2G3K | pdb_00002g3k

Crystal structure of the C-terminal domain of Vps28

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)
G	d2g3kg_	All alpha proteins	Four-helical up-and-down bundle	VPS28 C-terminal domain-like	VPS28 C-terminal domain-like	Vacuolar protein sorting-associated protein 28, VPS28	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d2g3kf_	All alpha proteins	Four-helical up-and-down bundle	VPS28 C-terminal domain-like	VPS28 C-terminal domain-like	Vacuolar protein sorting-associated protein 28, VPS28	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d2g3ke_	All alpha proteins	Four-helical up-and-down bundle	VPS28 C-terminal domain-like	VPS28 C-terminal domain-like	Vacuolar protein sorting-associated protein 28, VPS28	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d2g3kd_	All alpha proteins	Four-helical up-and-down bundle	VPS28 C-terminal domain-like	VPS28 C-terminal domain-like	Vacuolar protein sorting-associated protein 28, VPS28	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2g3kc_	All alpha proteins	Four-helical up-and-down bundle	VPS28 C-terminal domain-like	VPS28 C-terminal domain-like	Vacuolar protein sorting-associated protein 28, VPS28	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2g3kb_	All alpha proteins	Four-helical up-and-down bundle	VPS28 C-terminal domain-like	VPS28 C-terminal domain-like	Vacuolar protein sorting-associated protein 28, VPS28	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2g3ka1	All alpha proteins	Four-helical up-and-down bundle	VPS28 C-terminal domain-like	VPS28 C-terminal domain-like	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)
G	SCOP2B Superfamily	VPS28 C-terminal domain-like	8043070	3001082	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	VPS28 C-terminal domain-like	8043070	3001082	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	VPS28 C-terminal domain-like	8043070	3001082	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	VPS28 C-terminal domain-like	8043070	3001082	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	VPS28 C-terminal domain-like	8043070	3001082	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	VPS28 C-terminal domain-like	8043070	3001082	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	VPS28 C-terminal domain-like	8043070	3001082	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)
G	VPS28_C	e2g3kG1	A: alpha bundles	X: Four-helical up-and-down bundle	H: VPS28 C-terminal domain-like (From Topology)	T: VPS28 C-terminal domain-like	F: VPS28_C	ECOD (1.6)
F	VPS28_C	e2g3kF1	A: alpha bundles	X: Four-helical up-and-down bundle	H: VPS28 C-terminal domain-like (From Topology)	T: VPS28 C-terminal domain-like	F: VPS28_C	ECOD (1.6)
E	VPS28_C	e2g3kE1	A: alpha bundles	X: Four-helical up-and-down bundle	H: VPS28 C-terminal domain-like (From Topology)	T: VPS28 C-terminal domain-like	F: VPS28_C	ECOD (1.6)
D	VPS28_C	e2g3kD1	A: alpha bundles	X: Four-helical up-and-down bundle	H: VPS28 C-terminal domain-like (From Topology)	T: VPS28 C-terminal domain-like	F: VPS28_C	ECOD (1.6)
C	VPS28_C	e2g3kC1	A: alpha bundles	X: Four-helical up-and-down bundle	H: VPS28 C-terminal domain-like (From Topology)	T: VPS28 C-terminal domain-like	F: VPS28_C	ECOD (1.6)
B	VPS28_C	e2g3kB1	A: alpha bundles	X: Four-helical up-and-down bundle	H: VPS28 C-terminal domain-like (From Topology)	T: VPS28 C-terminal domain-like	F: VPS28_C	ECOD (1.6)
A	VPS28_C	e2g3kA1	A: alpha bundles	X: Four-helical up-and-down bundle	H: VPS28 C-terminal domain-like (From Topology)	T: VPS28 C-terminal domain-like	F: VPS28_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	1.20.120.1130	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Vps28 C-terminal domain	CATH (4.2.0)
F	1.20.120.1130	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Vps28 C-terminal domain	CATH (4.2.0)
E	1.20.120.1130	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Vps28 C-terminal domain	CATH (4.2.0)
D	1.20.120.1130	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Vps28 C-terminal domain	CATH (4.2.0)
C	1.20.120.1130	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Vps28 C-terminal domain	CATH (4.2.0)
B	1.20.120.1130	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Vps28 C-terminal domain	CATH (4.2.0)
A	1.20.120.1130	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Vps28 C-terminal domain	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G	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, B, C, D, E A, B, C, D, E, F, G	Vacuolar protein sorting-associated protein VPS28	protein-containing complex binding binding	establishment of protein localization cellular localization nitrogen compound transport 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 nitrogen compound transport 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 proteolysis involved in protein 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 proteolysis 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 establishment of protein localization to membrane localization within 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 intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle cytosol endosome membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure 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, B, C, D, E A, B, C, D, E, F, G	IPR037206	VPS28, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR007143	Vacuolar protein sorting-associated Vps28	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR017899	Vacuolar protein sorting-associated, VPS28, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR017898	Vacuolar protein sorting-associated, VPS28, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR038358	VPS28, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR037202	ESCRT assembly domain	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 R01GM157729.