3OLM

Structure and Function of a Ubiquitin Binding Site within the Catalytic Domain of a HECT Ubiquitin Ligase

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

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth D]	d3olmd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Hect E3 ligase catalytic domain	8084361	3000934	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Ubiquitin-like	8040187	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	WW	e3olmA2	A: beta meanders	X: WW domain-like	H: WW domain (From Topology)	T: WW domain	F: WW	ECOD (1.6)
A	HECT	e3olmA1	A: a+b complex topology	X: Hect, E3 ligase catalytic domain (From Topology)	H: Hect, E3 ligase catalytic domain (From Topology)	T: Hect, E3 ligase catalytic domain	F: HECT	ECOD (1.6)
B [auth D]	ubiquitin_1	e3olmD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1750.10	Alpha Beta	Alpha-Beta Complex	Hect, E3 ligase catalytic domain fold	Hect, E3 ligase catalytic domains	CATH (4.3.0)
A	3.30.2160.10	Alpha Beta	2-Layer Sandwich	Hect, E3 ligase catalytic domain	Hect, E3 ligase catalytic domain	CATH (4.3.0)
A	3.30.2410.10	Alpha Beta	2-Layer Sandwich	Hect, E3 ligase catalytic fold	Hect, E3 ligase catalytic domain	CATH (4.3.0)
B [auth D]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00397	WW domain (WW)	WW domain	The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.	Domain
A	PF00632	HECT-domain (ubiquitin-transferase) (HECT)	HECT-domain (ubiquitin-transferase)	The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.	Domain
B [auth D]	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	E3 ubiquitin-protein ligase RSP5	binding phospholipid binding lipid binding phosphatidylinositol 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 phospholipid binding lipid binding phosphatidylinositol 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 ubiquitin binding ubiquitin-like protein binding	cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway establishment of localization in cell cellular process vacuolar transport endosome transport via multivesicular body sorting pathway cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway establishment of localization in cell cellular process vacuolar transport endosome transport via multivesicular body sorting pathway cellular component organization regulation of cellular component size regulation of vesicle size biological regulation regulation of multivesicular body size cellular component organization or biogenesis regulation of biological quality regulation of endosome size regulation of anatomical structure size 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 organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process regulation of cellular process oxoacid metabolic process regulation of lipid metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process positive regulation of metabolic process cellular ketone metabolic process regulation of small molecule metabolic process organic substance biosynthetic process positive regulation of lipid metabolic process small molecule metabolic process regulation of biological process regulation of cellular ketone metabolic process cellular metabolic process regulation of cellular metabolic process biosynthetic process cellular lipid metabolic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process monocarboxylic acid metabolic process regulation of metabolic process cellular biosynthetic process positive regulation of biological process lipid biosynthetic process positive regulation of cellular metabolic process positive regulation of fatty acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of fatty acid metabolic process regulation of biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of cellular biosynthetic process positive regulation of lipid biosynthetic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process positive regulation of cellular biosynthetic process lipid metabolic process positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process positive regulation of macromolecule metabolic process regulation of protein metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein 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 cellular catabolic process ribophagy macroautophagy autophagy process utilizing autophagic mechanism regulation of steroid biosynthetic process organic hydroxy compound metabolic process steroid metabolic process sterol metabolic process alcohol metabolic process ergosterol biosynthetic process cellular lipid biosynthetic process ergosterol metabolic process steroid biosynthetic process phytosteroid metabolic process secondary alcohol biosynthetic process regulation of alcohol biosynthetic process regulation of ergosterol biosynthetic process regulation of steroid metabolic process organic cyclic compound metabolic process phytosteroid biosynthetic process secondary alcohol metabolic process sterol biosynthetic process organic hydroxy compound biosynthetic process regulation of sterol biosynthetic process organic cyclic compound biosynthetic process alcohol biosynthetic process polyprenol metabolic process polyprenol biosynthetic process regulation of dolichol biosynthetic process dolichol metabolic process isoprenoid biosynthetic process