4LCD | pdb_00004lcd

Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Hect, E3 ligase catalytic domain	8084361	3000934	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Hect, E3 ligase catalytic domain	8084361	3000934	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)
F		e4lcdF1	A: L-aspartase middle domain-like	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like	T: Cu_amine_oxidN2	F:	ECOD (20:10:01)
E		e4lcdE1	A: PRTase-like	X: PRTase-like	H: PRTase-like	T: Pribosyltran	F:	ECOD (20:10:01)
B		e4lcdB1	A: PRTase-like	X: PRTase-like	H: PRTase-like	T: Pribosyltran	F:	ECOD (20:10:01)
A		e4lcdA1	A: immunoglobulin/albumin-binding domain-like	X: EGF-related	H: Complement control module/SCR domain	T: Asp	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F	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
A, B	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, B	PF00632	HECT-domain (ubiquitin-transferase) (HECT)	HECT-domain (ubiquitin-transferase)	The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	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 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
C, D	Protein SNA3	ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization multivesicular body sorting pathway establishment of localization in cell cellular process endosome transport via multivesicular body sorting pathway catabolic process metabolic process primary metabolic process cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization multivesicular body sorting pathway establishment of localization in cell cellular process endosome transport via multivesicular body sorting pathway catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process	membrane-bounded organelle storage vacuole intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle cellular anatomical structure organelle cytoplasm membrane endosome membrane endosome membrane-bounded organelle storage vacuole intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle cellular anatomical structure organelle cytoplasm membrane endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome vesicle organelle membrane membrane-enclosed lumen vacuolar lumen intracellular organelle lumen organelle lumen fungal-type vacuole lumen
A, B	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-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity binding phospholipid binding lipid binding phosphatidylinositol 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 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 response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus 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 via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process regulation of cellular process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process positive regulation of biological process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process positive regulation of fatty acid biosynthetic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process positive regulation of lipid metabolic process small molecule metabolic process positive regulation of cellular process positive regulation of fatty acid metabolic process regulation of biosynthetic process fatty acid metabolic process regulation of biological process monocarboxylic acid biosynthetic process small molecule biosynthetic process biological regulation carboxylic acid metabolic process fatty acid biosynthetic process regulation of ketone metabolic process biosynthetic process positive regulation of lipid biosynthetic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process monocarboxylic acid metabolic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process regulation of metabolic 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 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 catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process 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 protein polymerization protein-containing complex organization homeostatic process free ubiquitin chain polymerization cellular component organization cellular component biogenesis cellular component assembly cellular homeostasis protein-containing complex assembly cellular component organization or biogenesis ubiquitin recycling ribophagy macroautophagy autophagy process utilizing autophagic mechanism regulation of steroid biosynthetic process steroid metabolic process sterol metabolic process alcohol metabolic process ergosterol biosynthetic process ergosterol metabolic process steroid biosynthetic process secondary alcohol biosynthetic process regulation of alcohol biosynthetic process regulation of ergosterol biosynthetic process regulation of steroid metabolic process phytosteroid biosynthetic process secondary alcohol metabolic process sterol biosynthetic process regulation of sterol biosynthetic process alcohol biosynthetic process phospholipid metabolic process phosphate-containing compound metabolic process phosphorus metabolic process dolichyl monophosphate biosynthetic process regulation of phospholipid metabolic process regulation of dolichyl monophosphate biosynthetic process phospholipid biosynthetic process regulation of phospholipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process regulation of phosphorus metabolic process import into cell regulation of localization ubiquitin-dependent endocytosis establishment of protein localization 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 intracellular protein localization regulation of ubiquitin-dependent endocytosis regulation of endocytosis regulation of 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 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 cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical response to amino acid regulation of ketone biosynthetic process ubiquinone biosynthetic process quinone metabolic process quinone biosynthetic process ubiquinone metabolic process regulation of ubiquinone biosynthetic process ketone biosynthetic process cellular response to nitrogen compound response to L-arginine response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to L-arginine positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription chromatin organization mitochondria-associated ubiquitin-dependent protein catabolic process nonfunctional rRNA decay rRNA catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process rRNA metabolic process RNA catabolic process nitrogen compound transport 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 cellular 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 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 response to nutrient levels regulation of response to nutrient levels nitrogen utilization regulation of nitrogen utilization chemical homeostasis regulation of response to stimulus intracellular nitrogen homeostasis intracellular chemical homeostasis establishment of protein localization to vacuole protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway protein localization to vacuole intracellular protein transport mitochondrion organization protein quality control for misfolded or incompletely synthesized proteins	cell cortex intracellular anatomical structure cortical cytoskeleton intracellular membraneless organelle actin cytoskeleton cell periphery intracellular organelle endocytic patch cellular anatomical structure cytoskeleton organelle membraneless organelle cortical actin cytoskeleton actin cortical patch cell cortex intracellular anatomical structure cortical cytoskeleton intracellular membraneless organelle actin cytoskeleton cell periphery intracellular organelle endocytic patch cellular anatomical structure cytoskeleton organelle membraneless organelle cortical actin cytoskeleton actin cortical patch cytoplasm 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 cytosol 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 nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR019954	Ubiquitin conserved site	Conserved Site
E, F	IPR000626	Ubiquitin-like domain	Domain
E, F	IPR019956	Ubiquitin domain	Domain
E, F	IPR050158	Ubiquitin and ubiquitin-like	Family
E, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C, D	IPR000612	Proteolipid membrane potential modulator	Family
A, B	IPR035983	HECT, E3 ligase catalytic domain	Homologous Superfamily
A, B	IPR036020	WW domain superfamily	Homologous Superfamily
A, B	IPR050409	E3 ubiquitin-protein ligase	Family
A, B	IPR000008	C2 domain	Domain
A, B	IPR000569	HECT domain	Domain
A, B	IPR024928	E3 ubiquitin-protein ligase, SMURF1 type	Family
A, B	IPR035892	C2 domain superfamily	Homologous Superfamily
A, B	IPR001202	WW domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F	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

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.