Annotations: 6OPC

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	CDC48_N	e6opcC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
C	CDC48	e6opcC6	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
C	Vps4_C_C	e6opcC5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
C	CDC48_2	e6opcC2	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)
C	Sigma54_activat	e6opcC4	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	CDC48_N	e6opcE3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
E	CDC48	e6opcE5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
E	Vps4_C_C	e6opcE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
E	CDC48_2	e6opcE4	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)
E	Sigma54_activat	e6opcE6	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)
A	CDC48_N	e6opcA6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
A	CDC48	e6opcA3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
A	Vps4_C_C	e6opcA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
A	CDC48_2	e6opcA5	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)
A	Sigma54_activat	e6opcA4	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	CDC48_N	e6opcB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
B	CDC48	e6opcB6	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
B	Vps4_C_C	e6opcB2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
B	CDC48_2	e6opcB3	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)
B	Sigma54_activat	e6opcB5	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	CDC48_N	e6opcD4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
D	CDC48	e6opcD2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
D	Vps4_C_C	e6opcD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
D	CDC48_2	e6opcD5	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)
D	Sigma54_activat	e6opcD6	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	CDC48_N	e6opcF3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
F	CDC48	e6opcF5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
F	Vps4_C_C	e6opcF6	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
F	CDC48_2	e6opcF1	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)
F	Sigma54_activat	e6opcF4	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)
H [auth Z]	UBX	e6opcZ1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UBX	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	PF02933	Cell division protein 48 (CDC48), domain 2 (CDC48_2)	Cell division protein 48 (CDC48), domain 2	This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at t ...	This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C-terminus. The VAT-N domain found in AAA ATPases Pfam:PF00004 is a substrate 185-residue recognition domain [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	PF02359	Cell division protein 48 (CDC48), N-terminal domain (CDC48_N)	Cell division protein 48 (CDC48), N-terminal domain	This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at t ...	This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases Pfam:PF00004 is a substrate 185-residue recognition domain [1].	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
H [auth Z]	PF00789	UBX domain (UBX)	UBX domain	This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module [2].	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	Cell division control protein 48	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 identical protein binding enzyme regulator activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity ubiquitin binding ubiquitin-like 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 response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress protein metabolic process organonitrogen compound catabolic process cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process cellular response to misfolded protein response to misfolded protein cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process cellular response to topologically incorrect protein primary metabolic process proteasomal protein catabolic process protein catabolic process nuclear protein quality control by the ubiquitin-proteasome system modification-dependent protein catabolic process response to topologically incorrect protein ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins cellular component disassembly cellular response to metal ion protein-containing complex organization protein-containing complex disassembly response to cadmium ion cellular component organization cellular response to chemical stimulus response to metal ion response to chemical cellular response to cadmium ion cellular component organization or biogenesis SCF complex disassembly in response to cadmium stress macroautophagy cellular metabolic process autophagy cellular catabolic process autophagosome maturation 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 response to organonitrogen compound response to nitrogen compound ERAD pathway response to endoplasmic reticulum stress ribosome disassembly cellular biosynthetic process rescue of stalled ribosome organonitrogen compound biosynthetic process translation gene expression macromolecule biosynthetic process biosynthetic process translational elongation piecemeal microautophagy of the nucleus microautophagy nucleophagy establishment of organelle localization cellular localization attachment of spindle microtubules to kinetochore sister chromatid biorientation chromosome organization sister chromatid segregation establishment of localization metaphase chromosome alignment localization chromosome localization organelle localization establishment of localization in cell nuclear chromosome segregation establishment of chromosome localization chromosome segregation ribosome-associated ubiquitin-dependent protein catabolic process ribophagy positive regulation of organelle organization positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization regulation of developmental process positive regulation of biological process positive regulation of developmental process anatomical structure development regulation of mitochondrial fusion mitochondrial fusion positive regulation of cellular process regulation of anatomical structure morphogenesis positive regulation of mitochondrial fusion mitochondrion organization developmental process regulation of biological process biological regulation regulation of organelle organization organelle fusion anatomical structure morphogenesis regulation of mitochondrion organization protein localization establishment of protein localization nitrogen compound transport transport establishment of protein localization to plasma membrane vesicle-mediated transport endocytic recycling cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane