3ZYQ

Crystal structure of the tandem VHS and FYVE domains of Hepatocyte growth factor-regulated tyrosine kinase substrate (HGS-Hrs) at 1.48 A resolution

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3zyqa1	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3zyqa2	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	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	VHS	e3zyqA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: VHS	ECOD (1.6)
A	FYVE	e3zyqA2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: FYVE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01363	FYVE zinc finger (FYVE)	FYVE zinc finger	The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions [1]. The FYVE finger has eight potential zinc coordinating cysteine positions. Man ...	The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions [1]. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE	binding phospholipid binding lipid binding phosphatidylinositol binding protein binding protein domain specific binding ubiquitin binding ubiquitin-like protein binding ubiquitin-like protein ligase binding enzyme binding cation binding ion binding metal ion binding small molecule binding	membrane organization cellular component organization membrane invagination cellular process cellular component organization or biogenesis cellular response to stimulus regulation of cellular process response to stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction regulation of platelet-derived growth factor receptor signaling pathway negative regulation of cell communication membrane organization cellular component organization membrane invagination cellular process cellular component organization or biogenesis cellular response to stimulus regulation of cellular process response to stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction regulation of platelet-derived growth factor receptor signaling pathway negative regulation of cell communication cell surface receptor protein tyrosine kinase signaling pathway cell communication negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of platelet-derived growth factor receptor signaling pathway biological regulation platelet-derived growth factor receptor signaling pathway negative regulation of signal transduction regulation of response to stimulus regulation of cell communication localization import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport organelle assembly multivesicular body assembly vesicle organization cellular component biogenesis organelle organization cellular component assembly multivesicular body organization endosome organization endomembrane system organization catabolic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process macromolecule catabolic process regulation of primary metabolic process metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process regulation of biosynthetic process positive regulation of biological process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process cellular response to growth factor stimulus negative regulation of cellular response to growth factor stimulus regulation of vascular endothelial growth factor receptor signaling pathway cellular response to endogenous stimulus negative regulation of vascular endothelial growth factor receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway response to growth factor cell surface receptor signaling pathway via STAT regulation of receptor signaling pathway via JAK-STAT negative regulation of receptor signaling pathway via JAK-STAT negative regulation of receptor signaling pathway via STAT regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT membrane fission macroautophagy autophagy process utilizing autophagic mechanism cellular localization establishment of localization in cell intracellular transport endosomal transport regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of transferase activity regulation of MAP kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process protein modification process protein phosphorylation phosphorylation regulation of protein kinase activity regulation of molecular function regulation of kinase activity regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation protein localization cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane establishment of protein localization nitrogen compound transport proteolysis involved in protein catabolic process establishment of protein localization to vacuole late endosome to vacuole transport modification-dependent macromolecule catabolic process late endosome to vacuole transport via multivesicular body sorting pathway proteolysis endosome transport via multivesicular body sorting pathway protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway protein localization to vacuole establishment of protein localization to organelle protein transport modification-dependent protein catabolic process multivesicular body sorting pathway protein localization to organelle ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process vacuolar transport intracellular protein transport exosomal secretion establishment of organelle localization regulation of localization positive regulation of secretion by cell positive regulation of exosomal secretion positive regulation of exocytosis secretion by cell regulation of secretion by cell positive regulation of secretion organelle localization vesicle localization positive regulation of cellular component biogenesis secretion regulation of transport regulation of exosomal secretion establishment of vesicle localization export from cell regulation of cellular component biogenesis regulation of vesicle-mediated transport extracellular exosome biogenesis regulation of secretion exocytosis positive regulation of transport extracellular vesicle biogenesis regulation of exocytosis protein targeting lysosomal transport protein targeting to lysosome protein targeting to vacuole protein localization to lysosome multicellular organismal process regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis system development blood vessel development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process endocytic recycling vesicle-mediated transport to the plasma membrane	membrane-bounded organelle endosome membrane intracellular anatomical structure endosome membrane multivesicular body membrane intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle membrane-bounded organelle endosome membrane intracellular anatomical structure endosome membrane multivesicular body membrane intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle late endosome cytoplasm vesicle organelle membrane multivesicular body ESCRT-0 complex protein-containing complex ESCRT complex extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol lytic vacuole vacuole lysosome phagocytic vesicle lumen membrane-enclosed lumen phagocytic vesicle intracellular organelle lumen organelle lumen endocytic vesicle lumen endocytic vesicle early endosome early endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR024641	Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain	Domain
A	IPR002014	VHS domain	Domain
A	IPR008942	ENTH/VHS	Homologous Superfamily
A	IPR017455	Zinc finger, FYVE-related	Domain
A	IPR000306	FYVE zinc finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR017073	Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27	Family
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR003903	Ubiquitin interacting motif	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O14964	corneal disease pancreatic ductal adenocarcinoma oligodendroglioma psoriasis osteosarcoma

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.