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- PDB-9lov: LGP2:MDA5:dsRNA filament -

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Basic information

Entry
Database: PDB / ID: 9lov
TitleLGP2:MDA5:dsRNA filament
Components
  • (RNA (45-MER)) x 2
  • ATP-dependent RNA helicase DHX58
  • Interferon-induced helicase C domain-containing protein 1
KeywordsIMMUNE SYSTEM/RNA / Innate immune system / RNA receptor / Cryo-EM / Filament / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


positive regulation of MDA-5 signaling pathway / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / MDA-5 signaling pathway / positive regulation of RIG-I signaling pathway / regulation of type III interferon production / detection of virus / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Modulation of host responses by IFN-stimulated genes ...positive regulation of MDA-5 signaling pathway / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / MDA-5 signaling pathway / positive regulation of RIG-I signaling pathway / regulation of type III interferon production / detection of virus / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Modulation of host responses by IFN-stimulated genes / TRAF6 mediated IRF7 activation / negative regulation of type I interferon production / negative regulation of viral genome replication / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / regulation of innate immune response / pattern recognition receptor activity / cellular response to exogenous dsRNA / TRAF6 mediated NF-kB activation / protein complex oligomerization / positive regulation of interferon-alpha production / protein sumoylation / positive regulation of type I interferon production / ribonucleoprotein complex binding / antiviral innate immune response / positive regulation of interferon-beta production / negative regulation of innate immune response / response to bacterium / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Evasion by RSV of host interferon responses / positive regulation of interleukin-6 production / response to virus / positive regulation of tumor necrosis factor production / SARS-CoV-1 activates/modulates innate immune responses / Ovarian tumor domain proteases / double-stranded RNA binding / TRAF3-dependent IRF activation pathway / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Helicase/UvrB, N-terminal ...RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Death-like domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / ATP-dependent RNA helicase DHX58 / Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
uncultured archaeon (environmental samples)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsKurihara, N. / Isayama, Y. / Nureki, O. / Kato, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H04768 Japan
CitationJournal: To Be Published
Title: LGP2:MDA5:dsRNA filament
Authors: Kurihara, N. / Isayama, Y. / Nureki, O. / Kato, K.
History
DepositionJan 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: RNA (45-MER)
X: RNA (45-MER)
A: ATP-dependent RNA helicase DHX58
B: Interferon-induced helicase C domain-containing protein 1
C: Interferon-induced helicase C domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,09914
Polymers275,5495
Non-polymers1,5519
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules YX

#1: RNA chain RNA (45-MER)


Mass: 14278.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) uncultured archaeon (environmental samples)
#2: RNA chain RNA (45-MER)


Mass: 14553.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) uncultured archaeon (environmental samples)

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Protein , 2 types, 3 molecules ABC

#3: Protein ATP-dependent RNA helicase DHX58 / ATP-dependent helicase LGP2 / Protein D11Lgp2 homolog / RIG-I-like receptor 3 / RLR-3 / RIG-I-like ...ATP-dependent helicase LGP2 / Protein D11Lgp2 homolog / RIG-I-like receptor 3 / RLR-3 / RIG-I-like receptor LGP2 / RLR


Mass: 76742.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX58, D11LGP2E, LGP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96C10, RNA helicase
#4: Protein Interferon-induced helicase C domain-containing protein 1 / Clinically amyopathic dermatomyositis autoantigen 140 kDa / CADM-140 autoantigen / Helicase with 2 ...Clinically amyopathic dermatomyositis autoantigen 140 kDa / CADM-140 autoantigen / Helicase with 2 CARD domains / Helicard / Interferon-induced with helicase C domain protein 1 / Melanoma differentiation-associated protein 5 / MDA-5 / Murabutide down-regulated protein / RIG-I-like receptor 2 / RLR-2 / RNA helicase-DEAD box protein 116


Mass: 84986.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFIH1, MDA5, RH116 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYX4, RNA helicase

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Non-polymers , 3 types, 9 molecules

#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Filament of LGP2, MDA5 and dsRNACOMPLEX#1-#40MULTIPLE SOURCES
2LGP2COMPLEX#31RECOMBINANT
3MDA5COMPLEX#41RECOMBINANT
4dsRNACOMPLEX#1-#21NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34uncultured archaeon (environmental samples)115547
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.83 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117189 / Symmetry type: POINT
RefinementHighest resolution: 3.07 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00218477
ELECTRON MICROSCOPYf_angle_d0.42625350
ELECTRON MICROSCOPYf_dihedral_angle_d13.53469
ELECTRON MICROSCOPYf_chiral_restr0.0362931
ELECTRON MICROSCOPYf_plane_restr0.0042896

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