Annotations: 6CHS

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth H]	CDC48	e6chsH2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
B [auth H]	Vps4_C_C	e6chsH1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
B [auth H]	Sigma54_activat	e6chsH3	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 [auth I]	CDC48	e6chsI2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
C [auth I]	Vps4_C_C	e6chsI1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
C [auth I]	Sigma54_activat	e6chsI4	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 [auth J]	CDC48	e6chsJ2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
D [auth J]	Vps4_C_C	e6chsJ1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
D [auth J]	Sigma54_activat	e6chsJ4	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 [auth D]	CDC48	e6chsD3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
E [auth D]	Vps4_C_C	e6chsD2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
E [auth D]	Sigma54_activat	e6chsD1	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 [auth E]	CDC48	e6chsE4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
F [auth E]	Vps4_C_C	e6chsE3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
F [auth E]	Sigma54_activat	e6chsE2	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 [auth F]	CDC48	e6chsF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
G [auth F]	Vps4_C_C	e6chsF2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
G [auth F]	Sigma54_activat	e6chsF4	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05020	NPL4 family, putative zinc binding region (zf-NPL4)	NPL4 family, putative zinc binding region	-	Family
A	PF05021	NPL4 family (NPL4)	NPL4 family	-	Family
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth 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
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth 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
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Npl4	protein binding binding ubiquitin binding ubiquitin-like protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cation binding ion binding metal ion binding small molecule binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process 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 metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process 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 metabolic process protein metabolic process macromolecule metabolic process RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport protein localization establishment of protein localization cellular localization protein transport cellular macromolecule localization cellular process	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane perinuclear region of cytoplasm membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane perinuclear region of cytoplasm cytoplasm
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	Putative cell division control protein	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 polyubiquitin modification-dependent protein binding protein binding modification-dependent protein 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 ATP-dependent activity	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 cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism 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 cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism spindle disassembly microtubule cytoskeleton organization mitotic cell cycle mitotic spindle organization organelle organization mitotic cell cycle process organelle disassembly mitotic spindle disassembly microtubule-based process cell cycle cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process cell division protein localization cellular response to stimulus protein exit from endoplasmic reticulum cellular localization establishment of protein localization nitrogen compound transport response to stimulus transport proteolysis involved in protein catabolic process macromolecule catabolic process localization ERAD pathway cellular response to stress response to stress proteolysis establishment of localization in cell cellular macromolecule localization protein metabolic process response to endoplasmic reticulum stress organonitrogen compound catabolic process organonitrogen compound metabolic process endoplasmic reticulum to cytosol transport response to organonitrogen compound intracellular transport response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process establishment of localization protein transport response to chemical retrograde protein transport, ER to cytosol macromolecule localization macromolecule metabolic process intracellular protein transport	membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane cytosol nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007717	Nuclear pore localisation protein NPL4, C-terminal	Domain
A	IPR007716	NPL4, zinc-binding putative	Domain
A	IPR016563	Nuclear protein localization protein 4	Family
A	IPR037518	MPN domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR041569	AAA ATPase, AAA+ lid domain	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR004201	CDC48, domain 2	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR015415	Spastin/Vps4, C-terminal	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR050168	AAA ATPase domain-containing protein	Family
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR005938	AAA ATPase, CDC48 family	Family
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR003338	CDC48, N-terminal subdomain	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR003593	AAA+ ATPase domain	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR003959	ATPase, AAA-type, core	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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 R01GM133198.