2ZME

Integrated structural and functional model of the human ESCRT-II complex

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2zmea1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	EAP30/Vps36-like	8084657	4000170	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8084658	3000034	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8091695	3000034	SCOP2 (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	EAP30_2nd	e2zmeA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EAP30_2nd	ECOD (1.6)
A	EAP30_1st	e2zmeA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EAP30_1st	ECOD (1.6)
B	EAP30_2nd	e2zmeB6	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EAP30_2nd	ECOD (1.6)
B	EAP30_1st	e2zmeB5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: EAP30_1st	ECOD (1.6)
C	ESCRT-II_N	e2zmeC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: ESCRT-II_N	ECOD (1.6)
D	ESCRT-II_N	e2zmeD1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: ESCRT-II_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04157	EAP30/Vps36 family (EAP30)	EAP30/Vps36 family	-	Family
B	PF04157	EAP30/Vps36 family (EAP30)	EAP30/Vps36 family	-	Family
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	Vacuolar-sorting protein SNF8	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity lipid binding channel regulator activity molecular function regulator activity transporter regulator activity	organelle assembly multivesicular body assembly vesicle organization cellular component organization cellular component biogenesis organelle organization cellular component assembly multivesicular body organization endosome organization cellular process cellular component organization or biogenesis endomembrane system organization organonitrogen compound catabolic process regulation of biological process organelle assembly multivesicular body assembly vesicle organization cellular component organization cellular component biogenesis organelle organization cellular component assembly multivesicular body organization endosome organization cellular process cellular component organization or biogenesis endomembrane system organization organonitrogen compound catabolic process regulation of biological process organonitrogen compound metabolic process catabolic process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process macromolecule catabolic process regulation of primary metabolic process organic substance metabolic process metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process organic substance catabolic process regulation of protein catabolic process regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of cellular biosynthetic process localization regulation of protein complex stability regulation of biological quality positive regulation of protein metabolic process positive regulation of protein catabolic process positive regulation of catabolic process membrane organization membrane fission transport multivesicular body sorting pathway establishment of localization vesicle-mediated transport cellular catabolic process macroautophagy autophagy process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport proteolysis involved in protein catabolic process establishment of protein localization to vacuole late endosome to vacuole transport modification-dependent macromolecule catabolic process late endosome to vacuole transport via multivesicular body sorting pathway proteolysis cellular macromolecule localization establishment of localization in cell endosome transport via multivesicular body sorting pathway organic substance transport protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway protein localization to vacuole intracellular transport endosomal transport establishment of protein localization to organelle protein transport modification-dependent protein catabolic process macromolecule localization protein localization to organelle ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process vacuolar transport intracellular protein transport exosomal secretion establishment of organelle localization regulation of localization positive regulation of secretion by cell positive regulation of exosomal secretion positive regulation of exocytosis secretion by cell regulation of secretion by cell positive regulation of secretion organelle localization vesicle localization positive regulation of cellular component biogenesis secretion regulation of transport regulation of exosomal secretion establishment of vesicle localization export from cell regulation of cellular component biogenesis regulation of vesicle-mediated transport extracellular exosome biogenesis regulation of secretion exocytosis positive regulation of transport extracellular vesicle biogenesis regulation of exocytosis RNA metabolic 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription vesicle-mediated transport between endosomal compartments early endosome to late endosome transport localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol endosome membrane protein-containing complex ESCRT complex endosome 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 membrane ESCRT II complex transcription regulator complex cell periphery plasma membrane late endosome membrane late endosome nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen recycling endosome perinuclear region of cytoplasm
B	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	membrane organization cellular component organization membrane fission cellular process cellular component organization or biogenesis cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism organelle assembly multivesicular body assembly membrane organization cellular component organization membrane fission cellular process cellular component organization or biogenesis cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism organelle assembly multivesicular body assembly vesicle organization cellular component biogenesis organelle organization cellular component assembly multivesicular body organization endosome organization endomembrane system organization protein localization establishment of protein localization cellular localization nitrogen compound transport transport proteolysis involved in protein catabolic process establishment of protein localization to vacuole macromolecule catabolic process vesicle-mediated transport localization 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 cellular macromolecule localization establishment of localization in cell protein metabolic process endosome transport via multivesicular body sorting pathway organonitrogen compound catabolic process organonitrogen compound metabolic process organic substance transport protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway primary metabolic process protein localization to vacuole intracellular transport protein catabolic process establishment of localization endosomal transport establishment of protein localization to organelle protein transport modification-dependent protein catabolic process multivesicular body sorting pathway macromolecule localization protein localization to organelle ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process vacuolar transport macromolecule metabolic process organic substance catabolic process intracellular protein 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 extracellular exosome extracellular vesicle 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 extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane protein-containing complex ESCRT complex membrane membrane protein complex cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane ESCRT II complex late endosome membrane late endosome lytic vacuole vacuole lysosome nucleus
