Annotations: 6CHS

Cdc48-Npl4 complex in the presence of ATP-gamma-S

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	HATPase_c_5	e6chsA01	A: beta barrels	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_5	ECOD (v294.2)
B [auth H]	Trypsin	e6chsH1	A: beta barrels	X: Surp module (SWAP domain)	H: ADP-ribosylation	T: ADP-ribosylation	F: Trypsin	ECOD (v294.2)
C [auth I]	Anoctamin	e6chsI1	A: beta barrels	X: Surp module (SWAP domain)	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (v294.2)
D [auth J]	Anoctamin	e6chsJ1	A: beta barrels	X: Surp module (SWAP domain)	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (v294.2)
E [auth D]	Anoctamin	e6chsD1	A: beta barrels	X: Surp module (SWAP domain)	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (v294.2)
F [auth E]	Anoctamin	e6chsE1	A: beta barrels	X: Surp module (SWAP domain)	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (v294.2)
G [auth F]	Anoctamin	e6chsF1	A: beta barrels	X: Surp module (SWAP domain)	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05020	NPL4 family, putative zinc binding region (zf-NPL4)	NPL4 family, putative zinc binding region	-	Family
A	PF05021	NPL4 family (NPL4)	NPL4 family	-	Family
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	PF09336	Vps4 C terminal oligomerisation domain (Vps4_C)	Vps4 C terminal oligomerisation domain	This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation [1].	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth 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
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Npl4	protein binding binding ubiquitin binding ubiquitin-like protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cation binding ion binding metal ion binding small molecule binding	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process RNA transport nitrogen compound transport transport catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport establishment of protein localization protein transport intracellular protein localization	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane perinuclear region of cytoplasm membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane perinuclear region of cytoplasm cytoplasm
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	Putative cell division control protein	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	cellular response to stimulus catabolic process response to stimulus 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 response to stress protein metabolic process cellular response to topologically incorrect protein primary metabolic process proteasomal protein catabolic process cellular response to stimulus catabolic process response to stimulus 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 response to stress protein 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 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 cell division protein exit from endoplasmic reticulum cellular localization establishment of protein localization transport localization ERAD pathway intercellular transport 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	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 cytosol mitochondrial membrane mitochondrion organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007717	Nuclear pore localisation protein NPL4, C-terminal	Domain
A	IPR007716	NPL4, zinc-binding putative	Domain
A	IPR016563	Nuclear protein localization protein 4	Family
A	IPR037518	MPN domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR041569	AAA ATPase, AAA+ lid domain	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR004201	CDC48, domain 2	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR015415	Spastin/Vps4, C-terminal	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR050168	AAA ATPase domain-containing protein	Family
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR005938	AAA ATPase, CDC48 family	Family
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR003338	CDC48, N-terminal subdomain	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR003593	AAA+ ATPase domain	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR003959	ATPase, AAA-type, core	Domain
B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], B [auth H], C [auth I], D [auth J], E [auth D], F [auth E], G [auth F]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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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.

6CHS | pdb_00006chs

Cdc48-Npl4 complex in the presence of ATP-gamma-S

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