolecule biosynthetic process biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process Golgi to plasma membrane transport establishment of protein localization cellular localization protein localization to cell periphery post-Golgi vesicle-mediated transport transport establishment of protein localization to membrane protein localization to plasma membrane establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization protein transport macromolecule localization intracellular protein localization Golgi vesicle transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum membrane organization vesicle budding from membrane Golgi vesicle budding cellular component organization vesicle organization organelle organization cellular component organization or biogenesis protein O-linked glycosylation via mannose protein O-linked glycosylation maintenance of protein location protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell protein localization to organelle protein retention in Golgi apparatus phosphatidylinositol metabolic process regulation of biological process regulation of cellular process regulation of dephosphorylation regulation of lipid metabolic process dephosphorylation biological regulation lipid modification regulation of macromolecule metabolic process regulation of primary metabolic process regulation of phosphatidylinositol dephosphorylation phosphatidylinositol dephosphorylation phosphate-containing compound metabolic process phospholipid dephosphorylation regulation of phosphorus metabolic process phosphorus metabolic process regulation of metabolic process lipid metabolic process cellular response to stimulus cellular response to topologically incorrect protein response to stimulus signaling endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein intracellular signal transduction cell communication cellular response to stress response to stress response to topologically incorrect protein signal transduction response to endoplasmic reticulum stress Golgi organization endomembrane system organization	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle Golgi stack cytoplasm Golgi medial cisterna membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle Golgi stack cytoplasm Golgi medial cisterna trans-Golgi network Golgi membrane membrane bounding membrane of organelle organelle membrane cytosol Golgi cisterna membrane nucleus
A [auth X]	Phosphoinositide phosphatase SAC1	phosphoric ester hydrolase activity phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity hydrolase activity, acting on ester bonds phosphatidylinositol bisphosphate phosphatase activity phosphatase activity hydrolase activity phosphatidylinositol-3,5-bisphosphate phosphatase activity phosphatidylinositol phosphate phosphatase activity catalytic activity phosphatidylinositol-3-phosphate phosphatase activity phosphatidylinositol monophosphate phosphatase activity phosphatidylinositol-4-phosphate phosphatase activity phosphatidylinositol phosphate 4-phosphatase activity	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism phosphatidylinositol metabolic process dephosphorylation lipid modification primary metabolic process phosphatidylinositol dephosphorylation phospholipid dephosphorylation phosphate-containing compound metabolic process phosphorus metabolic process lipid metabolic process 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 mitochondrion organelle cytoplasm intracellular membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna endomembrane system Golgi stack membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna endomembrane system Golgi stack Golgi medial cisterna cell cortex cortical endoplasmic reticulum cell periphery endoplasmic reticulum subcompartment endoplasmic reticulum endoplasmic reticulum tubular network Golgi membrane membrane bounding membrane of organelle organelle membrane mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane serine palmitoyltransferase complex protein-containing complex catalytic complex palmitoyltransferase complex transferase complex host intracellular membrane-bounded organelle host cellular component cytoplasmic viral factory host intracellular part other organism part host cell cytoplasm part host intracellular organelle host cell viral assembly compartment viral factory host cell cytoplasm host cell part host intracellular region nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR008628	Golgi phosphoprotein 3-like	Family
B [auth A]	IPR038261	Golgi phosphoprotein 3-like domain superfamily	Homologous Superfamily
A [auth X]	IPR002013	SAC domain	Domain

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.