7NIQ | pdb_00007niq

CryoEM structure of disease related M854K MDA5-dsRNA filament in complex with ADP-AlF4(Major class)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Mss4-like	8103694	3001994	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103696	3002019	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103697	3002019	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 [auth B]	Secretin_N	e7niqB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Secretin_N	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	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 [auth B]	PF04851	Type III restriction enzyme, res subunit (ResIII)	Type III restriction enzyme, res subunit	-	Family
A [auth B]	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-dependen ...	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-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity [1].	Domain
A [auth B]	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 [auth B]	Interferon-induced helicase C domain-containing protein 1	protein binding binding protein domain specific binding RNA binding double-stranded RNA binding nucleic acid binding single-stranded RNA binding ribonucleoprotein complex binding protein-containing complex binding molecular transducer activity pattern recognition receptor activity signaling receptor activity adenyl ribonucleotide binding nucleotide binding protein binding binding protein domain specific binding RNA binding double-stranded RNA binding nucleic acid binding single-stranded RNA binding ribonucleoprotein complex binding protein-containing complex binding molecular transducer activity pattern recognition receptor activity signaling receptor activity 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 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 catalytic activity ATP-dependent activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity cation binding transition metal ion binding zinc ion binding metal ion binding identical protein binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis interleukin-6 production multicellular organismal process regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of interleukin-6 production cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis interleukin-6 production multicellular organismal process regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of interleukin-6 production regulation of interleukin-6 production positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus cellular response to nitrogen compound cellular response to stimulus cellular response to dsRNA cellular response to exogenous dsRNA response to dsRNA response to nitrogen compound response to exogenous dsRNA cellular response to chemical stimulus response to chemical peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of interferon-beta production interferon-beta production positive regulation of type I interferon production type I interferon production positive regulation of interferon-beta production regulation of type I interferon production response to cytokine positive regulation of response to cytokine stimulus positive regulation of response to stimulus response to peptide regulation of response to cytokine stimulus regulation of response to stimulus RNA metabolic process nucleobase-containing compound biosynthetic process mRNA transcription mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process defense response to virus antiviral innate immune response response to virus negative regulation of viral genome replication negative regulation of biological process viral life cycle negative regulation of viral process regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication 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 positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway MDA-5 signaling pathway 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 innate immune response 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 regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress positive regulation of innate immune response interferon-alpha production regulation of interferon-alpha production positive regulation of interferon-alpha production cellular response to virus cytokine-mediated signaling pathway interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus cell surface receptor signaling pathway type I interferon-mediated signaling pathway response to type I interferon	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus
B [auth C]	RNA (5'-R(PCPAPAPGPCPCPGPAPGPGPAPGPAPU)-3')	-	-	-
C [auth G]	RNA (5'-R(PAPUPCPUPCPCPUPCPGPGPCPUPUPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR021673	RIG-I-like receptor, C-terminal regulatory domain	Domain
A [auth B]	IPR051363	RIG-I-like Receptor (RLR) Helicase	Family
A [auth B]	IPR041204	RIG-I-like receptor, C-terminal	Domain
A [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B]	IPR038557	RIG-I-like receptor, C-terminal domain superfamily	Homologous Superfamily
A [auth B]	IPR031964	Caspase recruitment domain	Domain
A [auth B]	IPR011029	Death-like domain superfamily	Homologous Superfamily
A [auth B]	IPR006935	Helicase/UvrB, N-terminal	Domain
A [auth B]	IPR001650	Helicase, C-terminal domain-like	Domain
A [auth B]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain

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.