Annotations: 11SY

Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth K]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B [auth H]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth H], C [auth I], D [auth J], E [auth K]	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
A [auth G]	PF05020	NPL4 family, putative zinc binding region (zf-NPL4)	NPL4 family, putative zinc binding region	-	Family
A [auth G]	PF05021	NPL4 family (NPL4)	NPL4 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth P]	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 system development 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 protein exit from endoplasmic reticulum cellular localization establishment of protein localization transport localization intercellular transport establishment of localization in cell intracellular protein localization endoplasmic reticulum to cytosol transport intracellular transport establishment of localization protein transport 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 UFD1-NPL4 complex cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B [auth H], C [auth I], D [auth J], E [auth K]	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
A [auth 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 cation binding transition metal ion binding 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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 protein exit from endoplasmic reticulum cellular localization establishment of protein localization transport localization intercellular transport establishment of localization in cell intracellular protein localization endoplasmic reticulum to cytosol transport intracellular transport establishment of localization protein transport retrograde protein transport, ER to cytosol macromolecule localization intracellular protein transport cellular component organization organelle organization cellular component organization or biogenesis 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 nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen UFD1-NPL4 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth P]	IPR055417	Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1	Domain
F [auth P]	IPR004854	Ubiquitin fusion degradation protein UFD1-like	Family
F [auth P]	IPR042299	UFD1-like, Nn domain	Homologous Superfamily
F [auth P]	IPR055418	Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2	Domain
B [auth H], C [auth I], D [auth J], E [auth K]	IPR019954	Ubiquitin conserved site	Conserved Site
B [auth H], C [auth I], D [auth J], E [auth K]	IPR000626	Ubiquitin-like domain	Domain
B [auth H], C [auth I], D [auth J], E [auth K]	IPR019956	Ubiquitin domain	Domain
B [auth H], C [auth I], D [auth J], E [auth K]	IPR050158	Ubiquitin and ubiquitin-like	Family
B [auth H], C [auth I], D [auth J], E [auth K]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A [auth G]	IPR007716	NPL4, zinc-binding putative	Domain
A [auth G]	IPR024682	Nuclear pore localisation protein Npl4, ubiquitin-like domain	Domain
A [auth G]	IPR007717	Nuclear pore localisation protein NPL4, C-terminal	Domain
A [auth G]	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
A [auth G]	IPR016563	Nuclear protein localization protein 4	Family
A [auth G]	IPR037518	MPN domain	Domain
A [auth G]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A [auth G]	IPR001876	Zinc finger, RanBP2-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
F [auth P]	: 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
B [auth H], C [auth I], D [auth J], E [auth K]	: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer
A [auth G]	: Q8TAT6	age-related macular degeneration wet macular degeneration corneal disease ovarian cancer

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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.