C, D	Vacuolar protein-sorting-associated protein 25	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity structural molecule activity	membrane organization cellular component organization membrane fission cellular process cellular component organization or biogenesis cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism organelle assembly multivesicular body assembly membrane organization cellular component organization membrane fission cellular process cellular component organization or biogenesis cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism organelle assembly multivesicular body assembly vesicle organization cellular component biogenesis organelle organization cellular component assembly multivesicular body organization endosome organization endomembrane system organization cellular response to stimulus regulation of cellular process response to stimulus negative regulation of protein tyrosine kinase activity regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of signal transduction regulation of transferase activity negative regulation of cellular metabolic process cell surface receptor protein tyrosine kinase signaling pathway regulation of primary metabolic process cell communication negative regulation of kinase activity negative regulation of transferase activity regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process negative regulation of protein modification process epidermal growth factor receptor signaling pathway signal transduction protein modification process phosphorus metabolic process negative regulation of protein metabolic process regulation of biological process regulation of ERBB signaling pathway protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process regulation of molecular function regulation of protein tyrosine kinase activity regulation of kinase activity regulation of response to stimulus negative regulation of protein phosphorylation negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway macromolecule modification regulation of phosphorus metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation signaling negative regulation of signaling regulation of epidermal growth factor-activated receptor activity regulation of signaling receptor activity negative regulation of ERBB signaling pathway negative regulation of phosphate metabolic process peptidyl-tyrosine modification negative regulation of cell communication organic substance metabolic process regulation of epidermal growth factor receptor signaling pathway negative regulation of cellular process protein metabolic process enzyme-linked receptor protein signaling pathway negative regulation of macromolecule metabolic process negative regulation of peptidyl-tyrosine phosphorylation regulation of signaling organonitrogen compound metabolic process cell surface receptor signaling pathway negative regulation of response to stimulus regulation of peptidyl-tyrosine phosphorylation biological regulation negative regulation of molecular function regulation of macromolecule metabolic process regulation of protein kinase activity negative regulation of protein kinase activity negative regulation of epidermal growth factor-activated receptor activity negative regulation of signal transduction negative regulation of phosphorus metabolic process regulation of cell communication regulation of phosphorylation negative regulation of phosphorylation peptidyl-tyrosine phosphorylation negative regulation of signaling receptor activity protein localization establishment of protein localization cellular localization nitrogen compound transport transport proteolysis involved in protein catabolic process establishment of protein localization to vacuole macromolecule catabolic process vesicle-mediated transport localization late endosome to vacuole transport modification-dependent macromolecule catabolic process late endosome to vacuole transport via multivesicular body sorting pathway proteolysis cellular macromolecule localization establishment of localization in cell endosome transport via multivesicular body sorting pathway organonitrogen compound catabolic process organic substance transport protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway protein localization to vacuole intracellular transport protein catabolic process establishment of localization endosomal transport establishment of protein localization to organelle protein transport modification-dependent protein catabolic process multivesicular body sorting pathway macromolecule localization protein localization to organelle ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process vacuolar transport organic substance catabolic process intracellular protein transport	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol endosome membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol 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 membrane ESCRT II complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B	IPR040608	Snf8/Vps36 family	Family
B	IPR011993	PH-like domain superfamily	Homologous Superfamily
B	IPR021648	Vacuolar protein sorting protein 36, GLUE domain	Domain
B	IPR037855	Vacuolar protein sorting protein 36	Family
C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
C, D	IPR008570	ESCRT-II complex, Vps25 subunit	Family
C, D	IPR014041	ESCRT-II complex, Vps25 subunit, N-terminal winged helix	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q96H20	heart disease lung cancer ovarian cancer
B	Pharos: Q86VN1	astrocytic tumor glioblastoma non-small cell lung carcinoma atypical teratoid rhabdoid tumor malignant ependymoma ovarian cancer breast cancer malignant glioma Pick disease
C, D	Pharos: Q9BRG1	diabetes mellitus pancreatic ductal adenocarcinoma

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.