5XMK

Cryo-EM structure of the ATP-bound Vps4 mutant-E233Q complex with Vta1 (masked)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Vps4_C_N	e5xmkA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_N	ECOD (1.6)
A	Sigma54_activat	e5xmkA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
B	Vps4_C_N	e5xmkB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_N	ECOD (1.6)
B	Sigma54_activat	e5xmkB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
C	Vps4_C_N	e5xmkC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_N	ECOD (1.6)
C	Sigma54_activat	e5xmkC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
D	Vps4_C_N	e5xmkD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_N	ECOD (1.6)
D	Sigma54_activat	e5xmkD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
E	Vps4_C_N	e5xmkE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_N	ECOD (1.6)
E	Sigma54_activat	e5xmkE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
F	Vps4_C_N	e5xmkF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_N	ECOD (1.6)
F	Sigma54_activat	e5xmkF2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
G	KOG0917	e5xmkG1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: KOG0917	ECOD (1.6)
H	KOG0917	e5xmkH1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: KOG0917	ECOD (1.6)
I	KOG0917	e5xmkI1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: KOG0917	ECOD (1.6)
J	KOG0917	e5xmkJ1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: KOG0917	ECOD (1.6)
K	KOG0917	e5xmkK1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: KOG0917	ECOD (1.6)
L	KOG0917	e5xmkL1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: KOG0917	ECOD (1.6)
M	KOG0917	e5xmkM1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: KOG0917	ECOD (1.6)
N	KOG0917	e5xmkN1	A: alpha bundles	X: Spectrin repeat-like	H: MIT domain (From Topology)	T: MIT domain	F: KOG0917	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF09336	Vps4 C terminal oligomerisation domain (Vps4_C)	Vps4 C terminal oligomerisation domain	This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation [1].	Domain
A, B, C, D, E A, B, C, D, E, F	PF17862	AAA+ lid domain (AAA_lid_3)	AAA+ lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	Domain
G, H, I, J, K G, H, I, J, K, L, M, N	PF18097	Vta1 C-terminal domain (Vta1_C)	Vta1 C-terminal domain	This is the C-terminal domain of Vta1 proteins Pfam:PF04652 . Structural and functional analysis indicate that this C-terminal domain promotes the ATP-dependent double ring assembly of Vps4. Furthermore, it has been shown that it is necessary and suf ...	This is the C-terminal domain of Vta1 proteins Pfam:PF04652 . Structural and functional analysis indicate that this C-terminal domain promotes the ATP-dependent double ring assembly of Vps4. Furthermore, it has been shown that it is necessary and sufficient for protein dimerization. Mutations in Lys-299 and Lys-302 completely abolished the ability of Vta1 to stimulate the ATPase activity of Vps4 while mutation in Lys-322 had no effect [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding 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 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 macroautophagy protein-containing complex organization cellular metabolic process autophagy protein-containing complex disassembly cellular catabolic process 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 organic hydroxy compound 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 protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule 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 entity 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 entity 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
G, H, I, J, K G, H, I, J, K, L, M, N	Vacuolar protein sorting-associated protein VTA1	ATPase activator activity molecular function activator activity molecular function regulator activity ATPase regulator activity protein-macromolecule adaptor activity molecular adaptor 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 macromolecule localization lipid localization lipid transport protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization	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 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 cellular anatomical entity intracellular membrane-bounded organelle cytoplasmic vesicle membrane organelle ESCRT IV complex cytoplasm organelle membrane late endosome multivesicular body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003959	ATPase, AAA-type, core	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR007330	MIT domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR015415	Spastin/Vps4, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050304	Microtubule-severing AAA ATPase	Family
A, B, C, D, E A, B, C, D, E, F	IPR045253	Vacuolar protein sorting-associated protein 4, MIT domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR036181	MIT domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L, M, N	IPR039431	Vta1/callose synthase, N-terminal	Domain
G, H, I, J, K G, H, I, J, K, L, M, N	IPR023175	Vta1/Callose synthase, N-terminal domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L, M, N	IPR041212	Vta1, C-terminal	Domain
G, H, I, J, K G, H, I, J, K, L, M, N	IPR044538	Vacuolar protein sorting-associated protein Vta1-like	Family

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 R01GM133198.

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5XMK

Cryo-EM structure of the ATP-bound Vps4 mutant-E233Q complex with Vta1 (masked)

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage