1JUQ

GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor

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)
A	d1juqa_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d1juqb1	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d1juqb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d1juqc_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth D]	d1juqd1	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth D]	d1juqd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	VHS domain	8025009	4001359	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ENTH/VHS domain-like	8037388	3000164	SCOP2 (2022-06-29)
C [auth B]	SCOP2B Superfamily	ENTH/VHS domain-like	8037388	3000164	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	ENTH/VHS domain-like	8037388	3000164	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	ENTH/VHS domain-like	8037388	3000164	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	VHS	e1juqA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: VHS	ECOD (1.6)
C [auth B]	VHS	e1juqB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: VHS	ECOD (1.6)
E [auth C]	VHS	e1juqC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: VHS	ECOD (1.6)
G [auth D]	VHS	e1juqD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: VHS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C [auth B]	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
E [auth C]	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
G [auth D]	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C], G [auth D]	PF00790	VHS domain (VHS)	VHS domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B], E [auth C], G [auth D]	ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3	binding phospholipid binding lipid binding phosphatidylinositol binding small GTPase binding protein binding enzyme binding GTPase binding ubiquitin binding ubiquitin-like protein binding protein-containing complex binding protein transporter activity transporter activity	protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport to the plasma membrane protein transport macromolecule localization cellular process Golgi vesicle transport protein destabilization regulation of protein stability biological regulation regulation of biological quality protein localization to cell surface catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process intracellular transport establishment of localization in cell intracellular protein transport amyloid precursor protein catabolic process regulation of amide metabolic process regulation of cellular process regulation of amyloid-beta formation negative regulation of biological process regulation of amyloid precursor protein catabolic process regulation of primary metabolic process negative regulation of amyloid precursor protein catabolic process amyloid-beta metabolic process negative regulation of cellular process amide metabolic process amyloid precursor protein metabolic process negative regulation of protein metabolic process amyloid-beta formation negative regulation of macromolecule metabolic process negative regulation of amyloid-beta formation regulation of biological process negative regulation of amide metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process in the vacuole positive regulation of protein metabolic process positive regulation of biological process lysosomal protein catabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of lysosomal protein catabolic process positive regulation of cellular process protein catabolic process in the vacuole regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of lysosomal protein catabolic process positive regulation of protein catabolic process in the vacuole regulation of protein catabolic process protein targeting establishment of protein localization to vacuole lysosomal transport protein targeting to lysosome protein targeting to vacuole protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein localization to organelle vacuolar transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle lytic vacuole vacuole cytoplasm intracellular membrane-bounded organelle lysosome protein-containing complex endosome membrane membrane endosome membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle lytic vacuole vacuole cytoplasm intracellular membrane-bounded organelle lysosome protein-containing complex endosome membrane membrane endosome intracellular vesicle recycling endosome endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane cytoplasmic vesicle vesicle organelle membrane Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network early endosome early endosome membrane
B [auth E], D [auth F], F [auth G], H	Cation-dependent mannose-6-phosphate receptor	protein binding binding protein domain specific binding protein transporter activity transporter activity protein-containing complex binding retromer complex binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization establishment of localization in cell cellular process vacuolar transport membrane lipid metabolic process sphingolipid catabolic process carbohydrate derivative catabolic process cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization establishment of localization in cell cellular process vacuolar transport membrane lipid metabolic process sphingolipid catabolic process carbohydrate derivative catabolic process glycosphingolipid catabolic process catabolic process lipid catabolic process glycolipid metabolic process glycosphingolipid metabolic process liposaccharide metabolic process carbohydrate derivative metabolic process primary metabolic process sphingolipid metabolic process membrane lipid catabolic process glycolipid catabolic process metabolic process lipid metabolic process protein localization establishment of protein localization nitrogen compound transport protein targeting establishment of protein localization to vacuole protein targeting to lysosome cellular macromolecule localization protein targeting to vacuole protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein transport secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell secretion of lysosomal enzymes import into cell receptor-mediated endocytosis endocytosis	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm organelle membrane lysosome Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network endosome intracellular vesicle cytoplasmic vesicle vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane trans-Golgi network membrane perinuclear region of cytoplasm cell periphery plasma membrane late endosome transport vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth C], G [auth D]	IPR046996	GGA3, VHS domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR002014	VHS domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR008942	ENTH/VHS	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR041198	N-terminal extension of GAT domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR044111	GGA3, GAT domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR008153	Gamma-adaptin ear (GAE) domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR038425	GAT domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR004152	GAT domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR008152	Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR027422	ADP-ribosylation factor-binding protein GGA1-3	Family
B [auth E], D [auth F], F [auth G], H	IPR028927	Mannose-6-phosphate receptor	Family
B [auth E], D [auth F], F [auth G], H	IPR009011	Mannose-6-phosphate receptor binding domain superfamily	Homologous Superfamily
B [auth E], D [auth F], F [auth G], H	IPR044865	MRH domain	Domain
B [auth E], D [auth F], F [auth G], H	IPR000296	Cation-dependent mannose-6-phosphate receptor	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth B], E [auth C], G [auth D]	Pharos: Q9NZ52	Malignant neoplasm of breast systemic lupus erythematosus non-alcoholic fatty liver disease systemic sclerosis osteosarcoma
B [auth E], D [auth F], F [auth G], H	Pharos: P20645	renal cell carcinoma prostate cancer chromophobe renal cell carcinoma papillary renal cell carcinoma sarcomatoid renal cell carcinoma collecting duct carcinoma Conventional (Clear Cell) Renal Cell Carcinoma glioblastoma lymphoplasmacytic lymphoma clear cell renal carcinoma depressive disorder gastric cancer hereditary diffuse gastric adenocarcinoma major depressive disorder osteosarcoma renal cell carcinoma prostate cancer chromophobe renal cell carcinoma papillary renal cell carcinoma sarcomatoid renal cell carcinoma collecting duct carcinoma Conventional (Clear Cell) Renal Cell Carcinoma glioblastoma lymphoplasmacytic lymphoma clear cell renal carcinoma depressive disorder gastric cancer hereditary diffuse gastric adenocarcinoma major depressive disorder osteosarcoma plasma cell myeloma renal carcinoma gastric neoplasm lung adenocarcinoma 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.