1P3Q | pdb_00001p3q

Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth V]	d1p3qv_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C [auth U]	d1p3qu_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B [auth R]	d1p3qr_	All alpha proteins	RuvA C-terminal domain-like	UBA-like	CUE domain	Vacuolar protein sorting-associated protein vps9	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A [auth Q]	d1p3qq_	All alpha proteins	RuvA C-terminal domain-like	UBA-like	CUE domain	Vacuolar protein sorting-associated protein vps9	baker's 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)
D [auth V]	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
C [auth U]	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
A [auth Q]	SCOP2B Superfamily	UBA-like	8032806	3001235	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)
D [auth V]	S4	e1p3qV1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: S4	ECOD (develop294)
C [auth U]	S4	e1p3qU1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: S4	ECOD (develop294)
B [auth R]	EF-hand_1,S_100	e1p3qR1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: EF-hand_1,S_100	ECOD (develop294)
A [auth Q]	EF-hand_1,S_100	e1p3qQ1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: EF-hand_1,S_100	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth V]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C [auth U]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A [auth Q]	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
C [auth U], D [auth V]	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 [auth Q], B [auth R]	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
C [auth U], D [auth V]	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme 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 mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane membrane-bounded organelle intracellular anatomical structure mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane cytoplasm organelle membrane nucleus
A [auth Q], B [auth R]	Vacuolar protein sorting-associated protein VPS9	small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity 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 organelle organization vacuole organization organelle inheritance vacuole inheritance cellular component organization or biogenesis establishment of protein localization protein targeting establishment of protein localization to vacuole protein localization to vacuole establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein localization protein targeting to vacuole intracellular protein transport protein localization to endosome Golgi to endosome transport post-Golgi vesicle-mediated transport cytosolic transport Golgi vesicle transport	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle cytosol membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle cytosol endocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth U], D [auth V]	IPR019956	Ubiquitin domain	Domain
C [auth U], D [auth V]	IPR019954	Ubiquitin conserved site	Conserved Site
C [auth U], D [auth V]	IPR050158	Ubiquitin and ubiquitin-like	Family
C [auth U], D [auth V]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C [auth U], D [auth V]	IPR000626	Ubiquitin-like domain	Domain
A [auth Q], B [auth R]	IPR041804	Vacuolar protein sorting-associated protein 9, CUE domain	Domain
A [auth Q], B [auth R]	IPR041545	RABX5, catalytic core helical domain	Domain
A [auth Q], B [auth R]	IPR037191	VPS9 domain superfamily	Homologous Superfamily
A [auth Q], B [auth R]	IPR045046	Vacuolar protein sorting-associated protein 9-like	Family
A [auth Q], B [auth R]	IPR009060	UBA-like superfamily	Homologous Superfamily
A [auth Q], B [auth R]	IPR003123	VPS9 domain	Domain
A [auth Q], B [auth R]	IPR003892	Ubiquitin system component CUE	Domain

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.