3CF1 | pdb_00003cf1

Structure of P97/vcp in complex with ADP/ADP.alfx

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
C	d3cf1c1	All beta proteins	Double psi beta-barrel	ADC-like	Cdc48 N-terminal domain-like	Membrane fusion ATPase p97 N-terminal domain , P97-Nn	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3cf1c2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Membrane fusion ATPase VCP/p97	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3cf1c4	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	Cdc48 domain 2-like	Membrane fusion atpase p97 domain 2, P97-Nc	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3cf1b1	All beta proteins	Double psi beta-barrel	ADC-like	Cdc48 N-terminal domain-like	Membrane fusion ATPase p97 N-terminal domain , P97-Nn	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3cf1b2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Membrane fusion ATPase VCP/p97	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3cf1b4	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	Cdc48 domain 2-like	Membrane fusion atpase p97 domain 2, P97-Nc	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3cf1a1	All beta proteins	Double psi beta-barrel	ADC-like	Cdc48 N-terminal domain-like	Membrane fusion ATPase p97 N-terminal domain , P97-Nn	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3cf1a2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Membrane fusion ATPase VCP/p97	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3cf1a4	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	Cdc48 domain 2-like	Membrane fusion atpase p97 domain 2, P97-Nc	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	ADC-like	8032511	3001132	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8032512	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cdc48 domain 2-like	8032514	3000725	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104156	3002834	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ADC-like	8032511	3001132	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104156	3002834	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8032512	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cdc48 domain 2-like	8032514	3000725	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8032512	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104156	3002834	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cdc48 domain 2-like	8032514	3000725	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ADC-like	8032511	3001132	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Redoxin	e3cf1C1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Redoxin	ECOD (v294.1)
C	AAA, RuvB_N	e3cf1C19	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: AAA, RuvB_N	ECOD (v294.1)
B	Redoxin	e3cf1B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Redoxin	ECOD (v294.1)
B	AAA, RuvB_N	e3cf1B19	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: AAA, RuvB_N	ECOD (v294.1)
A	DUF498	e3cf1A3	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: DUF498	ECOD (v294.1)
A	PolyA_pol	e3cf1A7	A: a/b three-layered sandwiches	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PolyA_pol	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, 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, 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, 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, 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, C	Transitional endoplasmic reticulum ATPase	polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding protein phosphatase binding phosphatase binding enzyme binding ubiquitin-specific protease binding protease binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding protein phosphatase binding phosphatase binding enzyme binding ubiquitin-specific protease binding protease 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 ADP binding protein-containing complex binding ubiquitin-modified protein reader activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding identical protein binding protein domain specific binding BAT3 complex binding lipid binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity deubiquitinase activator activity peptidase activator activity 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 MHC class I protein binding signaling receptor binding MHC protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process protein-DNA covalent cross-linking repair metabolic process macromolecule metabolic process DNA repair cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process protein-DNA covalent cross-linking repair metabolic process macromolecule metabolic process DNA repair cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation 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 proteasomal protein catabolic process protein catabolic process macromolecule catabolic process ERAD pathway response to chemical protein metabolic process response to endoplasmic reticulum stress regulation of biological process regulation of cellular process positive regulation of cellular component organization regulation of cellular component organization positive regulation of cellular component biogenesis biological regulation positive regulation of biological process regulation of cellular component biogenesis cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly positive regulation of cellular process cellular response to heat response to heat response to abiotic stimulus response to temperature stimulus protein deubiquitination regulation of protein modification process positive regulation of protein metabolic process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein modification by small protein removal positive regulation of macromolecule metabolic process protein modification process regulation of protein modification by small protein conjugation or removal regulation of protein K63-linked deubiquitination positive regulation of protein K63-linked deubiquitination positive regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification protein K63-linked deubiquitination regulation of protein metabolic process positive regulation of protein deubiquitination regulation of macromolecule metabolic process regulation of protein deubiquitination macromolecule modification post-translational protein modification regulation of metabolic process protein modification by small protein conjugation or removal interstrand cross-link repair