Annotations: 4NQK

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	DEATH domain	8092819	3000069	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DEATH domain	8092818	3000069	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DEATH domain	8092819	3000069	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DEATH domain	8092818	3000069	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DEATH domain	8092819	3000069	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DEATH domain	8092818	3000069	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DEATH domain	8092819	3000069	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DEATH domain	8092818	3000069	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	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)
B	CARD_2_1	e4nqkB1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD_2_1	ECOD (1.6)
B	CARD_2	e4nqkB2	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD_2	ECOD (1.6)
C	CARD_2_1	e4nqkC2	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD_2_1	ECOD (1.6)
C	CARD_2	e4nqkC1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD_2	ECOD (1.6)
D	CARD_2_1	e4nqkD2	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD_2_1	ECOD (1.6)
D	CARD_2	e4nqkD1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD_2	ECOD (1.6)
A	CARD_2_1	e4nqkA2	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD_2_1	ECOD (1.6)
A	CARD_2	e4nqkA1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD_2	ECOD (1.6)
E	ubiquitin_1	e4nqkE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
F	ubiquitin_1	e4nqkF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
G	ubiquitin_1	e4nqkG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
H	ubiquitin_1	e4nqkH1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
I	ubiquitin_1	e4nqkI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
J	ubiquitin_1	e4nqkJ1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
C	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
D	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
A	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
F	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
H	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
J	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF16739	Caspase recruitment domain (CARD_2)	Caspase recruitment domain	In the probable ATP-dependent RNA helicase DDX58 this CARD domain is found near the N-terminus and interacts with the C-terminal domain [1].	Domain
E, F, G, H, I E, F, G, H, I, J	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Probable ATP-dependent RNA helicase DDX58	RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid 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 RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid 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 catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA catalytic activity ATP-dependent activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding identical protein binding single-stranded RNA binding molecular transducer activity pattern recognition receptor activity signaling receptor activity guanyl nucleotide binding GTP binding guanyl ribonucleotide binding DNA binding double-stranded DNA 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 cation binding transition metal ion binding zinc ion binding metal ion binding	cellular response to stimulus cytoplasmic pattern recognition receptor signaling pathway regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus cell communication cellular response to stimulus cytoplasmic pattern recognition receptor signaling pathway regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response cellular process activation of immune response cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process positive regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of molecular function organic cyclic compound metabolic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process regulation of DNA-templated transcription RIG-I signaling pathway regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion response to organic substance response to cytokine positive regulation of response to cytokine stimulus regulation of response to cytokine stimulus response to chemical multicellular organismal process positive regulation of interleukin-8 production cytokine production regulation of cytokine production regulation of multicellular organismal process interleukin-8 production positive regulation of multicellular organismal process positive regulation of cytokine production regulation of interleukin-8 production regulation of immune effector process positive regulation of leukocyte mediated immunity regulation of myeloid leukocyte mediated immunity myeloid leukocyte mediated immunity dendritic cell cytokine production leukocyte mediated immunity regulation of cytokine production involved in immune response immune effector process regulation of leukocyte mediated immunity myeloid dendritic cell cytokine production positive regulation of myeloid leukocyte mediated immunity positive regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response positive regulation of dendritic cell cytokine production regulation of myeloid dendritic cell cytokine production positive regulation of myeloid leukocyte cytokine production involved in immune response regulation of dendritic cell cytokine production positive regulation of immune effector process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response positive regulation of myeloid dendritic cell cytokine production positive regulation of cytokine production involved in immune response regulation of defense response to virus defense response to virus positive regulation of defense response to virus by host regulation of defense response to virus by host response to virus transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of RNA biosynthetic process interferon-alpha production regulation of interferon-alpha production positive regulation of type I interferon production type I interferon production positive regulation of interferon-alpha production regulation of type I interferon production interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production response to dsRNA response to nitrogen compound response to exogenous dsRNA response to organic cyclic compound cellular response to nitrogen compound cellular response to dsRNA cellular response to exogenous dsRNA cellular response to organic cyclic compound cellular response to chemical stimulus cellular response to organic substance regulation of interferon-beta production interferon-beta production positive regulation of interferon-beta production antiviral innate immune response granulocyte macrophage colony-stimulating factor production positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of granulocyte macrophage colony-stimulating factor production protein metabolic process regulation of granulocyte macrophage colony-stimulating factor production organonitrogen compound metabolic process regulation of protein metabolic process detection of virus regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production type III interferon production regulation of type III interferon production	intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity actin cytoskeleton non-membrane-bounded organelle cytoplasm cytosol ruffle cell leading edge plasma membrane membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity actin cytoskeleton non-membrane-bounded organelle cytoplasm cytosol ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction protein-containing complex ribonucleoprotein complex
E, F, G, H, I E, F, G, H, I, J	Ubiquitin	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle 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 space 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR021673	RIG-I-like receptor, C-terminal regulatory domain	Domain
A, B, C, D	IPR042145	RIG-I, CARD domain repeat 2	Domain
A, B, C, D	IPR011545	DEAD/DEAH box helicase domain	Domain
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR038557	RIG-I-like receptor, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D	IPR041204	RIG-I-like receptor, C-terminal	Domain
A, B, C, D	IPR031964	Caspase recruitment domain	Domain
A, B, C, D	IPR011029	Death-like domain superfamily	Homologous Superfamily
E, F, G, H, I E, F, G, H, I, J	IPR019954	Ubiquitin conserved site	Conserved Site
E, F, G, H, I E, F, G, H, I, J	IPR000626	Ubiquitin-like domain	Domain
E, F, G, H, I E, F, G, H, I, J	IPR019956	Ubiquitin domain	Domain
E, F, G, H, I E, F, G, H, I, J	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O95786	psoriasis Singleton-Merten syndrome 2 influenza hepatitis C virus infection pilocytic astrocytoma pustulosis palmaris et plantaris tuberculosis atopic eczema dermatomyositis glioblastoma juvenile dermatomyositis malignant glioma ovarian cancer singleton-Merten dysplasia Sjogren syndrome psoriasis Singleton-Merten syndrome 2 influenza hepatitis C virus infection pilocytic astrocytoma pustulosis palmaris et plantaris tuberculosis atopic eczema dermatomyositis glioblastoma juvenile dermatomyositis malignant glioma ovarian cancer singleton-Merten dysplasia Sjogren syndrome cutaneous lupus erythematosus Disease Exacerbation intellectual disability lung cancer microphthalmia with limb anomalies pancreatic intraductal papillary-mucinous neoplasm Singleton-Merten syndrome 1 systemic lupus erythematosus cystic fibrosis hepatocellular carcinoma interstitial cystitis malignant ependymoma osteosarcoma
E, F, G, H, I E, F, G, H, I, J	Pharos: 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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.