9QWX | pdb_00009qwx

Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (N-term focused refinement)

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF19423	E3 ubiquitin-protein ligase UBR4 N-terminal (E3_UBR4_N)	E3 ubiquitin-protein ligase UBR4 N-terminal	This entry represents the N-terminal of E3 ubiquitin-protein ligases UBR4 (POE or PUSHOVER in Drosophila), which are components of the N-rule pathway, identified as noncanonical N-recognins implicated in bulk lysosomal degradation and autophagy. Thes ...	This entry represents the N-terminal of E3 ubiquitin-protein ligases UBR4 (POE or PUSHOVER in Drosophila), which are components of the N-rule pathway, identified as noncanonical N-recognins implicated in bulk lysosomal degradation and autophagy. These are extraordinarily large proteins that recognise and bind to proteins with N-terminal destabilising residues according to the N-end rule leading them to their ubiquitination and degradation. These proteins share a UBR box (Pfam:PF02207) with others E3-ligases UBR box proteins but UBR4 lacks the ubiquitylation domain, suggesting that it may interact with other catalytic proteins [1,2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	E3 ubiquitin-protein ligase UBR4	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein binding binding calmodulin binding cation binding transition metal ion binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein binding binding calmodulin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	protein polyubiquitination protein branched polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of protein stability protein polyubiquitination protein branched polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of protein stability biological regulation regulation of biological quality protein stabilization protein K27-linked ubiquitination cellular response to stimulus catabolic process cytoplasm protein quality control response to stimulus proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress cellular response to topologically incorrect protein cytoplasm protein quality control by the ubiquitin-proteasome system proteasomal protein catabolic process protein catabolic process modification-dependent protein catabolic process response to topologically incorrect protein ubiquitin-dependent protein catabolic process protein quality control for misfolded or incompletely synthesized proteins negative regulation of HRI-mediated signaling ubiquitin-dependent protein catabolic process via the N-end rule pathway protein K11-linked ubiquitination protein K48-linked ubiquitination response to oxidative stress regulation of cellular process negative regulation of small molecule metabolic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process negative regulation of biological process lipid biosynthetic process organic acid metabolic process organic acid biosynthetic process negative regulation of lipid biosynthetic process carboxylic acid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process negative regulation of cellular process small molecule metabolic process negative regulation of fatty acid biosynthetic process regulation of biosynthetic process regulation of biological process fatty acid metabolic process negative regulation of fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process negative regulation of metabolic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of ketone metabolic process biosynthetic process negative regulation of biosynthetic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process regulation of lipid biosynthetic process monocarboxylic acid metabolic process regulation of metabolic process negative regulation of lipid metabolic process lipid metabolic process positive regulation of autophagy autophagy positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process process utilizing autophagic mechanism positive regulation of cellular process vesicle organization cellular component organization organelle organization endosome organization cellular component organization or biogenesis endomembrane system organization	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule membrane specific granule centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytosol cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endosome ficolin-1-rich granule membrane ficolin-1-rich granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR047509	E3 ubiquitin-protein ligase UBR4-like, UBR-box	Domain
A, B	IPR025704	E3 ubiquitin ligase UBR4, C-terminal	Domain
A, B	IPR045189	E3 ubiquitin ligase UBR4-like	Family
A, B	IPR003126	Zinc finger, UBR-type	Domain
A, B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR056530	E3 ubiquitin-protein ligase UBR4-like domain	Domain
A, B	IPR045841	E3 ubiquitin-protein ligase UBR4, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q5T4S7	Ataxias, Hereditary tuberculosis hepatocellular carcinoma melanoma intellectual disability ovarian cancer

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.