Annotations: 9HYF

Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (composite map)

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], D	PF00569	Zinc finger, ZZ type (ZZ)	Zinc finger, ZZ type	Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure [2].	Domain
B [auth C], D	PF05605	Drought induced 19 protein (Di19), zinc-binding (zf-Di19)	Drought induced 19 protein (Di19), zinc-binding	This family consists of several drought induced 19 (Di19) like proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [1]. This domain is a zinc-binding domain.	Domain
A, C [auth B]	PF02207	Putative zinc finger in N-recognin (UBR box) (zf-UBR)	Putative zinc finger in N-recognin (UBR box)	This region is found in E3 ubiquitin ligases that recognise N-recognins [1].	Domain
A, C [auth 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
A, C [auth B]	PF02916	DNA polymerase processivity factor (DNA_PPF)	DNA polymerase processivity factor		Domain
A, C [auth B]	PF13764	E3 ubiquitin-protein ligase UBR4 (E3_UbLigase_R4)	E3 ubiquitin-protein ligase UBR4	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D	E3 ubiquitin-protein ligase kcmf-1	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion 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 DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion 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	regulation of signaling regulation of biological process signaling biological regulation synaptic signaling cell-cell signaling cellular process cell communication regulation of cellular process regulation of cell communication	cellular anatomical structure synapse cell junction cell periphery plasma membrane membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle cellular anatomical structure synapse cell junction cell periphery plasma membrane membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome cytoplasm vesicle lytic vacuole vacuole lysosome
A, C [auth B]	UBR-type domain-containing protein	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	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process ubiquitin-dependent protein catabolic process via the N-end rule pathway catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process ubiquitin-dependent protein catabolic process via the N-end rule pathway catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process protein metabolic process cytoplasm protein quality control protein quality control for misfolded or incompletely synthesized proteins	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR043145	Zinc finger, ZZ-type superfamily	Homologous Superfamily
B [auth C], D	IPR008598	Di19, zinc-binding domain	Domain
B [auth C], D	IPR050774	KCMF1 and Dystrophin	Family
B [auth C], D	IPR000433	Zinc finger, ZZ-type	Domain
A, C [auth B]	IPR025704	E3 ubiquitin ligase UBR4, C-terminal	Domain
A, C [auth B]	IPR045189	E3 ubiquitin ligase UBR4-like	Family
A, C [auth B]	IPR003126	Zinc finger, UBR-type	Domain
A, C [auth B]	IPR004190	DNA polymerase processivity factor	Domain
A, C [auth B]	IPR056530	E3 ubiquitin-protein ligase UBR4-like domain	Domain

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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.

9HYF | pdb_00009hyf

Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (composite map)

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage