7JL2 | pdb_00007jl2

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)
D [auth B]	UCR_14kD	e7jl2B1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UCR_14kD	ECOD (develop294)
F [auth D]	UCR_14kD	e7jl2D1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UCR_14kD	ECOD (develop294)
H [auth F]	UCR_14kD	e7jl2F1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UCR_14kD	ECOD (develop294)
C [auth A]	UCR_14kD	e7jl2A1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UCR_14kD	ECOD (develop294)
E [auth C]	UCR_14kD	e7jl2C1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UCR_14kD	ECOD (develop294)
G [auth E]	UCR_14kD	e7jl2E1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UCR_14kD	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth B], F [auth D], H [auth F]	PF00622	SPRY domain (SPRY)	SPRY domain	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of ...	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development [1,2,3,4]. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region [2]. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologues are domains in butyrophilin/ marenostrin/pyrin [1].	Domain
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-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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth Y]	RNA (44-MER)	-	-	-
D [auth B], F [auth D], H [auth F]	Tripartite motif-containing protein 65	protein binding binding protein domain specific 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 protein binding binding protein domain specific 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 metal ion binding small molecule binding	cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of NLRP3 inflammasome complex assembly negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication cellular component biogenesis immune response-activating signaling pathway cellular component assembly inflammasome-mediated signaling pathway cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of NLRP3 inflammasome complex assembly negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication cellular component biogenesis immune response-activating signaling pathway cellular component assembly inflammasome-mediated signaling pathway positive regulation of immune response canonical inflammasome complex assembly regulation of immune system process signal transduction negative regulation of NLRP3 inflammasome complex assembly positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process negative regulation of cellular component organization immune response response to other organism regulation of innate immune response response to external stimulus regulation of inflammasome-mediated signaling pathway negative regulation of protein-containing complex assembly regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly positive regulation of defense response activation of innate immune response regulation of immune response inflammatory 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 cellular component organization 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 cellular component organization regulation of protein-containing complex assembly 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 protein-containing complex assembly response to external biotic stimulus cellular component organization or biogenesis regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus protein-containing complex organization biological regulation defense response to symbiont regulation of cellular component biogenesis negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication cellular process negative regulation of inflammasome-mediated signaling pathway negative regulation of inflammatory response regulation of inflammatory response negative regulation of response to external stimulus negative regulation of defense response multicellular organismal process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production 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 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 metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of interferon-beta production positive regulation of cytokine production regulation of metabolic process regulation of type I interferon production positive regulation of cellular component organization positive regulation of cellular component biogenesis regulation of protein oligomerization positive regulation of protein-containing complex assembly positive regulation of protein oligomerization protein complex oligomerization 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 defense response to virus antiviral innate immune response response to virus protein K48-linked ubiquitination positive regulation of autophagy catabolic process autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process process utilizing autophagic mechanism interferon-alpha production regulation of interferon-alpha production positive regulation of interferon-alpha production response to cytokine cytokine-mediated signaling pathway interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus cell surface receptor signaling pathway response to peptide response to chemical type I interferon-mediated signaling pathway response to type I interferon	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
C [auth A], E [auth C], G [auth E]	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 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 intracellular signal transduction 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 intracellular signal transduction 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 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 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 cellular response to nitrogen compound 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 response to peptide 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 regulation of type III interferon production 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus
A [auth X]	RNA (44-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	IPR051051	E3 ubiquitin-protein ligase TRIM/RNF	Family
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]	IPR058030	TRIM8/14/16/25/29/45/65, coiled-coil region	Domain
D [auth B], F [auth D], H [auth F]	IPR001841	Zinc finger, RING-type	Domain
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]	IPR051363	RIG-I-like Receptor (RLR) Helicase	Family
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth B], F [auth D], H [auth F]	Pharos: Q6PJ69	osteosarcoma
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 acquired metabolic disease multiple sclerosis 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 acquired metabolic disease multiple sclerosis Aicardi-Goutieres syndrome 2 pancreatic intraductal papillary-mucinous neoplasm Crohn disease dermatomyositis glioblastoma Sjogren syndrome hypothyroidism thyrotoxicosis intellectual disability ulcerative colitis large cell medulloblastoma lung cancer malignant ependymoma medulloblastoma myositis pilocytic astrocytoma cutaneous lupus erythematosus diabetes mellitus skin disease inflammatory bowel disease tuberculosis interstitial lung disease leukodystrophy lung carcinoma malignant glioma microphthalmia with limb anomalies Aicardi-Goutieres syndrome 1 nasopharyngeal carcinoma autoimmune disease pseudo-TORCH syndrome cystic fibrosis pustulosis palmaris et plantaris Hashimoto thyroiditis type 1 diabetes mellitus 19