2KDI | pdb_00002kdi

Solution structure of a Ubiquitin/UIM fusion protein

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ubiquitin	e2kdiA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02809	Ubiquitin interaction motif (UIM)	Ubiquitin interaction motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein	protein binding binding protein domain specific binding polyubiquitin modification-dependent protein binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding protein heterodimerization activity protein dimerization activity ubiquitin binding ubiquitin-like protein binding K63-linked polyubiquitin modification-dependent protein binding phospholipid binding lipid binding phosphatidylinositol-3-phosphate binding protein binding binding protein domain specific binding polyubiquitin modification-dependent protein binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding protein heterodimerization activity protein dimerization activity ubiquitin binding ubiquitin-like protein binding K63-linked polyubiquitin modification-dependent protein binding phospholipid binding lipid binding phosphatidylinositol-3-phosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding cation binding transition metal ion binding zinc ion 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 cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus 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 cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation catabolic process proteolysis involved in protein catabolic process primary metabolic 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 metabolic process macromolecule metabolic process protein metabolic process multivesicular body sorting pathway regulation of protein maturation positive regulation of protein maturation regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process protein maturation positive regulation of metabolic process positive regulation of 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 biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process establishment of protein localization nitrogen compound transport 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 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 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 intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm membrane-bounded organelle ESCRT-0 complex protein-containing complex intracellular anatomical structure ESCRT complex endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure 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	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
A	IPR049425	Vacuolar protein sorting-associated protein 27, GAT-like 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.