Annotations: 31OQ

CryoEM structure of substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FAF1- State III

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	Transitional endoplasmic reticulum ATPase	protein phosphatase binding phosphatase binding protein binding binding enzyme 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 protein phosphatase binding phosphatase binding protein binding binding enzyme 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 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 protein domain specific 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 polyubiquitin modification-dependent protein binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin-specific protease binding protease binding ADP binding identical protein binding protein-containing complex binding BAT3 complex binding RNA binding nucleic acid binding	catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus protein deubiquitination catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus protein deubiquitination regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological 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 metabolic process protein modification process regulation of protein modification by small protein conjugation or removal regulation of protein K63-linked deubiquitination positive regulation of cellular process positive regulation of protein K63-linked deubiquitination positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification protein K63-linked deubiquitination regulation of protein metabolic process positive regulation of protein deubiquitination biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of protein deubiquitination macromolecule modification macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation or removal DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA damage response interstrand cross-link repair DNA 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 macromolecule catabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process proteasomal protein catabolic process protein 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 localization cellular localization transport establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization Golgi vesicle transport vesicle-mediated transport ribosome-associated ubiquitin-dependent protein catabolic process cytoplasm protein quality control protein quality control for misfolded or incompletely synthesized proteins cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein response to topologically incorrect protein signaling endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein intracellular signal transduction cell communication signal transduction response to endoplasmic reticulum stress establishment of protein localization 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 nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process nucleotide metabolic process purine-containing compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process NAD+ metabolic process regulation of cellular component organization cellular component organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of biological quality regulation of mitochondrial membrane potential positive regulation of mitochondrial membrane potential positive regulation of membrane potential regulation of membrane potential ERAD pathway protein transport response to chemical retrograde protein transport, ER to cytosol protein unfolding macroautophagy positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication 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 cell surface receptor signaling pathway regulation of Wnt signaling pathway cellular component disassembly ribosome disassembly translation gene expression protein biosynthetic process organelle organization organelle disassembly translational elongation cytoplasmic translation cytoplasmic translational elongation rescue of stalled cytosolic ribosome protein-DNA covalent cross-linking repair protein-containing complex organization protein-containing complex disassembly autophagosome maturation spindle disassembly microtubule cytoskeleton organization mitotic cell cycle mitotic spindle organization mitotic cell cycle process mitotic spindle disassembly microtubule-based process cell cycle cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process positive regulation of cellular component organization positive regulation of cellular component biogenesis 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 regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death peptidyl-lysine methylation protein methylation peptidyl-lysine modification peptidyl-lysine trimethylation macromolecule methylation protein alkylation methylation protein ubiquitination protein modification by small protein conjugation 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 negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of cell communication negative regulation of cellular process negative regulation of response to stimulus negative regulation of hippo signaling negative regulation of signal transduction regulation of hippo signaling nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic 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 regulation of nucleobase-containing compound metabolic process ribose phosphate biosynthetic process positive regulation of phosphorus 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 ribonucleotide metabolic process positive regulation of biosynthetic 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 positive regulation of purine nucleotide metabolic process positive regulation of ATP biosynthetic process regulation of ATP biosynthetic process positive regulation of small molecule metabolic process 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 protein-RNA complex disassembly cytoplasmic stress granule disassembly protein-RNA complex organization 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 negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway smoothened signaling pathway negative regulation of protein localization to chromatin negative regulation of protein localization endoplasmic reticulum stress-induced pre-emptive quality control 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 mitophagy autophagy of mitochondrion	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex intracellular protein-containing complex cytoplasmic ubiquitin ligase complex ubiquitin ligase complex catalytic complex transferase complex membrane-bounded organelle organelle subcompartment membrane membrane protein complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex intracellular protein-containing complex cytoplasmic ubiquitin ligase complex ubiquitin ligase complex catalytic complex transferase complex membrane-bounded organelle organelle subcompartment membrane membrane protein complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle Derlin-1 retrotranslocation complex organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane RQC complex peptidase complex proteasome complex endopeptidase complex extracellular region vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular organelle lumen cytoplasmic vesicle organelle lumen secretory granule secretory vesicle vesicle site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome extracellular exosome extracellular vesicle extracellular organelle extracellular membrane-bounded organelle synapse cell junction glutamatergic synapse perinuclear region of cytoplasm VCP-NPL4-UFD1 AAA ATPase complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule supramolecular complex cytoplasmic stress granule lytic vacuole vacuolar lumen lysosome azurophil granule vacuole azurophil granule lumen primary lysosome ficolin-1-rich granule ficolin-1-rich granule lumen nucleus nucleoplasm nuclear lumen ATPase complex VCP-NSFL1C complex lipid droplet
