1WRD

Crystal structure of Tom1 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)
A	d1wrda1	All alpha proteins	Spectrin repeat-like	GAT-like domain	GAT domain	Target of Myb protein 1, TOM1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1wrda2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1wrdb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GAT domain	8020072	4003696	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAT-like domain	8032452	3001306	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	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	GAT	e1wrdA1	A: alpha bundles	X: Spectrin repeat-like	H: GAT-like domain (From Topology)	T: GAT-like domain	F: GAT	ECOD (1.6)
B	ubiquitin_1	e1wrdB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Target of Myb protein 1	clathrin binding protein binding binding ubiquitin binding ubiquitin-like protein binding myosin VI binding cytoskeletal protein binding myosin binding clathrin heavy chain binding phosphatidylinositol-5-phosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding clathrin binding protein binding binding ubiquitin binding ubiquitin-like protein binding myosin VI binding cytoskeletal protein binding myosin binding clathrin heavy chain binding phosphatidylinositol-5-phosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding polyubiquitin modification-dependent protein binding modification-dependent protein binding	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism import into cell endocytosis protein localization establishment of protein localization cellular localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization positive regulation of organelle organization regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization regulation of autophagosome maturation positive regulation of biological process protein-containing complex disassembly regulation of autophagy regulation of protein-containing complex disassembly positive regulation of metabolic process autophagosome maturation positive regulation of macroautophagy positive regulation of protein-containing complex disassembly positive regulation of cellular process cellular component disassembly positive regulation of autophagy regulation of biological process protein-containing complex organization biological regulation regulation of catabolic process positive regulation of autophagosome maturation regulation of organelle organization positive regulation of catabolic process regulation of macroautophagy regulation of metabolic process cellular response to stimulus response to stimulus signaling signal transduction cell communication establishment of localization in cell intracellular transport endosomal transport regulation of endosome organization endosome organization endomembrane system organization substrate localization to autophagosome autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis cellular component assembly	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle lytic vacuole lysosome vacuolar membrane azurophil granule vacuole lytic vacuole membrane lysosomal membrane primary lysosome azurophil granule membrane cytosol cell periphery plasma membrane early endosome endosome endosome membrane early endosome membrane
B	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002014	VHS domain	Domain
A	IPR008942	ENTH/VHS	Homologous Superfamily
A	IPR014645	Target of Myb protein 1	Family
A	IPR038425	GAT domain superfamily	Homologous Superfamily
A	IPR004152	GAT domain	Domain
B	IPR019956	Ubiquitin domain	Domain
B	IPR019954	Ubiquitin conserved site	Conserved Site
B	IPR050158	Ubiquitin and ubiquitin-like	Family
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR000626	Ubiquitin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O60784	bipolar disorder ulcerative colitis major affective disorder 2 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.