4NIQ | pdb_00004niq

Crystal Structure of Vps4 MIT-Vfa1 MIM2

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)
C [auth B]	d4niqb_	All alpha proteins	Spectrin repeat-like	MIT domain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d4niqa_	All alpha proteins	Spectrin repeat-like	MIT domain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth B]	SCOP2B Superfamily	MIT domain	8067092	3001898	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MIT domain	8067092	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)
C [auth B]	MIT	e4niqB1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: MIT	ECOD (1.6)
A	MIT	e4niqA1	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)
C [auth B]	1.20.58.80	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
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, C [auth B]	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
B [auth C], D	VPS4-associated protein 1	ATPase activator activity molecular function activator activity molecular function regulator activity ATPase regulator activity	localization cellular localization transport establishment of localization in cell vacuolar transport intracellular transport cellular process establishment of localization establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle
A, C [auth B]	Vacuolar protein sorting-associated protein 4	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 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	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway cellular component disassembly catabolic process protein-containing complex organization macroautophagy 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 sterol metabolic process steroid metabolic process primary metabolic process lipid metabolic process late endosome to lysosome transport endosome to lysosome transport lysosomal transport endosome to lysosome transport via multivesicular body sorting pathway late endosome to lysosome transport via multivesicular body sorting pathway organelle assembly multivesicular body assembly vesicle organization multivesicular body organization endosome organization establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization cytoskeleton-dependent cytokinesis mitotic cytokinetic process mitotic cytokinesis cytokinesis mitotic cell cycle mitotic cell cycle process midbody abscission cytokinetic process cell cycle cell division cell cycle process membrane fission maintenance of protein location protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell protein localization to organelle protein retention in Golgi apparatus vesicle budding from membrane intralumenal vesicle formation wound healing response to stimulus plasma membrane repair response to stress plasma membrane organization response to wounding vacuole organization reticulophagy	midbody cellular anatomical structure membrane-bounded organelle endosome membrane protein-containing complex ATPase complex intracellular anatomical structure intracellular vesicle membrane protein complex endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane midbody cellular anatomical structure membrane-bounded organelle endosome membrane protein-containing complex ATPase complex intracellular anatomical structure intracellular vesicle membrane protein complex endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane vesicle catalytic complex ESCRT complex endosome membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane organelle ESCRT IV complex cytoplasm organelle membrane cell periphery plasma membrane nucleus nuclear protein-containing complex organelle envelope nuclear envelope nuclear pore endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR013640	VPS4-associated protein 1	Family
A, C [auth B]	IPR003593	AAA+ ATPase domain	Domain
A, C [auth B]	IPR003959	ATPase, AAA-type, core	Domain
A, C [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C [auth B]	IPR007330	MIT domain	Domain
A, C [auth B]	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A, C [auth B]	IPR015415	Spastin/Vps4, C-terminal	Domain
A, C [auth B]	IPR050304	Microtubule-severing AAA ATPase	Family
A, C [auth B]	IPR045253	Vacuolar protein sorting-associated protein 4, MIT domain	Domain
A, C [auth B]	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
A, C [auth B]	IPR036181	MIT domain superfamily	Homologous Superfamily

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.