8PMQ

Catalytic module of yeast GID E3 ligase bound to multiphosphorylated Ubc8~ubiquitin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth U]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 2]	PF10607	CTLH/CRA C-terminal to LisH motif domain (CTLH)	CTLH/CRA C-terminal to LisH motif domain	RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which ...	RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which is comprised of approximately 100 amino acids at the C terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X messenger ribonucleoprotein 1 (FMRP), but its functional significance has yet to be determined [5]. This region contains CTLH and CRA domains annotated by SMART; however, these may be a single domain, and it is refereed to as a C-terminal to LisH motif [6].	Domain
B [auth 9]	PF10607	CTLH/CRA C-terminal to LisH motif domain (CTLH)	CTLH/CRA C-terminal to LisH motif domain	RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which ...	RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which is comprised of approximately 100 amino acids at the C terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X messenger ribonucleoprotein 1 (FMRP), but its functional significance has yet to be determined [5]. This region contains CTLH and CRA domains annotated by SMART; however, these may be a single domain, and it is refereed to as a C-terminal to LisH motif [6].	Domain
C [auth E]	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain
D [auth U]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 2]	E3 ubiquitin-protein ligase RMD5	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 cation binding ion binding binding metal ion binding small molecule binding	organonitrogen compound catabolic process organonitrogen compound metabolic process 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 metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process 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 metabolic process protein metabolic process macromolecule metabolic process monosaccharide metabolic process negative regulation of small molecule metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process gluconeogenesis negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of gluconeogenesis regulation of small molecule metabolic process negative regulation of cellular process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process negative regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process negative regulation of metabolic process carbohydrate biosynthetic process cellular metabolic process biological regulation hexose metabolic process monosaccharide biosynthetic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process hexose biosynthetic process biosynthetic process negative regulation of biosynthetic process regulation of gluconeogenesis cellular process regulation of carbohydrate biosynthetic process regulation of metabolic process glucose metabolic 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 proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol GID complex protein-containing complex ubiquitin ligase complex catalytic complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol GID complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex nucleus
B [auth 9]	Protein FYV10	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 cation binding ion binding binding metal ion binding small molecule binding	regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death monosaccharide metabolic process regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death monosaccharide metabolic process negative regulation of small molecule metabolic process cellular biosynthetic process gluconeogenesis negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of gluconeogenesis regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process negative regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process small molecule biosynthetic process negative regulation of metabolic process carbohydrate biosynthetic process cellular metabolic process hexose metabolic process primary metabolic process monosaccharide biosynthetic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process hexose biosynthetic process biosynthetic process negative regulation of biosynthetic process regulation of gluconeogenesis metabolic process regulation of carbohydrate biosynthetic process regulation of metabolic process glucose metabolic process organonitrogen compound metabolic process protein ubiquitination macromolecule modification 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 organonitrogen compound catabolic process catabolic process proteolysis involved in protein 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 proteolysis ubiquitin-dependent protein catabolic process	GID complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
C [auth E]	Ubiquitin-conjugating enzyme E2-24 kDa	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity	monosaccharide metabolic process negative regulation of small molecule metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process gluconeogenesis negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of gluconeogenesis regulation of small molecule metabolic process negative regulation of cellular process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process monosaccharide metabolic process negative regulation of small molecule metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process gluconeogenesis negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of gluconeogenesis regulation of small molecule metabolic process negative regulation of cellular process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process negative regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process negative regulation of metabolic process carbohydrate biosynthetic process cellular metabolic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process hexose biosynthetic process biosynthetic process negative regulation of biosynthetic process regulation of gluconeogenesis metabolic process cellular process regulation of carbohydrate biosynthetic process regulation of metabolic process glucose metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein metabolic process macromolecule metabolic process protein polyubiquitination 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 proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
D [auth U]	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process 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 metabolic process protein metabolic process macromolecule metabolic process protein ubiquitination organonitrogen compound catabolic process organonitrogen compound metabolic process 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 metabolic process protein metabolic process macromolecule metabolic 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle 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 space 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 2]	IPR044063	Gid-type RING finger domain	Domain
A [auth 2]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth 2]	IPR024964	CTLH/CRA C-terminal to LisH motif domain	Domain
A [auth 2]	IPR006595	CTLH, C-terminal LisH motif	Domain
A [auth 2]	IPR037683	Rmd5, degenerated RING (dRING) finger	Domain
A [auth 2]	IPR045098	Fyv10 family	Family
B [auth 9]	IPR044063	Gid-type RING finger domain	Domain
B [auth 9]	IPR024964	CTLH/CRA C-terminal to LisH motif domain	Domain
B [auth 9]	IPR006595	CTLH, C-terminal LisH motif	Domain
B [auth 9]	IPR045098	Fyv10 family	Family
C [auth E]	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
C [auth E]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
C [auth E]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
D [auth U]	IPR019954	Ubiquitin conserved site	Conserved Site
D [auth U]	IPR000626	Ubiquitin-like domain	Domain
D [auth U]	IPR019956	Ubiquitin domain	Domain
D [auth U]	IPR050158	Ubiquitin and ubiquitin-like	Family
D [auth U]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth U]	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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth E]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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 R01GM133198.