7JL2

Cryo-EM structure of MDA5-dsRNA filament in complex with TRIM65 PSpry domain (Trimer)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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)
C [auth A]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103684	3002019	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Mss4-like	8103682	3001994	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103685	3002019	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103684	3002019	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103685	3002019	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Mss4-like	8103682	3001994	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103684	3002019	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103685	3002019	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Mss4-like	8103682	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)
C [auth A]	RIG-I_C-RD	e7jl2A2	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 [auth A]	MDA5_ID	e7jl2A1	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)
C [auth A]	DEAD_1	e7jl2A4	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)
C [auth A]	Helicase_C_1	e7jl2A3	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)
E [auth C]	RIG-I_C-RD	e7jl2C2	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 [auth C]	MDA5_ID	e7jl2C1	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)
E [auth C]	DEAD_1	e7jl2C4	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 [auth C]	Helicase_C_1	e7jl2C3	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)
G [auth E]	RIG-I_C-RD	e7jl2E4	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 [auth E]	MDA5_ID	e7jl2E3	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)
G [auth E]	DEAD_1	e7jl2E1	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 [auth E]	Helicase_C_1	e7jl2E2	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)
D [auth B]	SPRY	e7jl2B1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
F [auth D]	SPRY	e7jl2D1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
H [auth F]	SPRY	e7jl2F1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], E [auth C], G [auth E]	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
C [auth A], E [auth C], G [auth E]	PF04851	Type III restriction enzyme, res subunit (ResIII)	Type III restriction enzyme, res subunit	-	Family
C [auth A], E [auth C], G [auth E]	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
C [auth A], E [auth C], G [auth E]	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
D [auth B], F [auth D], H [auth F]	PF00622	SPRY domain (SPRY)	SPRY domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth X]	RNA (44-MER)	-	-	-
B [auth Y]	RNA (44-MER)	-	-	-
C [auth A], E [auth C], G [auth E]	Interferon-induced helicase C domain-containing protein 1	RNA binding double-stranded RNA binding binding organic cyclic compound 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 RNA binding double-stranded RNA binding binding organic cyclic compound 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 catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA cation binding transition metal ion binding zinc ion binding metal ion binding identical protein binding protein 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 component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis interleukin-6 production multicellular organismal process cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of interleukin-6 production regulation of interleukin-6 production positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process regulation of cytokine production organic substance biosynthetic process cytokine production regulation of multicellular organismal 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 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 positive regulation of cellular biosynthetic process cellular response to nitrogen compound response to organic substance cellular response to dsRNA cellular response to exogenous dsRNA cellular response to organic cyclic compound response to dsRNA response to nitrogen compound response to exogenous dsRNA cellular response to chemical stimulus response to chemical cellular response to organic substance response to organic cyclic compound organonitrogen compound metabolic process 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 regulation of response to cytokine stimulus 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 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 MDA-5 signaling pathway 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 intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol nucleus
