3HTU | pdb_00003htu

Crystal structure of the human VPS25-VPS20 subcomplex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Stathmin	e3htuA1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: SH3	T: SH3	F: Stathmin	ECOD (v294.1)
C	HTH_3	e3htuC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3	ECOD (v294.1)
E	HTH_3	e3htuE1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3	ECOD (v294.1)
G	HTH_3	e3htuG1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3	ECOD (v294.1)

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)
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)
E	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)
G	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
A, C, E, G	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, D, F, H	Vacuolar protein-sorting-associated protein 20	protein-containing complex binding binding	cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization intercellular transport late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway establishment of localization in cell cellular process vacuolar transport cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization intercellular transport late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway establishment of localization in cell cellular process vacuolar transport endosome transport via multivesicular body sorting pathway membrane fusion organelle membrane fusion endosome to lysosome transport lysosomal transport multivesicular body-lysosome fusion cellular component organization vesicle organization endosome to lysosome transport via multivesicular body sorting pathway lysosome organization cellular component organization or biogenesis membrane organization vacuole organization lytic vacuole organization lysosomal membrane organization organelle fusion organelle organization vesicle fusion cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly autophagosome maturation metabolic process process utilizing autophagic mechanism membrane biogenesis nuclear membrane reassembly membrane assembly nuclear membrane organization cellular component biogenesis nucleus organization cellular component assembly nuclear envelope organization endomembrane system organization organelle assembly multivesicular body assembly multivesicular body organization endosome 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 cell surface receptor protein tyrosine kinase signaling pathway cell communication regulation of primary metabolic process negative regulation of kinase activity 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 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 signaling regulation of protein phosphorylation negative regulation of signaling 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 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 cell surface receptor signaling pathway negative regulation of response to stimulus biological regulation negative regulation of molecular function regulation of peptidyl-tyrosine phosphorylation 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 negative regulation of signaling receptor activity peptidyl-tyrosine phosphorylation protein catabolic process regulation of catabolic process macromolecule catabolic process regulation of protein catabolic process establishment of protein localization protein transport macromolecule localization intracellular protein localization 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 mitotic nuclear division mitotic metaphase chromosome alignment organelle fission chromosome organization sister chromatid segregation mitotic cell cycle metaphase chromosome alignment nuclear division mitotic cell cycle process chromosome localization organelle localization nuclear chromosome segregation mitotic sister chromatid segregation cell cycle chromosome segregation cell cycle process regulation of cytoskeleton organization regulation of cellular component organization microtubule cytoskeleton organization regulation of mitotic spindle organization membraneless organelle assembly regulation of mitotic spindle assembly regulation of cell cycle microtubule cytoskeleton organization involved in mitosis spindle organization regulation of cell cycle process regulation of microtubule-based process regulation of spindle organization regulation of cellular component biogenesis spindle assembly regulation of organelle organization mitotic spindle organization regulation of spindle assembly mitotic spindle assembly regulation of organelle assembly microtubule-based process cytoskeleton organization regulation of microtubule cytoskeleton organization cytoskeleton-dependent cytokinesis mitotic cytokinetic process mitotic cytokinesis cytokinesis midbody abscission cytokinetic process cell division virion assembly viral process viral budding viral budding via host ESCRT complex viral life cycle vesicle budding from membrane membrane fission ESCRT III complex assembly ESCRT complex assembly protein-containing complex assembly biological process involved in interspecies interaction between organisms non-lytic viral release biological process involved in interaction with host biological process involved in symbiotic interaction exit from host cell viral budding from plasma membrane viral release from host cell late endosome to lysosome transport wound healing plasma membrane repair response to stress plasma membrane organization response to wounding vesicle fusion with vacuole vacuole fusion	midbody cellular anatomical structure membrane membrane-bounded organelle endosome membrane intracellular anatomical structure endosome multivesicular body membrane intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane midbody cellular anatomical structure membrane membrane-bounded organelle endosome membrane intracellular anatomical structure endosome multivesicular body membrane intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle late endosome cytoplasm vesicle organelle membrane multivesicular body extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytosol protein-containing complex ESCRT complex membrane protein complex ESCRT III complex cell periphery plasma membrane vacuolar membrane autophagosome membrane vacuole autophagosome amphisome membrane amphisome nucleus nuclear protein-containing complex organelle envelope nuclear envelope nuclear pore polymeric cytoskeletal fiber spindle intracellular membraneless organelle spindle microtubule kinetochore microtubule cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton lytic vacuole lytic vacuole membrane lysosomal membrane lysosome chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region condensed chromosome
A, C, E, G	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 catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism organelle assembly multivesicular body assembly vesicle organization cellular component biogenesis membrane organization cellular component organization membrane fission cellular process cellular component organization or biogenesis catabolic process macroautophagy 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 cell surface receptor protein tyrosine kinase signaling pathway cell communication regulation of primary metabolic process negative regulation of kinase activity 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 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 signaling regulation of protein phosphorylation negative regulation of signaling 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 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 cell surface receptor signaling pathway negative regulation of response to stimulus biological regulation negative regulation of molecular function regulation of peptidyl-tyrosine phosphorylation 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 negative regulation of signaling receptor activity peptidyl-tyrosine phosphorylation establishment of protein localization cellular localization transport establishment of protein localization to vacuole macromolecule catabolic process vesicle-mediated transport localization intercellular transport late endosome to vacuole transport modification-dependent macromolecule catabolic process late endosome to vacuole transport via multivesicular body sorting pathway establishment of localization in cell intracellular protein localization endosome transport via multivesicular body sorting pathway 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 protein localization to organelle macromolecule localization ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process vacuolar transport intracellular protein transport	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol endosome membrane protein-containing complex extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle 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
B, D, F, H	IPR005024	Snf7 family	Family
A, C, E, G	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, C, E, G	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, C, E, G	IPR008570	ESCRT-II complex, Vps25 subunit	Family
A, C, E, G	IPR014041	ESCRT-II complex, Vps25 subunit, N-terminal winged helix	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H	Pharos: Q96FZ7	endogenous depression ovarian cancer psoriasis
A, C, E, G	Pharos: Q9BRG1	diabetes mellitus pancreatic ductal adenocarcinoma

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.