5HPL | pdb_00005hpl

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: Rsp5 and UbV R5.4

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)
D	d5hpld1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5hpld2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5hplc1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5hplc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5hplb_	Alpha and beta proteins (a+b)	Hect, E3 ligase catalytic domain	Hect, E3 ligase catalytic domain	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d5hpla_	Alpha and beta proteins (a+b)	Hect, E3 ligase catalytic domain	Hect, E3 ligase catalytic domain	automated matches	automated matches	(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)
D	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
C	SCOP2 Family	Ubiquitin-related	8066186	4000962	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ubiquitin-like	8066187	3000157	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Hect, E3 ligase catalytic domain	8084361	3000934	SCOP2B (2022-06-29)
A	SCOP2 Family	Hect, E3 ligase catalytic domain	8084360	4002196	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Hect, E3 ligase catalytic domain	8084361	3000934	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	HABP4_PAI-RBP1	e5hplD1	A: alpha bundles	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (develop294)
C	HABP4_PAI-RBP1	e5hplC1	A: alpha bundles	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (develop294)
B	HABP4_PAI-RBP1	e5hplB1	A: alpha bundles	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (develop294)
A	HABP4_PAI-RBP1	e5hplA1	A: alpha bundles	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	3.30.2160.10	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
C, 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
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
C, D	Ubiquitin variant R5.4	structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process protein catabolic process macromolecule catabolic process protein ubiquitination post-translational protein modification macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process protein catabolic process macromolecule catabolic process protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation response to stimulus response to chemical response to insecticide response to toxic substance	membrane-bounded organelle cellular anatomical structure organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery membrane-bounded organelle cellular anatomical structure organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome cytosolic ribosome membraneless organelle intracellular membraneless organelle ribosome endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit
A, B	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
C, D	IPR019954	Ubiquitin conserved site	Conserved Site
C, D	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
C, D	IPR050158	Ubiquitin and ubiquitin-like	Family
C, D	IPR000626	Ubiquitin-like domain	Domain
C, D	IPR019956	Ubiquitin domain	Domain
C, D	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
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
C, D	Pharos: P62987	attention deficit hyperactivity disorder, inattentive type heart disease dental caries lung cancer gastroesophageal reflux disease plasma cell myeloma

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.