5F9H

Crystal structure of RIG-I helicase-RD in complex with 24-mer 5' triphosphate hairpin RNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Mss4-like	8103677	3001994	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)
A	RIG-I_C-RD	e5f9hA2	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: RIG-I_C-RD	ECOD (1.6)
A	MDA5_ID,Helicase_C_1	e5f9hA4	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: MDA5_ID,Helicase_C_1	ECOD (1.6)
A	DEAD_1	e5f9hA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
E	RIG-I_C-RD	e5f9hE1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: RIG-I_C-RD	ECOD (1.6)
E	MDA5_ID,Helicase_C_1	e5f9hE3	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: MDA5_ID,Helicase_C_1	ECOD (1.6)
E	DEAD_1	e5f9hE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
G	RIG-I_C-RD	e5f9hG2	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: RIG-I_C-RD	ECOD (1.6)
G	MDA5_ID,Helicase_C_1	e5f9hG4	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: MDA5_ID,Helicase_C_1	ECOD (1.6)
G	DEAD_1	e5f9hG3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
K	RIG-I_C-RD	e5f9hK4	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: RIG-I_C-RD	ECOD (1.6)
K	MDA5_ID	e5f9hK6	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: MDA5_ID	ECOD (1.6)
K	DEAD_1	e5f9hK3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
K	Helicase_C_1	e5f9hK5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_1	ECOD (1.6)
C	RIG-I_C-RD	e5f9hC2	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: RIG-I_C-RD	ECOD (1.6)
C	MDA5_ID,Helicase_C_1	e5f9hC1	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: MDA5_ID,Helicase_C_1	ECOD (1.6)
C	DEAD_1	e5f9hC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
I	RIG-I_C-RD	e5f9hI1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: RIG-I_C-RD	ECOD (1.6)
I	MDA5_ID,Helicase_C_1	e5f9hI4	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: MDA5_ID,Helicase_C_1	ECOD (1.6)
I	DEAD_1	e5f9hI3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (4.3.0)
A	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (4.3.0)
E	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
G	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (4.3.0)
G	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
K	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
K	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (4.3.0)
K	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (4.3.0)
C	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
I	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
I	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (4.3.0)
I	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
A, C, E, G, I A, C, E, G, I, K	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
A, C, E, G, I A, C, E, G, I, K	PF11648	C-terminal domain of RIG-I (RIG-I_C-RD)	C-terminal domain of RIG-I	This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependan ...	This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity [1].	Domain
A, C, E, G, I A, C, E, G, I, K	PF18119	RIG-I receptor C-terminal domain (RIG-I_C)	RIG-I receptor C-terminal domain	This is the C-terminal domain of Innate Immune Pattern-Recognition Receptor RIG-I present in homo sapiens. RIG-I is a key cytosolic pattern-recognition receptors of the vertebrate innate immune system that form the first line of defense against RNA v ...	This is the C-terminal domain of Innate Immune Pattern-Recognition Receptor RIG-I present in homo sapiens. RIG-I is a key cytosolic pattern-recognition receptors of the vertebrate innate immune system that form the first line of defense against RNA viral infection. RNA binding to RIG-I is mediated both by the C-terminal domain and by the helicase domain. The C-terminal domain specifically binds the 5'triphosphate end with a 10-fold higher affinity compared to 5'OH-dsRNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	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
B, D, F, H, J B, D, F, H, J, L	RNA (5'-R(PAPAPUPAPUPAPAPUPAPGPUPGPAPUPAPUPUPAPUPAPUPUP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR021673	RIG-I-like receptor, C-terminal regulatory domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR042145	RIG-I, CARD domain repeat 2	Domain
A, C, E, G, I A, C, E, G, I, K	IPR011545	DEAD/DEAH box helicase domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR038557	RIG-I-like receptor, C-terminal domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR001650	Helicase, C-terminal domain-like	Domain
A, C, E, G, I A, C, E, G, I, K	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR041204	RIG-I-like receptor, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K	IPR031964	Caspase recruitment domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR011029	Death-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K	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

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.