intracellular transport localization within membrane protein localization to membrane endosomal transport vesicle-mediated transport to the plasma membrane endosome to plasma membrane protein transport protein transport macromolecule localization intracellular protein transport stress-induced homeostatically regulated protein degradation pathway mitotic DNA replication cell cycle DNA replication termination DNA-templated DNA replication nuclear DNA replication cell cycle DNA replication DNA metabolic process DNA replication termination nucleic acid metabolic process nucleobase-containing compound metabolic process nuclear DNA replication termination DNA replication mitotic DNA replication termination regulation of localization regulation of protein localization positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus regulation of cellular localization protein localization to organelle positive regulation of protein localization ribose phosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process purine nucleoside triphosphate metabolic process nucleotide metabolic process purine-containing compound metabolic process organophosphate metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process mitochondria-associated ubiquitin-dependent protein catabolic process nonfunctional rRNA decay RNA metabolic process rRNA catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process rRNA metabolic process RNA catabolic process cytoplasm protein quality control cytoplasm protein quality control by the ubiquitin-proteasome system membrane organization membrane fusion organelle membrane fusion endoplasmic reticulum organization endoplasmic reticulum membrane organization endoplasmic reticulum membrane fusion endomembrane system organization protein exit from endoplasmic reticulum endoplasmic reticulum to cytosol transport retrograde protein transport, ER to cytosol establishment of protein localization to vacuole late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway protein localization to vacuole establishment of protein localization to organelle multivesicular body sorting pathway ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway vacuolar transport	cell projection mating projection cell tip mating projection tip cell pole cellular anatomical entity plasma membrane bounded cell projection site of polarized growth intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex cell projection mating projection cell tip mating projection tip cell pole cellular anatomical entity plasma membrane bounded cell projection site of polarized growth intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex mitochondrial membrane mitochondrion outer mitochondrial membrane protein complex membrane membrane protein complex organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle Cdc48p-Npl4p-Vms1p AAA ATPase complex organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane cytoplasmic ubiquitin ligase complex ubiquitin ligase complex transferase complex endomembrane system ER ubiquitin ligase complex endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex Doa10p ubiquitin ligase complex organelle subcompartment endoplasmic reticulum intracellular protein-containing complex VCP-NPL4-UFD1 AAA ATPase complex RQC complex Hrd1p ubiquitin ligase ERAD-L complex Hrd1p ubiquitin ligase complex protein-DNA complex chromosome intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle nucleus
G	Substrate bound to the central pore of the Cdc48 hexamer	-	-	-
H [auth Z]	UBX domain-containing protein 1	enzyme regulator activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin binding ubiquitin-like protein binding	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis membrane biogenesis nuclear membrane reassembly membrane assembly nuclear membrane organization cellular component biogenesis nucleus organization organelle organization cellular component assembly nuclear envelope organization membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis 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 cellular response to stimulus organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process response to stimulus response to organonitrogen compound proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress autophagosome assembly organelle assembly vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular catabolic process process utilizing autophagic mechanism piecemeal microautophagy of the nucleus microautophagy nucleophagy establishment of organelle localization cellular localization attachment of spindle microtubules to kinetochore sister chromatid biorientation chromosome organization sister chromatid segregation establishment of localization metaphase chromosome alignment localization chromosome localization organelle localization establishment of localization in cell nuclear chromosome segregation cell cycle establishment of chromosome localization chromosome segregation cell cycle process developmental process sexual sporulation resulting in formation of a cellular spore sexual reproduction cellular developmental process reproductive process reproductive process in single-celled organism meiotic cell cycle cell development developmental process involved in reproduction meiotic cell cycle process sporulation resulting in formation of a cellular spore anatomical structure morphogenesis ascospore formation sexual sporulation cell differentiation anatomical structure formation involved in morphogenesis anatomical structure development sporulation proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process carbohydrate metabolic process energy derivation by oxidation of organic compounds glycogen metabolic process generation of precursor metabolites and energy glucan metabolic process polysaccharide metabolic process energy reserve metabolic process Golgi organization	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR005938	AAA ATPase, CDC48 family	Family
A, B, C, D, E A, B, C, D, E, F	IPR003338	CDC48, N-terminal subdomain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004201	CDC48, domain 2	Domain
A, B, C, D, E A, B, C, D, E, F	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
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	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050168	AAA ATPase domain-containing protein	Family
A, B, C, D, E A, B, C, D, E, F	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
H [auth Z]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
H [auth Z]	IPR036241	NSFL1 cofactor p47, SEP domain superfamily	Homologous Superfamily
H [auth Z]	IPR001012	UBX domain	Domain
H [auth Z]	IPR012989	SEP domain	Domain