3LDZ | pdb_00003ldz

Crystal structure of human STAM1 VHS 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)
F [auth E]	d3ldze_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
G	d3ldzg_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A [auth F]	d3ldzf_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B [auth A]	d3ldza_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d3ldzd_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d3ldzb_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d3ldzc_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	automated matches	automated matches	(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)
F [auth E]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
A [auth F]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B [auth A]	SCOP2 Family	VHS domain	8066260	4001359	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	ENTH/VHS domain-like	8066261	3000164	SCOP2 (2022-06-29)
C [auth D]	SCOP2B Superfamily	ENTH/VHS domain-like	8066261	3000164	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	ENTH/VHS domain-like	8066261	3000164	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	ENTH/VHS domain-like	8066261	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)
F [auth E]	RVP	e3ldzE1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
G	RVP	e3ldzG1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
A [auth F]	RVP	e3ldzF1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
B [auth A]	ecTbetaR2	e3ldzA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: HTH	T: winged helix domain	F: ecTbetaR2	ECOD (v294.1)
C [auth D]	RVP	e3ldzD1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
D [auth B]	RVP	e3ldzB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
E [auth C]	RVP	e3ldzC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth E]	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)
A [auth F]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B [auth A]	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C [auth D]	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
D [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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth F], F [auth E], G	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
B [auth A], C [auth D], D [auth B], E [auth C]	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 [auth F], F [auth E], G	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid 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 membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B [auth A], C [auth D], D [auth B], E [auth C]	Signal transducing adapter molecule 1	ion binding binding anion binding phosphatidylinositol binding small molecule binding protein binding ubiquitin-like protein ligase binding enzyme binding ubiquitin binding ubiquitin-like protein binding	membrane organization cellular component organization membrane fission cellular process cellular component organization or biogenesis catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism organelle assembly multivesicular body assembly vesicle organization cellular component biogenesis membrane organization cellular component organization membrane fission cellular process cellular component organization or biogenesis catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism organelle assembly multivesicular body assembly vesicle organization cellular component biogenesis organelle organization cellular component assembly multivesicular body organization endosome organization endomembrane system organization establishment of protein localization cellular localization transport establishment of protein localization to vacuole macromolecule catabolic process vesicle-mediated transport localization intercellular transport late endosome to vacuole transport modification-dependent macromolecule catabolic process late endosome to vacuole transport via multivesicular body sorting pathway establishment of localization in cell protein metabolic process intracellular protein localization endosome transport via multivesicular body sorting pathway protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway primary metabolic process protein localization to vacuole intracellular transport protein catabolic process establishment of localization endosomal transport establishment of protein localization to organelle protein transport modification-dependent protein catabolic process multivesicular body sorting pathway protein localization to organelle macromolecule localization ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process vacuolar transport macromolecule metabolic process intracellular protein transport exosomal secretion establishment of organelle localization regulation of localization regulation of cellular process positive regulation of biological process positive regulation of secretion by cell positive regulation of exosomal secretion positive regulation of exocytosis secretion by cell regulation of secretion by cell positive regulation of secretion organelle localization positive regulation of cellular process vesicle localization regulation of biological process positive regulation of cellular component biogenesis secretion regulation of transport regulation of exosomal secretion establishment of vesicle localization biological regulation export from cell regulation of cellular component biogenesis regulation of vesicle-mediated transport extracellular exosome biogenesis regulation of secretion exocytosis positive regulation of transport extracellular vesicle biogenesis regulation of exocytosis regulation of cellular component organization regulation of extracellular exosome assembly regulation of organelle organization regulation of organelle assembly extracellular exosome assembly cellular response to stimulus response to stimulus signaling signal transduction cell communication	membrane-bounded organelle endosome membrane intracellular anatomical structure early endosome endosome membrane intracellular vesicle early endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle membrane-bounded organelle endosome membrane intracellular anatomical structure early endosome endosome membrane intracellular vesicle early endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle cytoplasm vesicle organelle membrane ESCRT-0 complex protein-containing complex ESCRT complex cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth F], F [auth E], G	IPR019954	Ubiquitin conserved site	Conserved Site
A [auth F], F [auth E], G	IPR000626	Ubiquitin-like domain	Domain
A [auth F], F [auth E], G	IPR019956	Ubiquitin domain	Domain
A [auth F], F [auth E], G	IPR050158	Ubiquitin and ubiquitin-like	Family
A [auth F], F [auth E], G	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth A], C [auth D], D [auth B], E [auth C]	IPR047492	STAM1, non-canonical GAT domain	Domain
B [auth A], C [auth D], D [auth B], E [auth C]	IPR002014	VHS domain	Domain
B [auth A], C [auth D], D [auth B], E [auth C]	IPR008942	ENTH/VHS	Homologous Superfamily
B [auth A], C [auth D], D [auth B], E [auth C]	IPR050670	Signal Transducing Adapter Molecule	Family
B [auth A], C [auth D], D [auth B], E [auth C]	IPR035657	STAM1, SH3 domain	Domain
B [auth A], C [auth D], D [auth B], E [auth C]	IPR001452	SH3 domain	Domain
B [auth A], C [auth D], D [auth B], E [auth C]	IPR036028	SH3-like domain superfamily	Homologous Superfamily
B [auth A], C [auth D], D [auth B], E [auth C]	IPR047528	STAM1, VHS domain	Domain
B [auth A], C [auth D], D [auth B], E [auth C]	IPR003903	Ubiquitin interacting motif	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth F], F [auth E], G	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer
B [auth A], C [auth D], D [auth B], E [auth C]	Pharos: Q92783	B-cell chronic lymphocytic leukemia myopathy psoriasis colorectal cancer ovarian cancer juvenile dermatomyositis 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.