D [auth B], F [auth D], H [auth F]	Tripartite motif-containing protein 65	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus biological regulation negative regulation of biological process response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus biological regulation negative regulation of biological process response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response multicellular organismal process regulation of cellular process cellular biosynthetic process positive regulation of biological 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 cytokine production organic substance biosynthetic process regulation of cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of interferon-beta production interferon-beta production positive regulation of cellular process regulation of biosynthetic process positive regulation of type I interferon production type I interferon production 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 positive regulation of multicellular organismal process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of interferon-beta production positive regulation of cytokine production regulation of metabolic process positive regulation of cellular biosynthetic process regulation of type I interferon production regulation of cellular component organization positive regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of protein oligomerization regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly positive regulation of protein oligomerization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis organonitrogen compound metabolic process protein polyubiquitination primary metabolic process protein K63-linked ubiquitination protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont response to biotic stimulus defense response to virus immune system process defense response to other organism innate immune response antiviral innate immune response response to external biotic stimulus response to virus protein K48-linked ubiquitination positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of phosphorus metabolic process regulation of phosphorylation positive regulation of autophagy catabolic process autophagy regulation of catabolic process regulation of autophagy cellular catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process process utilizing autophagic mechanism interferon-alpha production regulation of interferon-alpha production positive regulation of interferon-alpha production cellular response to stimulus response to organic substance signaling response to cytokine cytokine-mediated signaling pathway cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus cellular response to organic substance signal transduction cell surface receptor signaling pathway cellular response to chemical stimulus response to chemical type I interferon-mediated signaling pathway response to type I interferon	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], E [auth C], G [auth E]	IPR021673	RIG-I-like receptor, C-terminal regulatory domain	Domain
C [auth A], E [auth C], G [auth E]	IPR041204	RIG-I-like receptor, C-terminal	Domain
C [auth A], E [auth C], G [auth E]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth A], E [auth C], G [auth E]	IPR038557	RIG-I-like receptor, C-terminal domain superfamily	Homologous Superfamily
C [auth A], E [auth C], G [auth E]	IPR031964	Caspase recruitment domain	Domain
C [auth A], E [auth C], G [auth E]	IPR011029	Death-like domain superfamily	Homologous Superfamily
C [auth A], E [auth C], G [auth E]	IPR006935	Helicase/UvrB, N-terminal	Domain
C [auth A], E [auth C], G [auth E]	IPR001650	Helicase, C-terminal domain-like	Domain
C [auth A], E [auth C], G [auth E]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
D [auth B], F [auth D], H [auth F]	IPR048222	E3 ubiquitin-protein ligase TRIM65, PRY/SPRY domain	Domain
D [auth B], F [auth D], H [auth F]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
D [auth B], F [auth D], H [auth F]	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
D [auth B], F [auth D], H [auth F]	IPR003877	SPRY domain	Domain
D [auth B], F [auth D], H [auth F]	IPR018957	Zinc finger, C3HC4 RING-type	Domain
D [auth B], F [auth D], H [auth F]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
D [auth B], F [auth D], H [auth F]	IPR000315	B-box-type zinc finger	Domain
D [auth B], F [auth D], H [auth F]	IPR001870	B30.2/SPRY domain	Domain
D [auth B], F [auth D], H [auth F]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
D [auth B], F [auth D], H [auth F]	IPR003879	Butyrophylin-like, SPRY domain	Domain
D [auth B], F [auth D], H [auth F]	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A], E [auth C], G [auth E]	Pharos: Q9BYX4	Aicardi-Goutieres syndrome psoriasis selective IgA deficiency disease Aicardi-Goutieres syndrome 7 vitiligo Singleton-Merten syndrome 1 systemic lupus erythematosus influenza singleton-Merten dysplasia Graves disease juvenile dermatomyositis Libman-Sacks Disease malignant mesothelioma multiple sclerosis acquired metabolic disease Aicardi-Goutieres syndrome psoriasis selective IgA deficiency disease Aicardi-Goutieres syndrome 7 vitiligo Singleton-Merten syndrome 1 systemic lupus erythematosus influenza singleton-Merten dysplasia Graves disease juvenile dermatomyositis Libman-Sacks Disease malignant mesothelioma multiple sclerosis acquired metabolic disease pancreatic intraductal papillary-mucinous neoplasm Aicardi-Goutieres syndrome 2 Crohn disease dermatomyositis Sjogren syndrome glioblastoma thyrotoxicosis hypothyroidism ulcerative colitis intellectual disability large cell medulloblastoma lung cancer malignant ependymoma medulloblastoma myositis pilocytic astrocytoma cutaneous lupus erythematosus diabetes mellitus skin disease tuberculosis inflammatory bowel disease interstitial lung disease leukodystrophy lung carcinoma malignant glioma microphthalmia with limb anomalies nasopharyngeal carcinoma Aicardi-Goutieres syndrome 1 pseudo-TORCH syndrome autoimmune disease pustulosis palmaris et plantaris cystic fibrosis Hashimoto thyroiditis type 1 diabetes mellitus 19
D [auth B], F [auth D], H [auth F]	Pharos: Q6PJ69	osteosarcoma