L [auth T]	FAS-associated factor 1	protein binding binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding heat shock protein binding ubiquitin binding ubiquitin-like protein binding kinase binding enzyme binding protein kinase binding enzyme regulator activity protein binding binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding heat shock protein binding ubiquitin binding ubiquitin-like protein binding kinase binding enzyme binding protein kinase binding enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding	cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress cellular process metabolic process protein metabolic process cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of catabolic process regulation of primary metabolic process regulation of metabolic process regulation of protein catabolic process signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of canonical NF-kappaB signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death positive regulation of cellular process positive regulation of DNA replication nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process DNA metabolic process nucleic acid metabolic process DNA replication positive regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA replication positive regulation of protein metabolic process positive regulation of protein catabolic process positive regulation of catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process cell surface receptor signaling pathway Fas signaling pathway	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 organelle envelope nuclear envelope nucleus cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen CD95 death-inducing signaling complex cell periphery plasma membrane protein complex plasma membrane death-inducing signaling complex ATPase complex catalytic complex perinuclear region of cytoplasm
I [auth J], J [auth K], K [auth M], M [auth I], N, I [auth J], J [auth K], K [auth M], M [auth I], N, O [auth L]	Polyubiquitin-B	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding protein tag activity molecular tag activity	regulation of mitochondrial membrane potential biological regulation regulation of biological quality regulation of membrane potential protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular process regulation of mitochondrial membrane potential biological regulation regulation of biological quality regulation of membrane potential protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process regulation of biological process neuron apoptotic process regulation of cellular process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule modification post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction intrinsic apoptotic signaling pathway regulation of signaling positive regulation of programmed cell death positive regulation of intracellular signal transduction signal transduction by p53 class mediator positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway positive regulation of signaling multicellular organismal process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development animal gross anatomical part developmental process positive regulation of protein monoubiquitination protein monoubiquitination regulation of protein monoubiquitination proteasomal protein catabolic process regulation of catabolic process regulation of proteasomal protein catabolic process regulation of protein catabolic process establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated mitochondrion transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cell projection neuron projection plasma membrane bounded cell projection intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle cytosolic ribosome membraneless organelle intracellular membraneless organelle ribosome endosome membrane endosome mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane somatodendritic compartment cell body neuronal cell body
H	Ubiquitin recognition factor in ER-associated degradation protein 1	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein 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 cellular response to stimulus positive regulation of response to biotic stimulus negative regulation of RIG-I signaling pathway 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 cellular response to stimulus positive regulation of response to biotic stimulus negative regulation of RIG-I signaling pathway regulation of cellular process pattern recognition receptor signaling pathway response to stimulus negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process immune response response to other organism regulation of innate immune response response to external stimulus regulation of RIG-I signaling pathway RIG-I signaling pathway regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction positive regulation of biological process regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response negative regulation of cellular process response to external biotic stimulus regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus biological regulation defense response to symbiont negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication multicellular organismal process negative regulation of type I interferon production cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process type I interferon production negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production proteasomal protein catabolic process ERAD pathway cellular response to stress response to chemical response to endoplasmic reticulum stress developmental process multicellular organism development skeletal system development anatomical structure development animal gross anatomical part developmental process system development cellular component disassembly ribosome disassembly translation protein biosynthetic process cellular component organization organelle organization organelle disassembly translational elongation cytoplasmic translation cytoplasmic translational elongation cellular component organization or biogenesis rescue of stalled cytosolic ribosome cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein response to topologically incorrect protein proteasome-mediated ubiquitin-dependent protein catabolic process establishment of protein localization transport localization intracellular protein localization establishment of localization protein transport retrograde protein transport, ER to cytosol macromolecule localization ribosome-associated ubiquitin-dependent protein catabolic process	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 ATPase complex catalytic complex UFD1-NPL4 complex cytosol RQC complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
