Annotations: 2JQK

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2jqka_	All alpha proteins	Spectrin repeat-like	MIT domain	MIT domain	Vacuolar sorting protein 4b (VPS4B, SKD1 protein)	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	8033242	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	e2jqkA1	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-associating protein 4B	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-containing complex binding identical protein binding protein binding protein homodimerization activity protein dimerization activity 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 ATP-dependent activity	cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism membrane organization membrane biogenesis cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular process 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 protein depolymerization cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication signal transduction Wnt signaling pathway 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 macromolecule metabolic process protein metabolic process mitotic nuclear division mitotic metaphase chromosome alignment organelle fission chromosome organization sister chromatid segregation mitotic cell cycle metaphase chromosome alignment localization 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 organelle assembly 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 transport macromolecule localization lipid localization cholesterol transport lipid transport sterol transport organic hydroxy compound transport establishment of localization microtubule organizing center organization regulation of centrosome cycle centrosome duplication centrosome cycle regulation of centrosome duplication virion assembly viral process viral budding viral budding via host ESCRT complex viral life cycle multivesicular body sorting pathway vesicle-mediated transport cellular localization establishment of localization in cell intracellular transport endosomal transport late endosomal microautophagy microautophagy positive regulation of organelle organization positive regulation of centriole elongation positive regulation of cellular component organization positive regulation of biological process positive regulation of cell cycle process positive regulation of cellular process regulation of centriole replication centriole replication centriole assembly centriole elongation positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of centriole elongation positive regulation of cell cycle positive regulation of centriole replication positive regulation of organelle assembly response to lipid response to chemical ESCRT III complex disassembly ESCRT complex disassembly developmental process multicellular organismal process cellular developmental process establishment of blood-brain barrier cell development nervous system development multicellular organism development central nervous system development cell differentiation anatomical structure development system development 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 blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development multivesicular body assembly vesicle organization multivesicular body organization endosome organization establishment of protein localization nitrogen compound transport protein transport intracellular protein localization cytoskeleton-dependent cytokinesis mitotic cytokinetic process mitotic cytokinesis cytokinesis midbody abscission cytokinetic process cell division exosomal secretion establishment of organelle localization regulation of localization negative regulation of biological process negative regulation of transport secretion by cell regulation of secretion by cell negative regulation of secretion negative regulation of exocytosis negative regulation of exosomal secretion negative regulation of cellular process negative regulation of secretion by cell vesicle localization secretion regulation of transport regulation of exosomal secretion establishment of vesicle localization export from cell regulation of vesicle-mediated transport extracellular exosome biogenesis regulation of secretion exocytosis extracellular vesicle biogenesis regulation of exocytosis ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway monoatomic ion transport potassium ion transport monoatomic cation transport metal ion transport membrane fission 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 positive regulation of secretion by cell positive regulation of exosomal secretion positive regulation of exocytosis positive regulation of secretion positive regulation of transport wound healing plasma membrane repair response to stress plasma membrane organization response to wounding vacuole organization regulation of cell cycle phase transition G2/M transition of mitotic cell cycle cell cycle phase transition regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle cell cycle G2/M phase transition positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition regulation of mitotic cell cycle phase transition positive regulation of cell cycle phase transition mitotic cell cycle phase transition	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 midbody centrosome microtubule organizing center cell periphery plasma membrane ATPase complex catalytic complex Flemming body
B	Charged multivesicular body protein 2b	cell adhesion molecule binding cadherin binding protein binding binding protein domain specific binding	cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism membrane organization membrane biogenesis cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation cellular process 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 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 macromolecule metabolic process protein metabolic process mitotic nuclear division mitotic metaphase chromosome alignment organelle fission chromosome organization sister chromatid segregation mitotic cell cycle metaphase chromosome alignment localization 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 regulation of cellular process 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 biological process organelle assembly regulation of cell cycle process biological regulation 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 microtubule organizing center organization regulation of centrosome cycle centrosome duplication centrosome cycle regulation of centrosome duplication cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport multivesicular body sorting pathway establishment of localization in cell endosome transport via multivesicular body sorting pathway multicellular organismal process system process nervous system process cognition virion assembly viral process viral budding viral budding via host ESCRT complex viral life cycle trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication postsynapse organization regulation of postsynapse organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of biological quality vesicle organization endosome organization cellular homeostasis neuron cellular homeostasis homeostatic process regulation of modification of synaptic structure regulation of modification of postsynaptic structure modification of synaptic structure modification of postsynaptic structure ESCRT III complex disassembly ESCRT complex disassembly late endosome to vacuole transport vacuolar transport membrane fusion organelle membrane fusion endosome to lysosome transport lysosomal transport multivesicular body-lysosome fusion endosome to lysosome transport via multivesicular body sorting pathway lysosome organization vacuole organization lytic vacuole organization lysosomal membrane organization organelle fusion vesicle fusion multivesicular body assembly multivesicular body organization establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization cytoskeleton-dependent cytokinesis mitotic cytokinetic process mitotic cytokinesis cytokinesis midbody abscission cytokinetic process cell division 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 late endosome to lysosome transport wound healing response to stimulus plasma membrane repair response to stress plasma membrane organization response to wounding vesicle fusion with vacuole vacuole fusion	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol endosome membrane extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure 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 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 ESCRT III complex organelle membrane vacuolar membrane autophagosome membrane vacuole autophagosome amphisome membrane amphisome nucleus nuclear protein-containing complex organelle envelope nuclear envelope nuclear pore synapse cell junction glutamatergic synapse lytic vacuole lytic vacuole membrane lysosomal membrane lysosome midbody multivesicular body membrane late endosome membrane late endosome multivesicular body cell periphery plasma membrane polymeric cytoskeletal fiber spindle intracellular membraneless organelle spindle microtubule kinetochore microtubule cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region condensed chromosome postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse

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
B	IPR005024	Snf7 family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O75351	dentin dysplasia type I plasma cell myeloma dermatomyositis prostate carcinoma ovarian cancer
B	Pharos: Q9UQN3	amyotrophic lateral sclerosis frontotemporal dementia and/or amyotrophic lateral sclerosis 7 frontotemporal dementia Frontotemporal Lobar Degeneration behavioral variant of frontotemporal dementia plasma cell myeloma progressive supranuclear palsy semantic dementia IgA glomerulonephritis neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm prostate carcinoma spina bifida dementia large cell medulloblastoma amyotrophic lateral sclerosis frontotemporal dementia and/or amyotrophic lateral sclerosis 7 frontotemporal dementia Frontotemporal Lobar Degeneration behavioral variant of frontotemporal dementia plasma cell myeloma progressive supranuclear palsy semantic dementia IgA glomerulonephritis neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm prostate carcinoma spina bifida dementia large cell medulloblastoma ovarian cancer Pick disease progressive non-fluent aphasia psoriasis dermatomyositis lung cancer 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.