1XB4

Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II

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)
A	d1xb4a1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Vacuolar sorting protein domain	Vacuolar protein sorting-associated protein VPS25	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1xb4b1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Vacuolar sorting protein domain	Vacuolar protein sorting-associated protein VPS25	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1xb4c1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Vacuolar sorting protein domain	Vacuolar protein sorting-associated protein VPS25	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1xb4d1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Vacuolar sorting protein domain	Vacuolar protein sorting-associated protein VPS25	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)
A	SCOP2 Family	Vps25-like	8002870	4000337	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8002871	3000034	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8002872	3000034	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8002871	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8002872	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002871	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002872	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8002872	3000034	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	PF05871	e1xb4A2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05871	ECOD (1.6)
B	PF05871	e1xb4B2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05871	ECOD (1.6)
C	PF05871	e1xb4C2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05871	ECOD (1.6)
D	PF05871	e1xb4D4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05871	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.570	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	"Winged helix" DNA-binding domain. Chain C. Domain 1	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	1.10.10.570	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	"Winged helix" DNA-binding domain. Chain C. Domain 1	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	1.10.10.570	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	"Winged helix" DNA-binding domain. Chain C. Domain 1	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D	1.10.10.570	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	"Winged helix" DNA-binding domain. Chain C. Domain 1	CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05871	ESCRT-II complex subunit (ESCRT-II)	ESCRT-II complex subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity structural molecule activity	protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting organic substance transport establishment of protein localization to vacuole protein localization to vacuole intracellular transport establishment of localization localization establishment of protein localization to organelle protein transport cellular macromolecule localization protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting organic substance transport establishment of protein localization to vacuole protein localization to vacuole intracellular transport establishment of localization localization establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle establishment of localization in cell cellular process vacuolar transport protein targeting to vacuole intracellular protein transport catabolic process proteolysis involved in protein catabolic process macromolecule catabolic process vesicle-mediated transport organic substance metabolic process late endosome to vacuole transport modification-dependent macromolecule catabolic process late endosome to vacuole transport via multivesicular body sorting pathway proteolysis protein metabolic process endosome transport via multivesicular body sorting pathway organonitrogen compound catabolic process organonitrogen compound metabolic process protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway primary metabolic process protein catabolic process endosomal transport modification-dependent protein catabolic process multivesicular body sorting pathway ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process metabolic process macromolecule metabolic process organic substance catabolic process cellular response to stimulus regulation of cellular process response to stimulus regulation of transcription from RNA polymerase II promoter by glucose negative regulation of biological process carbon catabolite regulation of transcription negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of transcription from RNA polymerase II promoter by glucose catabolite repression negative regulation of cellular biosynthetic process carbon catabolite repression organic cyclic compound metabolic process regulation of gene expression cellular response to nutrient levels carbon catabolite regulation of transcription from RNA polymerase II promoter biosynthetic process negative regulation of macromolecule biosynthetic process response to chemical organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to nutrient levels cellular biosynthetic process negative regulation of transcription by glucose RNA metabolic process carbon catabolite repression of transcription from RNA polymerase II promoter by glucose RNA biosynthetic process carbon catabolite repression of transcription nucleic acid biosynthetic process carbon catabolite repression of transcription by glucose negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation response to nutrient regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process cellular response to chemical stimulus negative regulation of biosynthetic process cellular response to nutrient regulation of transcription by glucose ATP transport organic anion transport nucleotide transport purine ribonucleotide transport carbohydrate derivative transport purine nucleotide transport adenine nucleotide transport ATP export nucleobase-containing compound transport organophosphate ester transport	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle endosome membrane protein-containing complex ESCRT complex endosome membrane intracellular vesicle membrane protein complex intracellular membrane-bounded organelle endomembrane system intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle endosome membrane protein-containing complex ESCRT complex endosome membrane intracellular vesicle membrane protein complex intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle vesicle organelle membrane ESCRT II complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR008570	ESCRT-II complex, Vps25 subunit	Family
A, B, C, D	IPR014041	ESCRT-II complex, Vps25 subunit, N-terminal winged helix	Homologous Superfamily

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 R01GM133198.