G	Nuclear protein localization protein 4 homolog	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 K63-linked polyubiquitin modification-dependent protein binding protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding ATPase binding	cellular response to stimulus positive regulation of response to biotic stimulus negative regulation of RIG-I signaling pathway regulation of cellular process pattern recognition receptor signaling pathway response to stimulus negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process cellular response to stimulus positive regulation of response to biotic stimulus negative regulation of RIG-I signaling pathway regulation of cellular process pattern recognition receptor signaling pathway response to stimulus negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process immune response response to other organism regulation of innate immune response response to external stimulus regulation of RIG-I signaling pathway RIG-I signaling pathway regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction positive regulation of biological process regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response negative regulation of cellular process response to external biotic stimulus regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus biological regulation defense response to symbiont negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication cellular process multicellular organismal process negative regulation of type I interferon production cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process type I interferon production negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical protein metabolic process response to endoplasmic reticulum stress proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process establishment of protein localization transport localization intracellular protein localization establishment of localization protein transport retrograde protein transport, ER to cytosol macromolecule localization ribosome-associated ubiquitin-dependent protein catabolic process cellular component disassembly ribosome disassembly translation protein biosynthetic process cellular component organization organelle organization organelle disassembly translational elongation cytoplasmic translation cytoplasmic translational elongation cellular component organization or biogenesis rescue of stalled cytosolic ribosome Golgi organization endomembrane system organization	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 RQC complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen ATPase complex catalytic complex UFD1-NPL4 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR003959	ATPase, AAA-type, core	Domain
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR005938	AAA ATPase, CDC48 family	Family
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR003338	CDC48, N-terminal subdomain	Domain
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR004201	CDC48, domain 2	Domain
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR003593	AAA+ ATPase domain	Domain
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR050168	AAA ATPase domain-containing protein	Family
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
L [auth T]	IPR044541	FAF1, UBA-like domain	Domain
L [auth T]	IPR033043	FAS-associated factor 1-like, UBX domain	Domain
L [auth T]	IPR049483	Fas-associated factor 1/2-like, UAS domain	Domain
L [auth T]	IPR050730	UBX domain-containing protein	Family
L [auth T]	IPR006577	UAS	Domain
L [auth T]	IPR001012	UBX domain	Domain
L [auth T]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
L [auth T]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
I [auth J], J [auth K], K [auth M], M [auth I], N, I [auth J], J [auth K], K [auth M], M [auth I], N, O [auth L]	IPR019954	Ubiquitin conserved site	Conserved Site
I [auth J], J [auth K], K [auth M], M [auth I], N, I [auth J], J [auth K], K [auth M], M [auth I], N, O [auth L]	IPR050158	Ubiquitin and ubiquitin-like	Family
I [auth J], J [auth K], K [auth M], M [auth I], N, I [auth J], J [auth K], K [auth M], M [auth I], N, O [auth L]	IPR000626	Ubiquitin-like domain	Domain
I [auth J], J [auth K], K [auth M], M [auth I], N, I [auth J], J [auth K], K [auth M], M [auth I], N, O [auth L]	IPR019956	Ubiquitin domain	Domain
I [auth J], J [auth K], K [auth M], M [auth I], N, I [auth J], J [auth K], K [auth M], M [auth I], N, O [auth L]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
H	IPR055417	Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1	Domain
H	IPR004854	Ubiquitin fusion degradation protein UFD1-like	Family
H	IPR042299	UFD1-like, Nn domain	Homologous Superfamily
H	IPR055418	Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2	Domain
G	IPR007716	NPL4, zinc-binding putative	Domain
G	IPR024682	Nuclear pore localisation protein Npl4, ubiquitin-like domain	Domain
G	IPR007717	Nuclear pore localisation protein NPL4, C-terminal	Domain
G	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
G	IPR016563	Nuclear protein localization protein 4	Family
G	IPR037518	MPN domain	Domain
G	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
G	IPR001876	Zinc finger, RanBP2-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	: P55072	amyotrophic lateral sclerosis Charcot-Marie-Tooth disease type 2Y inclusion body myopathy with Paget disease of bone and frontotemporal dementia frontotemporal dementia and/or amyotrophic lateral sclerosis 6 Charcot-Marie-Tooth disease Stevens-Johnson syndrome inclusion body myopathy with Paget disease of bone and frontotemporal dementia type 1 behavioral variant of frontotemporal dementia peripheral neuropathy neurodegenerative disease Mycoplasma-Induced Stevens-Johnson Syndrome osteosarcoma peripheral nervous system disease plasma cell myeloma prostate cancer amyotrophic lateral sclerosis Charcot-Marie-Tooth disease type 2Y inclusion body myopathy with Paget disease of bone and frontotemporal dementia frontotemporal dementia and/or amyotrophic lateral sclerosis 6 Charcot-Marie-Tooth disease Stevens-Johnson syndrome inclusion body myopathy with Paget disease of bone and frontotemporal dementia type 1 behavioral variant of frontotemporal dementia peripheral neuropathy neurodegenerative disease Mycoplasma-Induced Stevens-Johnson Syndrome osteosarcoma peripheral nervous system disease plasma cell myeloma prostate cancer dementia lymphoplasmacytic lymphoma myopathy ovarian cancer arthrogryposis psoriasis bone Paget disease motor peripheral neuropathy pancreatic ductal adenocarcinoma Pick disease progressive non-fluent aphasia astrocytic tumor spastic paraplegia-Paget disease of bone syndrome toxic epidermal necrolysis cytomegalovirus infection distal myopathy frontotemporal dementia with motor neuron disease limb-girdle muscular dystrophy
L [auth T]	: Q9UNN5	androgenetic alopecia atypical teratoid rhabdoid tumor large cell medulloblastoma osteosarcoma type 2 diabetes mellitus atrial fibrillation cerebrovascular disorder maturity-onset diabetes of the young ovarian cancer attention deficit hyperactivity disorder, inattentive type glioblastoma medulloblastoma renal cell carcinoma
I [auth J], J [auth K], K [auth M], M [auth I], N, I [auth J], J [auth K], K [auth M], M [auth I], N, O [auth L]	: P0CG47	astrocytic tumor cleft soft palate lung cancer Cleft of hard palate ovarian cancer isolated cleft palate
H	: Q92890	DiGeorge syndrome Craniofacial Abnormalities congenital heart disease ovarian cancer breast cancer glioblastoma pancreatic ductal adenocarcinoma velocardiofacial syndrome 22q11.2 deletion syndrome lung cancer schizophrenia
G	: Q8TAT6	age-related macular degeneration wet macular degeneration corneal disease ovarian cancer

31OQ | pdb_000031oq

CryoEM structure of substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FAF1- State III

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation