2F6M

Structure of a Vps23-C:Vps28-N subcomplex

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2f6ma2	All alpha proteins	Long alpha-hairpin	Endosomal sorting complex assembly domain	VPS23 C-terminal domain	Vacuolar protein sorting-associated protein 23, VPS23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2f6ma3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2f6mc2	All alpha proteins	Long alpha-hairpin	Endosomal sorting complex assembly domain	VPS23 C-terminal domain	Vacuolar protein sorting-associated protein 23, VPS23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2f6mc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2f6mb2	All alpha proteins	Long alpha-hairpin	Endosomal sorting complex assembly domain	VPS28 N-terminal domain	Vacuolar protein sorting-associated protein 28, VPS28	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2f6mb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d2f6md_	All alpha proteins	Long alpha-hairpin	Endosomal sorting complex assembly domain	VPS28 N-terminal domain	Vacuolar protein sorting-associated protein 28, VPS28	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	VPS23 C-terminal domain	8028208	4001058	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Endosomal sorting complex assembly domain-like	8040587	3000610	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8040587	3000610	SCOP2B (2022-06-29)
B	SCOP2 Family	VPS28 N-terminal domain	8028211	4001061	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Endosomal sorting complex assembly domain-like	8040590	3000610	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8040590	3000610	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	Vps23_core	e2f6mA1	A: alpha bundles	X: Long alpha-hairpin	H: Endosomal sorting complex assembly domains (From Topology)	T: Endosomal sorting complex assembly domains	F: Vps23_core	ECOD (1.6)
C	Vps23_core	e2f6mC1	A: alpha bundles	X: Long alpha-hairpin	H: Endosomal sorting complex assembly domains (From Topology)	T: Endosomal sorting complex assembly domains	F: Vps23_core	ECOD (1.6)
B	VPS28_N	e2f6mB1	A: alpha bundles	X: Long alpha-hairpin	H: Endosomal sorting complex assembly domains (From Topology)	T: Endosomal sorting complex assembly domains	F: VPS28_N	ECOD (1.6)
D	VPS28_N	e2f6mD1	A: alpha bundles	X: Long alpha-hairpin	H: Endosomal sorting complex assembly domains (From Topology)	T: Endosomal sorting complex assembly domains	F: VPS28_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.140.820	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C	6.10.140.820	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	1.20.1440.200	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	Vps28 N-terminal domain	CATH (4.3.0)
D	1.20.1440.200	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	Vps28 N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF09454	Vps23 core domain (Vps23_core)	Vps23 core domain	ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. The core domain of the Vps23 subunit of the heterotrimeric ESCRT-I complex is a helical hairpin sandwiched in a fan-like formation between two other helical ...	ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. The core domain of the Vps23 subunit of the heterotrimeric ESCRT-I complex is a helical hairpin sandwiched in a fan-like formation between two other helical hairpins from Vps28 (Pfam:PF03997) and Vps37. Vps23 gives ESCRT-I complex its stability [1].	Domain
B, D	PF03997	VPS28 protein (VPS28)	VPS28 protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease	protein binding binding ubiquitin binding ubiquitin-like protein binding	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosome to lysosome transport lysosomal transport organic substance metabolic process organonitrogen compound metabolic process localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosome to lysosome transport lysosomal transport organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process protein localization establishment of protein localization nitrogen compound transport protein targeting organic substance transport establishment of protein localization to vacuole protein localization to vacuole establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle protein targeting to vacuole intracellular protein transport organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process organic substance catabolic process negative regulation of post-translational protein modification regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination regulation of primary metabolic process protein ubiquitination negative regulation of protein modification process regulation of protein modification by small protein conjugation or removal negative regulation of protein ubiquitination negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process regulation of protein polyubiquitination negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process biological regulation protein polyubiquitination regulation of macromolecule metabolic process negative regulation of protein polyubiquitination post-translational protein modification protein modification by small protein conjugation regulation of metabolic process protein modification by small protein conjugation or removal establishment of protein localization to membrane localization within membrane protein localization to membrane protein targeting to membrane 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 cellular component disassembly macroautophagy cellular metabolic process autophagy cellular component organization cellular catabolic process organelle organization organelle disassembly reticulophagy cellular component organization or biogenesis process utilizing autophagic mechanism	membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle cytosol endosome membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle cytosol endosome membrane protein-containing complex ESCRT complex membrane membrane protein complex ESCRT I complex cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane late endosome membrane late endosome cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane plasma membrane side of membrane
B, D	Vacuolar protein sorting-associated protein VPS28	protein-containing complex binding binding	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 establishment of protein localization to membrane localization within membrane protein localization to membrane protein targeting to membrane 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	membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle cytosol endosome membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle cytosol endosome membrane protein-containing complex ESCRT complex membrane membrane protein complex ESCRT I complex cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane late endosome membrane late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR017916	Steadiness box (SB) domain	Domain
A, C	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A, C	IPR008883	Ubiquitin E2 variant, N-terminal	Domain
A, C	IPR037202	ESCRT assembly domain	Homologous Superfamily
B, D	IPR037206	VPS28, C-terminal domain superfamily	Homologous Superfamily
B, D	IPR007143	Vacuolar protein sorting-associated Vps28	Family
B, D	IPR017899	Vacuolar protein sorting-associated, VPS28, C-terminal	Domain
B, D	IPR017898	Vacuolar protein sorting-associated, VPS28, N-terminal	Domain
B, D	IPR038358	VPS28, N-terminal domain superfamily	Homologous Superfamily
B, D	IPR037202	ESCRT assembly domain	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.