dolichol biosynthetic process regulation of isoprenoid metabolic process isoprenoid metabolic process protein localization import into cell regulation of localization ubiquitin-dependent endocytosis establishment of protein localization nitrogen compound transport regulation of cellular component organization positive regulation of cellular component organization regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of endocytosis cellular macromolecule localization regulation of ubiquitin-dependent endocytosis regulation of endocytosis regulation of transport organic substance transport regulation of establishment of protein localization regulation of protein transport regulation of vesicle-mediated transport establishment of protein localization to organelle positive regulation of transport protein transport regulation of cellular localization macromolecule localization protein localization to organelle positive regulation of ubiquitin-dependent endocytosis positive regulation of protein localization endocytosis positive regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis receptor-mediated endocytosis ubiquinone metabolic process regulation of ketone biosynthetic process ubiquinone biosynthetic process quinone metabolic process quinone biosynthetic process regulation of ubiquinone biosynthetic process ketone biosynthetic process regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process phosphorus metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process protein-DNA complex organization protein-containing complex organization chromatin organization mitochondria-associated ubiquitin-dependent protein catabolic process nonfunctional rRNA decay rRNA catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process ncRNA metabolic process nucleic acid catabolic process rRNA metabolic process RNA catabolic process nucleocytoplasmic transport regulation of mRNA export from nucleus nuclear transport mRNA transport mRNA export from nucleus RNA localization nuclear export nucleobase-containing compound transport ribonucleoprotein complex localization regulation of intracellular transport regulation of ribonucleoprotein complex localization RNA transport regulation of RNA export from nucleus regulation of nucleobase-containing compound transport nucleic acid transport regulation of nucleocytoplasmic transport RNA export from nucleus establishment of RNA localization regulation of cytoskeleton organization regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cytoskeleton organization ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis RNA processing regulation of rRNA processing regulation of tRNA processing tRNA processing tRNA metabolic process regulation of tRNA metabolic process tRNA export from nucleus regulation of tRNA export from nucleus tRNA transport poly(A)+ mRNA export from nucleus protein polyubiquitination protein K63-linked ubiquitination establishment of organelle localization ribosomal large subunit export from nucleus organelle localization ribosome localization regulation of ribosomal large subunit export from nucleus ribosomal subunit export from nucleus regulation of ribosomal subunit export from nucleus protein-containing complex localization response to nutrient levels regulation of response to nutrient levels response to stimulus homeostatic process nitrogen utilization regulation of nitrogen utilization cellular homeostasis chemical homeostasis regulation of response to stimulus intracellular nitrogen homeostasis intracellular chemical homeostasis mitochondrion organization	intracellular anatomical structure cell cortex cortical cytoskeleton cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch cytoplasm intracellular anatomical structure cell cortex cortical cytoskeleton cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch cytoplasm non-membrane-bounded organelle cellular bud cellular bud tip site of polarized growth protein-containing complex catalytic complex RSP5-BUL ubiquitin ligase complex transferase complex intracellular protein-containing complex membrane-bounded organelle Golgi apparatus intracellular membrane-bounded organelle endomembrane system endosome membrane membrane endosome intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle organelle membrane ubiquitin ligase complex mitochondrion plasma membrane cytosolic ribosome ribosome cytosol nucleus
B [auth D]	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme 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 organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis 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 organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR035983	HECT, E3 ligase catalytic domain	Homologous Superfamily
A	IPR036020	WW domain superfamily	Homologous Superfamily
A	IPR000008	C2 domain	Domain
A	IPR000569	HECT domain	Domain
A	IPR024928	E3 ubiquitin-protein ligase, SMURF1 type	Family
A	IPR035892	C2 domain superfamily	Homologous Superfamily
A	IPR001202	WW domain	Domain
B [auth D]	IPR019956	Ubiquitin domain	Domain
B [auth D]	IPR019954	Ubiquitin conserved site	Conserved Site
B [auth D]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth D]	IPR000626	Ubiquitin-like domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.