2LVO | pdb_00002lvo

Structure of the gp78CUE domain bound to monubiquitin

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2lvoa_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	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	RRM_1	e2lvoA1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
B [auth C]	Rrf2	e2lvoC1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: Rrf2	ECOD (v294.1)

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 (4.3.0)
B [auth C]	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
B [auth C]	PF02845	CUE domain (CUE)	CUE domain	CUE domains have been shown to bind ubiquitin [3-4]. It has been suggested that CUE domains are related to Pfam:PF00627 [4] and this has been confirmed by the structure of the domain [5]. CUE domains also occur in two protein of the IL-1 signal trans ...	CUE domains have been shown to bind ubiquitin [3-4]. It has been suggested that CUE domains are related to Pfam:PF00627 [4] and this has been confirmed by the structure of the domain [5]. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2 [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process 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	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B [auth C]	E3 ubiquitin-protein ligase AMFR	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity molecular transducer activity signaling receptor activity protein binding binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity molecular transducer activity signaling receptor activity protein binding binding ubiquitin binding ubiquitin-like protein binding protein-containing complex binding BAT3 complex binding protein-folding chaperone binding protein-macromolecule adaptor activity molecular adaptor activity ubiquitin-specific protease binding enzyme binding protease binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding	cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress cellular process metabolic process protein metabolic process cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress protein polyubiquitination protein K27-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 regulation of cellular process signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus biological regulation negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication protein autoubiquitination regulation of cellular response to stress intracellular signal transduction regulation of intracellular signal transduction regulation of response to stress ER-nucleus signaling pathway cellular response to sterol depletion regulation of SREBP signaling pathway response to sterol depletion SREBP signaling pathway non-canonical NF-kappaB signal transduction intracellular signaling cassette protein alpha-1,2-demannosylation carbohydrate derivative metabolic process glycoprotein metabolic process protein deglycosylation protein demannosylation endoplasmic reticulum mannose trimming modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process protein K48-linked ubiquitination behavior multicellular organismal process system process learning or memory nervous system process cognition cellular response to topologically incorrect protein endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein response to topologically incorrect protein	cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane protein complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle Derlin-1 retrotranslocation complex organelle nuclear outer membrane-endoplasmic reticulum membrane network cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane protein complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle Derlin-1 retrotranslocation complex organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection growth cone axon distal axon site of polarized growth endoplasmic reticulum quality control compartment Golgi apparatus perinuclear region of cytoplasm cell body neuronal cell body ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR019954	Ubiquitin conserved site	Conserved Site
A	IPR000626	Ubiquitin-like domain	Domain
A	IPR019956	Ubiquitin domain	Domain
A	IPR050158	Ubiquitin and ubiquitin-like	Family
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth C]	IPR057992	E3 ubiquitin-protein ligase synoviolin-like, TPR repeats	Domain
B [auth C]	IPR003892	Ubiquitin system component CUE	Domain
B [auth C]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth C]	IPR040675	E3 ubiquitin-protein ligase AMFR, Ube2g2-binding region	Domain
B [auth C]	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer
B [auth C]	Pharos: Q9UKV5	Alzheimer disease urinary bladder cancer Acute Confusional Senile Dementia cerebrovascular disorder osteosarcoma urinary bladder neoplasm cystic fibrosis medulloblastoma Pick disease spina bifida atypical teratoid rhabdoid tumor large cell medulloblastoma multiple sclerosis pituitary 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.