1W7P | pdb_00001w7p

The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36)

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)
B	d1w7pb1	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	d1w7pc1	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	d1w7pd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Vacuolar sorting protein domain	Vacuolar protein sorting-associated protein VPS36	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1w7pa1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Vacuolar sorting protein domain	Vacuolar sorting protein SNF8	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)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8002872	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8002871	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	8058022	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8058023	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8002878	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8002879	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)
B	Phage_CII	e1w7pB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (v294.1)
C	Phage_CII	e1w7pC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (v294.1)
D	EAP30	e1w7pD1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: EAP30	ECOD (v294.1)
A	Phage_CII	e1w7pA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	1.10.10.10	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)
A	6.10.140.180	Special	Helix non-globular	Helix Hairpins		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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C	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
B, C	VPS25, YJR102C	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity structural molecule activity	establishment of protein localization cellular localization transport protein targeting establishment of protein localization to vacuole intracellular transport protein localization to vacuole establishment of localization localization establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle macromolecule localization establishment of protein localization cellular localization transport protein targeting establishment of protein localization to vacuole intracellular transport protein localization to vacuole establishment of localization localization establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle macromolecule localization vacuolar transport cellular process intracellular protein localization protein targeting to vacuole intracellular protein transport catabolic process macromolecule catabolic process vesicle-mediated transport late endosome to vacuole transport modification-dependent macromolecule catabolic process late endosome to vacuole transport via multivesicular body sorting pathway protein metabolic process 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 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 regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process ATP transport nitrogen compound 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle endosome membrane protein-containing complex ESCRT complex endosome membrane intracellular vesicle membrane protein complex intracellular membrane-bounded organelle endomembrane system cellular anatomical structure intracellular anatomical structure cytoplasm 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
D	VPS36P, YLR417W	protein binding binding ubiquitin binding ubiquitin-like protein binding phospholipid binding lipid binding phosphatidylinositol-3-phosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding protein binding binding ubiquitin binding ubiquitin-like protein binding phospholipid binding lipid binding phosphatidylinositol-3-phosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	catabolic process macroautophagy autophagy cellular process metabolic process process utilizing autophagic mechanism establishment of protein localization cellular localization transport protein targeting establishment of protein localization to vacuole intracellular transport protein localization to vacuole establishment of localization catabolic process macroautophagy autophagy cellular process metabolic process process utilizing autophagic mechanism establishment of protein localization cellular localization transport protein targeting establishment of protein localization to vacuole intracellular transport protein localization to vacuole establishment of localization localization establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle macromolecule localization vacuolar transport intracellular protein localization protein targeting to vacuole intracellular protein transport macromolecule catabolic process vesicle-mediated transport late endosome to vacuole transport modification-dependent macromolecule catabolic process late endosome to vacuole transport via multivesicular body sorting pathway protein metabolic process 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 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 macromolecule metabolic process cytoplasm to vacuole targeting by the Cvt pathway maintenance of protein location protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell protein retention in Golgi apparatus regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process ATP transport nitrogen compound 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	membrane-bounded organelle endosome membrane protein-containing complex intracellular anatomical structure ESCRT complex endosome membrane intracellular vesicle membrane protein complex intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane membrane-bounded organelle endosome membrane protein-containing complex intracellular anatomical structure ESCRT complex endosome membrane intracellular vesicle membrane protein complex 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 II complex late endosome membrane late endosome
A	VPS22, YPL002C	binding lipid binding	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of cellular process negative regulation of biological process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process establishment of protein localization cellular localization transport protein targeting establishment of protein localization to vacuole intracellular transport protein localization to vacuole establishment of localization localization establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle macromolecule localization vacuolar transport intracellular protein localization protein targeting to vacuole intracellular protein transport vesicle-mediated transport late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway endosomal transport multivesicular body sorting pathway ATP transport nitrogen compound 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	membrane-bounded organelle endosome membrane protein-containing complex intracellular anatomical structure ESCRT complex endosome membrane intracellular vesicle membrane protein complex intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane membrane-bounded organelle endosome membrane protein-containing complex intracellular anatomical structure ESCRT complex endosome membrane intracellular vesicle membrane protein complex 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 II complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B, C	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B, C	IPR008570	ESCRT-II complex, Vps25 subunit	Family
B, C	IPR014041	ESCRT-II complex, Vps25 subunit, N-terminal winged helix	Homologous Superfamily
D	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
D	IPR040608	Snf8/Vps36 family	Family
D	IPR011993	PH-like domain superfamily	Homologous Superfamily
D	IPR031558	Vacuolar protein-sorting-associated protein 36, NZF-N zinc-finger domain	Domain
D	IPR001876	Zinc finger, RanBP2-type	Domain
D	IPR021648	Vacuolar protein sorting protein 36, GLUE domain	Domain
D	IPR037855	Vacuolar protein sorting protein 36	Family
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR016689	ESCRT-2 complex, Snf8	Family
A	IPR040608	Snf8/Vps36 family	Family

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.