6OAB

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 2

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 [auth D]	CDC48	e6oabD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
A [auth D]	Vps4_C_C	e6oabD3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
A [auth D]	Sigma54_activat	e6oabD2	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 [auth E]	PRK03992	e6oabE3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK03992	ECOD (1.6)
B [auth E]	Sigma54_activat	e6oabE2	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 [auth E]	Sigma54_activat,CDC48	e6oabE1	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,CDC48	ECOD (1.6)
C [auth B]	CDC48	e6oabB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
C [auth B]	Vps4_C_C	e6oabB3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
C [auth B]	Sigma54_activat	e6oabB4	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 C]	CDC48	e6oabC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
D [auth C]	Vps4_C_C	e6oabC4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
D [auth C]	Sigma54_activat	e6oabC3	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 A]	CDC48	e6oabA4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
E [auth A]	Vps4_C_C	e6oabA3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
E [auth A]	Sigma54_activat	e6oabA2	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 [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	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 [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	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 [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	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 response to organic substance 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 organic substance metabolic process cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress cellular response to stimulus response to organic substance 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 organic substance metabolic process cellular response to stress modification-dependent macromolecule catabolic process proteolysis response to stress protein metabolic process cellular response to organic substance 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 cellular response to chemical stimulus modification-dependent protein catabolic process response to chemical 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 organic substance catabolic process cellular component disassembly cellular response to inorganic substance cellular response to metal ion protein-containing complex organization protein-containing complex disassembly response to cadmium ion response to inorganic substance cellular component organization response to metal ion 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 cellular biosynthetic process rescue of stalled ribosome organonitrogen compound biosynthetic process organic substance biosynthetic process ribosome disassembly 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 stress-induced homeostatically regulated protein degradation pathway response to organonitrogen compound response to nitrogen compound protein localization 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 cellular macromolecule localization macromolecule localization protein localization to organelle positive regulation of protein localization ribose phosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process nucleobase-containing compound 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 organic cyclic 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 nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process ncRNA metabolic 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 DNA-templated DNA replication DNA metabolic process DNA replication termination DNA replication protein exit from endoplasmic reticulum establishment of protein localization nitrogen compound transport transport ERAD pathway response to endoplasmic reticulum stress endoplasmic reticulum to cytosol transport organic substance transport intracellular transport protein transport retrograde protein transport, ER to cytosol intracellular protein transport establishment of protein localization to vacuole vesicle-mediated transport 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 endosomal transport 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
F [auth H]	poly(alanine) substrate	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR003959	ATPase, AAA-type, core	Domain
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR005938	AAA ATPase, CDC48 family	Family
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR003338	CDC48, N-terminal subdomain	Domain
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR004201	CDC48, domain 2	Domain
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR003593	AAA+ ATPase domain	Domain
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A [auth D], B [auth E], C [auth B], D [auth C], E [auth A]	IPR003960	ATPase, AAA-type, conserved site	Conserved Site

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.