1WR6 | pdb_00001wr6

Crystal structure of GGA3 GAT domain in complex with ubiquitin

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)
H	d1wr6h_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
G	d1wr6g_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
F	d1wr6f_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
E	d1wr6e_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D	d1wr6d_	All alpha proteins	Spectrin repeat-like	GAT-like domain	GAT domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1wr6c_	All alpha proteins	Spectrin repeat-like	GAT-like domain	GAT domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1wr6b_	All alpha proteins	Spectrin repeat-like	GAT-like domain	GAT domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1wr6a1	All alpha proteins	Spectrin repeat-like	GAT-like domain	GAT domain	ADP-ribosylation factor binding protein Gga3	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)
H	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GAT-like domain	8032447	3001306	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAT-like domain	8032447	3001306	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAT-like domain	8032447	3001306	SCOP2B (2022-06-29)
A	SCOP2 Family	GAT domain	8020067	4003696	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAT-like domain	8032447	3001306	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)
H		e1wr6H1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
G		e1wr6G1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
F		e1wr6F1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
E		e1wr6E1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
D		e1wr6D2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: EF-hand_1, EF-hand_5, EF-hand_7	F:	ECOD (20:10:01)
C		e1wr6C2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: EF-hand_1, EF-hand_5, EF-hand_7	F:	ECOD (20:10:01)
B		e1wr6B2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: EF-hand_1, EF-hand_5, EF-hand_7	F:	ECOD (20:10:01)
A		e1wr6A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
G	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
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)
D	1.20.58.160	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
C	1.20.58.160	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	1.20.58.160	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	1.20.58.160	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F, G, H	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, C, D	PF03127	GAT domain (GAT)	GAT domain	The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 [1] and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	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, B, C, 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	Golgi to plasma membrane transport establishment of protein localization cellular localization protein localization to cell periphery post-Golgi vesicle-mediated transport transport establishment of protein localization to membrane protein localization to plasma membrane establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane Golgi to plasma membrane transport establishment of protein localization cellular localization protein localization to cell periphery post-Golgi vesicle-mediated transport transport establishment of protein localization to membrane protein localization to plasma membrane establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization protein transport macromolecule localization cellular process intracellular protein localization 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 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 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 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 protein localization to vacuole lysosomal transport protein localization to lysosome establishment of protein localization to organelle protein targeting to lysosome protein localization to organelle vacuolar transport protein targeting to vacuole endocytic recycling endosomal 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR019956	Ubiquitin domain	Domain
E, F, G, H	IPR019954	Ubiquitin conserved site	Conserved Site
E, F, G, H	IPR050158	Ubiquitin and ubiquitin-like	Family
E, F, G, H	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
E, F, G, H	IPR000626	Ubiquitin-like domain	Domain
A, B, C, D	IPR046996	GGA3, VHS domain	Domain
A, B, C, D	IPR002014	VHS domain	Domain
A, B, C, D	IPR008942	ENTH/VHS	Homologous Superfamily
A, B, C, D	IPR041198	N-terminal extension of GAT domain	Domain
A, B, C, D	IPR044111	GGA3, GAT domain	Domain
A, B, C, D	IPR008153	Gamma-adaptin ear (GAE) domain	Domain
A, B, C, D	IPR038425	GAT domain superfamily	Homologous Superfamily
A, B, C, D	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
A, B, C, D	IPR004152	GAT domain	Domain
A, B, C, D	IPR008152	Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain	Domain
A, B, C, D	IPR027422	ADP-ribosylation factor-binding protein GGA1-3	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9NZ52	Malignant neoplasm of breast systemic lupus erythematosus non-alcoholic fatty liver disease systemic sclerosis osteosarcoma

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.