3R42

Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3r42a_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UEV domain	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	UBC-like	8035336	3000570	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	PF05743	e3r42A1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF05743	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05743	UEV domain (UEV)	UEV domain	This family includes the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other human malignancies. However, the involvement of this gene in neoplastic ...	This family includes the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other human malignancies. However, the involvement of this gene in neoplastic transformation and tumorigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but that this gene is not a tumour suppressor for sporadic forms of breast cancer [1]. This family is related to the ubiquitin conjugating enzymes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease	protein binding binding ubiquitin binding ubiquitin-like protein binding	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosome to lysosome transport lysosomal transport organic substance metabolic process organonitrogen compound metabolic process localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosome to lysosome transport lysosomal transport organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process protein localization establishment of protein localization nitrogen compound transport protein targeting organic substance transport establishment of protein localization to vacuole protein localization to vacuole establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle protein targeting to vacuole intracellular protein transport organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process organic substance catabolic process negative regulation of post-translational protein modification regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination regulation of primary metabolic process protein ubiquitination negative regulation of protein modification process regulation of protein modification by small protein conjugation or removal negative regulation of protein ubiquitination negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process regulation of protein polyubiquitination negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process biological regulation protein polyubiquitination regulation of macromolecule metabolic process negative regulation of protein polyubiquitination post-translational protein modification protein modification by small protein conjugation regulation of metabolic process protein modification by small protein conjugation or removal establishment of protein localization to membrane localization within membrane protein localization to membrane protein targeting to membrane ATP transport organic anion transport nucleotide transport purine ribonucleotide transport carbohydrate derivative transport purine nucleotide transport adenine nucleotide transport ATP export nucleobase-containing compound transport organophosphate ester transport cellular component disassembly macroautophagy cellular metabolic process autophagy cellular component organization cellular catabolic process organelle organization organelle disassembly reticulophagy cellular component organization or biogenesis process utilizing autophagic mechanism	membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle cytosol endosome membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle cytosol endosome membrane protein-containing complex ESCRT complex membrane membrane protein complex ESCRT I complex cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane late endosome membrane late endosome cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane plasma membrane side of membrane
B	Vacuolar protein sorting-associated protein 27	protein binding binding protein domain specific binding protein heterodimerization activity protein dimerization activity ubiquitin binding ubiquitin-like protein binding phospholipid binding lipid binding phosphatidylinositol-3-phosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding cation binding ion binding protein binding binding protein domain specific binding protein heterodimerization activity protein dimerization activity ubiquitin binding ubiquitin-like protein binding phospholipid binding lipid binding phosphatidylinositol-3-phosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding cation binding ion binding metal ion binding small molecule binding	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process multivesicular body sorting pathway regulation of protein maturation positive regulation of protein maturation regulation of cellular process positive regulation of protein metabolic process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process protein maturation positive regulation of metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of cellular biosynthetic process protein localization establishment of protein localization nitrogen compound transport protein targeting organic substance transport establishment of protein localization to vacuole protein localization to vacuole establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle protein targeting to vacuole intracellular protein transport late endosome to vacuole transport via multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway endosomal transport secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell cellular catabolic process autophagy microautophagy process utilizing autophagic mechanism microlipophagy maintenance of protein location protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell protein retention in Golgi apparatus ATP transport organic anion transport nucleotide transport purine ribonucleotide transport carbohydrate derivative transport purine nucleotide transport adenine nucleotide transport ATP export nucleobase-containing compound transport organophosphate ester transport	membrane-bounded organelle ESCRT-0 complex protein-containing complex intracellular anatomical structure ESCRT complex endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm membrane-bounded organelle ESCRT-0 complex protein-containing complex intracellular anatomical structure ESCRT complex endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle endosome membrane membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane vacuolar membrane vacuole

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017916	Steadiness box (SB) domain	Domain
A	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A	IPR008883	Ubiquitin E2 variant, N-terminal	Domain
A	IPR037202	ESCRT assembly domain	Homologous Superfamily
B	IPR002014	VHS domain	Domain
B	IPR008942	ENTH/VHS	Homologous Superfamily
B	IPR017455	Zinc finger, FYVE-related	Domain
B	IPR000306	FYVE zinc finger	Domain
B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B	IPR017073	Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27	Family
B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B	IPR003903	Ubiquitin interacting motif	Conserved Site
B	IPR049425	Vacuolar protein sorting-associated protein 27, GAT-like domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.