9QWZ | pdb_00009qwz

Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (BP 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
B	PF24079	E3 ubiquitin-protein ligase UBR4-like domain (UBR4)	E3 ubiquitin-protein ligase UBR4-like domain	This domain is found in human E3 ubiquitin-protein ligase UBR4 and similar proteins mainly found in eukaryotes. UBR4 is a component of the N-end rule pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabili ...	This domain is found in human E3 ubiquitin-protein ligase UBR4 and similar proteins mainly found in eukaryotes. UBR4 is a component of the N-end rule pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilising	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D]	E3 ubiquitin-protein ligase KCMF1	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule 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 cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule 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	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process biological regulation negative regulation of HRI-mediated signaling protein polyubiquitination catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process biological regulation negative regulation of HRI-mediated signaling protein polyubiquitination protein K63-linked ubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein K48-linked ubiquitination synaptic signaling regulation of biological process signaling cell-cell signaling cell communication response to oxidative stress response to stimulus response to stress proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	cellular anatomical structure extracellular region synapse cell junction intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle cellular anatomical structure extracellular region synapse cell junction intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome vesicle membrane-enclosed lumen ficolin-1-rich granule intracellular organelle lumen organelle lumen ficolin-1-rich granule lumen secretory granule secretory vesicle lytic vacuole vacuole lysosome
B	E3 ubiquitin-protein ligase UBR4	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity 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 ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity 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 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 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 cytosol cell periphery plasma membrane cytoskeleton membraneless organelle intracellular membraneless organelle endosome ficolin-1-rich granule membrane ficolin-1-rich granule nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D]	IPR043145	Zinc finger, ZZ-type superfamily	Homologous Superfamily
A [auth D]	IPR013087	Zinc finger C2H2-type	Domain
A [auth D]	IPR008598	Di19, zinc-binding domain	Domain
A [auth D]	IPR050774	KCMF1 and Dystrophin	Family
A [auth D]	IPR000433	Zinc finger, ZZ-type	Domain
B	IPR016024	Armadillo-type fold	Homologous Superfamily
B	IPR047509	E3 ubiquitin-protein ligase UBR4-like, UBR-box	Domain
B	IPR025704	E3 ubiquitin ligase UBR4, C-terminal	Domain
B	IPR045189	E3 ubiquitin ligase UBR4-like	Family
B	IPR003126	Zinc finger, UBR-type	Domain
B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B	IPR056530	E3 ubiquitin-protein ligase UBR4-like domain	Domain
B	IPR045841	E3 ubiquitin-protein ligase UBR4, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D]	Pharos: Q9P0J7	astrocytic tumor malignant glioma ovarian cancer subependymal giant cell astrocytoma lung cancer malignant pancreatic neoplasm pancreatic ductal adenocarcinoma malignant ependymoma osteosarcoma plasma cell myeloma
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.