2J9U

2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from 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	d2j9ua_	All alpha proteins	Four-helical up-and-down bundle	VPS28 C-terminal domain-like	VPS28 C-terminal domain-like	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2j9uc_	All alpha proteins	Four-helical up-and-down bundle	VPS28 C-terminal domain-like	VPS28 C-terminal domain-like	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2j9ub1	Small proteins	Rubredoxin-like	Ran binding protein zinc finger-like	Ran binding protein zinc finger-like	Vacuolar protein-sorting-associated protein 36, VPS36	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d2j9ud_	Small proteins	Rubredoxin-like	Ran binding protein zinc finger-like	Ran binding protein zinc finger-like	automated matches	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	VPS28 C-terminal domain-like	8030691	4001213	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	VPS28 C-terminal domain-like	8043070	3001082	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	VPS28 C-terminal domain-like	8043070	3001082	SCOP2B (2022-06-29)
B	SCOP2 Family	Ran binding protein zinc finger-like	8003494	4000343	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ran binding protein zinc finger-like	8003495	3000133	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Ran binding protein zinc finger-like	8003495	3000133	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	PF03997	e2j9uA1	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: PF03997	ECOD (1.6)
C	PF03997	e2j9uC1	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: PF03997	ECOD (1.6)
B	PF16988	e2j9uB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF16988	ECOD (1.6)
D	PF16988	e2j9uD1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF16988	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.1130	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Vps28 C-terminal domain	CATH (4.3.0)
C	1.20.120.1130	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Vps28 C-terminal domain	CATH (4.3.0)
B	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	CATH (4.3.0)
D	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF03997	VPS28 protein (VPS28)	VPS28 protein	-	Family
B, D	PF16988	Vacuolar protein sorting 36 NZF-N zinc-finger domain (Vps36-NZF-N)	Vacuolar protein sorting 36 NZF-N zinc-finger domain	The vacuolar protein sorting 36 NZF-N zinc-finger domain interacts with the C-terminus of vacuolar protein sorting 28 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28	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
B, D	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 36	protein binding binding ubiquitin binding ubiquitin-like protein binding phospholipid binding lipid binding phosphatidylinositol-3-phosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding cation binding ion binding metal ion binding small molecule binding	cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting establishment of protein localization to vacuole cytoplasm to vacuole targeting by the Cvt pathway localization cellular macromolecule localization establishment of localization in cell protein targeting to vacuole organic substance transport protein localization to vacuole intracellular transport establishment of localization establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle vacuolar transport intracellular protein transport 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 macromolecule metabolic process organic substance catabolic process 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 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 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	membrane-bounded organelle endosome membrane protein-containing complex intracellular anatomical structure ESCRT complex endosome membrane intracellular vesicle membrane protein complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane membrane-bounded organelle endosome membrane protein-containing complex intracellular anatomical structure ESCRT complex endosome membrane intracellular vesicle membrane protein complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle cytoplasm vesicle organelle membrane ESCRT II complex late endosome membrane late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR037206	VPS28, C-terminal domain superfamily	Homologous Superfamily
A, C	IPR007143	Vacuolar protein sorting-associated Vps28	Family
A, C	IPR017899	Vacuolar protein sorting-associated, VPS28, C-terminal	Domain
A, C	IPR017898	Vacuolar protein sorting-associated, VPS28, N-terminal	Domain
A, C	IPR038358	VPS28, N-terminal domain superfamily	Homologous Superfamily
A, C	IPR037202	ESCRT assembly domain	Homologous Superfamily
B, D	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
B, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B, D	IPR040608	Snf8/Vps36 family	Family
B, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
B, D	IPR031558	Vacuolar protein-sorting-associated protein 36, NZF-N zinc-finger domain	Domain
B, D	IPR001876	Zinc finger, RanBP2-type	Domain
B, D	IPR021648	Vacuolar protein sorting protein 36, GLUE domain	Domain
B, D	IPR037855	Vacuolar protein sorting protein 36	Family

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.