Annotations: 1YXR

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1yxra1	All alpha proteins	Spectrin repeat-like	MIT domain	MIT domain	Vacuolar protein sorting factor 4a (VPS4A, SKD2)	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	SCOP2B Superfamily	MIT domain	8034724	3001898	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	MIT	e1yxrA1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: MIT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.58.80	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04212	MIT (microtubule interacting and transport) domain (MIT)	MIT (microtubule interacting and transport) domain	The MIT domain forms an asymmetric three-helix bundle [3] and binds ESCRT-III (endosomal sorting complexes required for transport) substrates [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	vacuolar protein sorting factor 4A	protein-containing complex destabilizing activity ATP-dependent protein disaggregase activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding protein-containing complex destabilizing activity ATP-dependent protein disaggregase activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-containing complex binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	regulation of cytokinesis regulation of biological process regulation of cellular process negative regulation of cytokinesis regulation of cell cycle process biological regulation negative regulation of biological process negative regulation of cell cycle cytokinesis negative regulation of cell cycle process regulation of cell division negative regulation of cell division negative regulation of cellular process cellular process regulation of cytokinesis regulation of biological process regulation of cellular process negative regulation of cytokinesis regulation of cell cycle process biological regulation negative regulation of biological process negative regulation of cell cycle cytokinesis negative regulation of cell cycle process regulation of cell division negative regulation of cell division negative regulation of cellular process cellular process cell cycle cell division regulation of cell cycle cell cycle process cellular component disassembly catabolic process macroautophagy protein-containing complex organization autophagy protein-containing complex disassembly cellular component organization autophagosome maturation metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism membrane organization membrane biogenesis nuclear membrane reassembly membrane assembly nuclear membrane organization cellular component biogenesis nucleus organization organelle organization cellular component assembly nuclear envelope organization endomembrane system organization positive regulation of viral life cycle positive regulation of viral process positive regulation of biological process viral budding viral budding via host ESCRT complex viral life cycle regulation of viral budding via host ESCRT complex virion assembly regulation of viral process regulation of viral life cycle viral process positive regulation of viral budding via host ESCRT complex proteolysis involved in protein catabolic process primary metabolic 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 protein metabolic process macromolecule metabolic process establishment of organelle localization cellular localization mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment localization chromosome localization organelle localization establishment of localization in cell mitotic sister chromatid segregation chromosome segregation mitotic nuclear division organelle fission chromosome organization sister chromatid segregation establishment of localization nuclear division mitotic cell cycle process nuclear chromosome segregation establishment of chromosome localization transport intracellular lipid transport intracellular cholesterol transport lipid localization lipid transport intracellular transport organic hydroxy compound transport intracellular sterol transport macromolecule localization cholesterol transport sterol transport vesicle budding from membrane vesicle-mediated transport vesicle organization multivesicular body sorting pathway endosomal transport late endosomal microautophagy microautophagy endosomal vesicle fusion membrane fusion organelle membrane fusion organelle fusion vesicle fusion protein localization regulation of localization protein localization to cell periphery regulation of protein localization protein localization to plasma membrane localization within membrane regulation of protein localization to cell periphery protein localization to membrane regulation of cellular localization cellular macromolecule localization regulation of protein localization to plasma membrane regulation of protein localization to membrane vesicle uncoating protein depolymerization ESCRT III complex disassembly ESCRT complex disassembly cytoskeleton-dependent cytokinesis late endosome to lysosome transport endosome to lysosome transport lysosomal transport endosome to lysosome transport via multivesicular body sorting pathway late endosome to vacuole transport late endosome to lysosome transport via multivesicular body sorting pathway vacuolar transport endosome transport via multivesicular body sorting pathway organelle assembly multivesicular body assembly multivesicular body organization endosome organization cellular response to stimulus regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle cell cycle phase transition intracellular signal transduction negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle negative regulation of cell cycle phase transition signal transduction mitotic cytokinesis checkpoint signaling cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition mitotic cytokinetic process mitotic cytokinesis midbody abscission cytokinetic process ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway mitotic nuclear membrane reassembly mitotic nuclear membrane organization actin cytoskeleton organization actomyosin structure organization cortical cytoskeleton organization contractile ring contraction cortical actin cytoskeleton organization actomyosin contractile ring contraction actin filament-based process actomyosin contractile ring organization cytoskeleton organization membrane fission exit from host cell biological process involved in interspecies interaction between organisms viral release from host cell biological process involved in interaction with host biological process involved in symbiotic interaction non-lytic viral release viral budding from plasma membrane exosomal secretion 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 positive regulation of cellular process 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 establishment of protein localization nitrogen compound transport protein targeting establishment of protein localization to vacuole protein targeting to lysosome protein targeting to vacuole protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein transport protein localization to organelle intracellular protein transport wound healing plasma membrane repair response to stress plasma membrane organization response to wounding vacuole organization developmental process multicellular organism development multicellular organismal process abscission anatomical structure development	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle endomembrane system organelle envelope nuclear envelope nuclear pore endosome membrane endosome membrane intracellular vesicle late endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome organelle membrane perinuclear region of cytoplasm midbody centrosome microtubule organizing center cell periphery plasma membrane lytic vacuole vacuole lysosome early endosome ATPase complex catalytic complex Flemming body vacuolar membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003959	ATPase, AAA-type, core	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR007330	MIT domain	Domain
A	IPR036181	MIT domain superfamily	Homologous Superfamily
A	IPR003593	AAA+ ATPase domain	Domain
A	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A	IPR015415	Spastin/Vps4, C-terminal	Domain
A	IPR050304	Microtubule-severing AAA ATPase	Family
A	IPR045253	Vacuolar protein sorting-associated protein 4, MIT domain	Domain
A	IPR003960	ATPase, AAA-type, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9UN37	cataract ovarian cancer congenital dyserythropoietic anemia psoriasis familial hemolytic anemia

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.