6OAA

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1

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 B]	CDC48	e6oaaB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
A [auth B]	Vps4_C_C	e6oaaB3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
A [auth B]	Sigma54_activat	e6oaaB2	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 C]	CDC48	e6oaaC3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
B [auth C]	Vps4_C_C	e6oaaC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
B [auth C]	Sigma54_activat	e6oaaC4	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 D]	CDC48	e6oaaD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: CDC48	ECOD (1.6)
C [auth D]	Vps4_C_C	e6oaaD4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Vps4_C_C	ECOD (1.6)
C [auth D]	Sigma54_activat	e6oaaD2	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 G]	UNK_F_TYPE	e6oaaG2	A: alpha arrays	X: C-terminal domain of Npl4 (From Topology)	H: C-terminal domain of Npl4 (From Topology)	T: C-terminal domain of Npl4	F: UNK_F_TYPE	ECOD (1.6)
E [auth G]	UNK_F_TYPE	e6oaaG1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: UNK_F_TYPE	ECOD (1.6)
E [auth G]	UNK_F_TYPE	e6oaaG3	A: few secondary structure elements	X: Npl4 zinc binding domain (From Topology)	H: Npl4 zinc binding domain (From Topology)	T: Npl4 zinc binding domain	F: UNK_F_TYPE	ECOD (1.6)
F [auth H]	ubiquitin	e6oaaH1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth C], C [auth D], D [auth E]	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 B], B [auth C], C [auth D], D [auth E]	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
E [auth G]	PF05021	NPL4 family (NPL4)	NPL4 family	-	Family
F [auth H]	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth C], C [auth D], D [auth E]	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
E [auth G]	Nuclear protein localization protein 4	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 ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	protein localization localization cellular localization protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to vacuole cellular process regulation of localization regulation of biological process regulation of cellular process regulation of protein localization positive regulation of protein localization to nucleus biological regulation protein localization localization cellular localization protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to vacuole cellular process regulation of localization regulation of biological process regulation of cellular process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus regulation of cellular localization positive regulation of protein localization positive regulation of cellular process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process mitochondria-associated ubiquitin-dependent protein catabolic process proteasome-mediated ubiquitin-dependent 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 cellular component disassembly spindle disassembly microtubule cytoskeleton organization mitotic cell cycle mitotic spindle organization cellular component organization organelle organization mitotic cell cycle process organelle disassembly mitotic spindle disassembly microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization establishment of RNA localization RNA localization nucleobase-containing compound transport nonfunctional rRNA decay RNA metabolic process rRNA catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process rRNA metabolic process RNA catabolic process cellular response to stimulus response to stimulus response to organonitrogen compound response to nitrogen compound ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress ribosome disassembly cellular biosynthetic process cellular metabolic process rescue of stalled ribosome organonitrogen compound biosynthetic process translation gene expression macromolecule biosynthetic process biosynthetic process translational elongation cytoplasm protein quality control cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein cytoplasm protein quality control by the ubiquitin-proteasome system response to topologically incorrect protein protein quality control for misfolded or incompletely synthesized proteins DNA-templated DNA replication DNA replication DNA metabolic process DNA replication termination protein exit from endoplasmic reticulum establishment of protein localization establishment of localization in cell endoplasmic reticulum to cytosol transport intracellular transport protein transport retrograde protein transport, ER to cytosol intracellular protein transport ribosome-associated ubiquitin-dependent protein catabolic process establishment of protein localization to plasma membrane vesicle-mediated transport endocytic recycling protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane endosomal transport vesicle-mediated transport to the plasma membrane endosome to plasma membrane 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 nuclear membrane nucleus organelle envelope nuclear envelope RQC complex cytoplasmic ubiquitin ligase complex ubiquitin ligase complex transferase complex ER ubiquitin ligase complex catalytic complex Hrd1p ubiquitin ligase ERAD-L complex Hrd1p ubiquitin ligase complex intracellular protein-containing complex mitochondrial protein-containing complex mitochondrial membrane mitochondrion outer mitochondrial membrane protein complex organelle outer membrane bounding membrane of organelle Cdc48p-Npl4p-Vms1p AAA ATPase complex mitochondrial envelope mitochondrial outer membrane outer membrane Doa10p ubiquitin ligase complex perinuclear region of cytoplasm protein-DNA complex chromosome intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle
F [auth H]	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding structural molecule activity structural constituent of ribosome	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal establishment of organelle localization cellular localization nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus ribosomal large subunit export from nucleus intracellular transport establishment of localization protein-containing complex localization localization organelle localization establishment of localization in cell nuclear export ribosome localization	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome large ribosomal subunit intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome large ribosomal subunit non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth C], C [auth D], D [auth E]	IPR003959	ATPase, AAA-type, core	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B], B [auth C], C [auth D], D [auth E]	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
A [auth B], B [auth C], C [auth D], D [auth E]	IPR005938	AAA ATPase, CDC48 family	Family
A [auth B], B [auth C], C [auth D], D [auth E]	IPR003338	CDC48, N-terminal subdomain	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	IPR004201	CDC48, domain 2	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A [auth B], B [auth C], C [auth D], D [auth E]	IPR003593	AAA+ ATPase domain	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	IPR050168	AAA ATPase domain-containing protein	Family
A [auth B], B [auth C], C [auth D], D [auth E]	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
E [auth G]	IPR007716	NPL4, zinc-binding putative	Domain
E [auth G]	IPR007717	Nuclear pore localisation protein NPL4, C-terminal	Domain
E [auth G]	IPR016563	Nuclear protein localization protein 4	Family
E [auth G]	IPR037518	MPN domain	Domain
E [auth G]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
F [auth H]	IPR019954	Ubiquitin conserved site	Conserved Site
F [auth H]	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
F [auth H]	IPR000626	Ubiquitin-like domain	Domain
F [auth H]	IPR019956	Ubiquitin domain	Domain
F [auth H]	IPR050158	Ubiquitin and ubiquitin-like	Family
F [auth H]	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
F [auth H]	IPR029071	Ubiquitin-like 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 R01GM133198.

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6OAA

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1

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