6HD3 | pdb_00006hd3

Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth C]	d6hd3c1	All beta proteins	Double psi beta-barrel	ADC-like	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B [auth C]	d6hd3c3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B [auth C]	d6hd3c2	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth C]		e6hd3C1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: Hydrolase	F:	ECOD (20:10:01)
A		e6hd3A1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: Hydrolase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (utative)
B [auth C]	3.10.330.10	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (utative)
B [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
B [auth C]	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (utative)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C]	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 [auth C]	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 [auth C]	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
A, B [auth C]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C]	Cell division control protein 48 homolog A	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 identical protein binding	multi-multicellular organism process multicellular organismal process pollination reproductive process pollen germination response to oxidative stress regulation of biological process response to stimulus regulation of response to stimulus response to stress regulation of response to stress regulation of response to oxidative stress biological regulation cellular component disassembly multi-multicellular organism process multicellular organismal process pollination reproductive process pollen germination response to oxidative stress regulation of biological process response to stimulus regulation of response to stimulus response to stress regulation of response to stress regulation of response to oxidative stress biological regulation cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly 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 protein destabilization regulation of protein stability regulation of biological quality cell division proteasomal protein catabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process regulation of cellular process regulation of protein metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis regulation of metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process cellular response to stimulus protein exit from endoplasmic reticulum cellular localization establishment of protein localization transport localization ERAD pathway cellular response to stress establishment of localization in cell intracellular protein localization response to endoplasmic reticulum stress endoplasmic reticulum to cytosol transport intracellular transport establishment of localization protein transport response to chemical retrograde protein transport, ER to cytosol macromolecule localization intracellular protein transport developmental process cellular developmental process developmental cell growth developmental growth growth unidimensional cell growth cell development cell tip growth developmental process involved in reproduction cell growth cell morphogenesis developmental growth involved in morphogenesis anatomical structure morphogenesis pollen tube growth cell differentiation anatomical structure development pollen tube development cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound response to reactive oxygen species cellular response to reactive oxygen species cellular response to chemical stimulus regulation of defense response negative regulation of response to stimulus defense response negative regulation of biological process negative regulation of defense response	membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure 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 intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen phragmoplast organelle envelope nuclear envelope cytosol cell periphery plasma membrane external encapsulating structure plant-type cell wall cell wall plastid membrane plastid chloroplast envelope organelle outer membrane plastid outer membrane chloroplast outer membrane bounding membrane of organelle chloroplast membrane outer membrane plastid envelope chloroplast cytosolic ribosome ribosome Golgi apparatus lipid droplet cell-cell junction symplast anchoring junction cell junction plasmodesma cytoskeleton spindle microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR004201	CDC48, domain 2	Domain
A, B [auth C]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, B [auth C]	IPR003593	AAA+ ATPase domain	Domain
A, B [auth C]	IPR003959	ATPase, AAA-type, core	Domain
A, B [auth C]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B [auth C]	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
A, B [auth C]	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A, B [auth C]	IPR050168	AAA ATPase domain-containing protein	Family
A, B [auth C]	IPR005938	AAA ATPase, CDC48 family	Family
A, B [auth C]	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
A, B [auth C]	IPR003338	CDC48, N-terminal subdomain	Domain

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.