translesion synthesis nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process DNA synthesis involved in DNA replication nucleic acid biosynthetic process DNA replication biosynthetic process DNA biosynthetic process positive regulation of proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process protein ubiquitination protein modification by small protein conjugation cellular localization transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization vesicle-mediated transport localization intercellular transport establishment of localization in cell Golgi vesicle transport cellular response to arsenic-containing substance response to oxygen-containing compound response to arsenic-containing substance cellular response to oxygen-containing compound cellular response to chemical stimulus response to arsenite ion cellular response to arsenite ion hippo signaling signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of hippo signaling negative regulation of signal transduction regulation of response to stimulus regulation of cell communication regulation of hippo signaling cytoplasm protein quality control protein quality control for misfolded or incompletely synthesized proteins aggresome assembly inclusion body assembly nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process positive regulation of phosphate metabolic process purine ribonucleoside triphosphate biosynthetic process positive regulation of nucleotide biosynthetic process regulation of nucleotide biosynthetic process regulation of ATP metabolic process ribonucleotide biosynthetic process purine nucleoside triphosphate biosynthetic process regulation of small molecule metabolic process positive regulation of purine nucleotide biosynthetic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process positive regulation of phosphorus metabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process ribonucleoside triphosphate biosynthetic process positive regulation of ATP metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process positive regulation of nucleotide metabolic process purine nucleotide metabolic process ribonucleotide metabolic process positive regulation of biosynthetic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process purine-containing compound biosynthetic process purine nucleoside triphosphate metabolic process regulation of biosynthetic process carbohydrate derivative biosynthetic process regulation of purine nucleotide biosynthetic process nucleoside triphosphate biosynthetic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of ATP biosynthetic process regulation of ATP biosynthetic process organophosphate metabolic process positive regulation of small molecule metabolic process cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein response to topologically incorrect protein cellular respiration aerobic respiration energy derivation by oxidation of organic compounds regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration oxidative phosphorylation positive regulation of oxidative phosphorylation positive regulation of cellular respiration regulation of oxidative phosphorylation canonical NF-kappaB signal transduction intracellular signaling cassette protein-RNA complex disassembly protein-RNA complex organization stress granule disassembly flavin-containing compound metabolic process flavin adenine dinucleotide catabolic process organophosphate catabolic process flavin adenine dinucleotide metabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process flavin-containing compound catabolic process nucleotide catabolic process viral genome replication viral process viral life cycle regulation of localization protein localization to chromatin regulation of protein localization protein localization to chromosome macromolecule localization protein localization to organelle regulation of protein localization to chromatin intracellular protein localization nicotinamide nucleotide metabolic process pyridine-containing compound metabolic process NAD+ metabolic process regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of biological quality regulation of mitochondrial membrane potential positive regulation of mitochondrial membrane potential positive regulation of membrane potential regulation of membrane potential negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway cell surface receptor signaling pathway smoothened signaling pathway protein exit from endoplasmic reticulum establishment of protein localization endoplasmic reticulum to cytosol transport protein transport retrograde protein transport, ER to cytosol intracellular protein transport negative regulation of protein localization to chromatin negative regulation of protein localization endoplasmic reticulum stress-induced pre-emptive quality control positive regulation of cell communication positive regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction positive regulation of response to stimulus non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of Wnt signaling pathway double-strand break repair endosome to lysosome transport lysosomal transport endosomal transport endosome to lysosome transport via multivesicular body sorting pathway multivesicular body sorting pathway vacuolar transport endosome transport via multivesicular body sorting pathway	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse perinuclear region of cytoplasm cytoplasmic ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse perinuclear region of cytoplasm cytoplasmic ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular membraneless organelle cilium plasma membrane bounded cell projection intracellular organelle ciliary basal body cell projection microtubule organizing center cytoskeleton organelle membraneless organelle microtubule cytoskeleton organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane cytoplasmic ribonucleoprotein granule ribonucleoprotein granule supramolecular complex cytoplasmic stress granule myelin sheath Derlin-1 retrotranslocation complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen peptidase complex proteasome complex endopeptidase complex ATPase complex VCP-NSFL1C complex lipid droplet site of double-strand break site of DNA damage chromosome

InterPro: Protein Family Classification InterPro Database Homepage

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

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.