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- PDB-9lou: LGP2:dsRNA complex -

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Basic information

Entry
Database: PDB / ID: 9lou
TitleLGP2:dsRNA complex
Components
  • (RNA) x 2
  • ATP-dependent RNA helicase DHX58
KeywordsIMMUNE SYSTEM/RNA / Innate immune system / RNA receptor / Cryo-EM / 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 / positive regulation of RIG-I signaling pathway / negative regulation of type I interferon production / cytoplasmic pattern recognition receptor signaling pathway / regulation of innate immune response / positive regulation of type I interferon production / antiviral innate immune response / negative regulation of innate immune response ...positive regulation of MDA-5 signaling pathway / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / positive regulation of RIG-I signaling pathway / negative regulation of type I interferon production / cytoplasmic pattern recognition receptor signaling pathway / regulation of innate immune response / positive regulation of type I interferon production / antiviral innate immune response / negative regulation of innate immune response / response to bacterium / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / double-stranded RNA binding / RNA helicase activity / single-stranded RNA binding / RNA helicase / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / 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. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain ...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. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
uncultured archaeon (environmental samples)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 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:dsRNA complex
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

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DHX58
X: RNA
Y: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0286
Polymers84,5113
Non-polymers5173
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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Protein , 1 types, 1 molecules A

#1: 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: 76726.820 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

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RNA chain , 2 types, 2 molecules XY

#2: RNA chain RNA


Mass: 4035.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) uncultured archaeon (environmental samples)
#3: RNA chain RNA


Mass: 3749.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) uncultured archaeon (environmental samples)

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Non-polymers , 3 types, 3 molecules

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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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
1Complex of LGP2 and dsRNACOMPLEX#1-#30MULTIPLE SOURCES
2LGP2COMPLEX#11RECOMBINANT
3dsRNACOMPLEX#2-#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23uncultured archaeon (environmental samples)115547
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50094 / Symmetry type: POINT
RefinementHighest resolution: 3.36 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025424
ELECTRON MICROSCOPYf_angle_d0.4317457
ELECTRON MICROSCOPYf_dihedral_angle_d12.397993
ELECTRON MICROSCOPYf_chiral_restr0.036862
ELECTRON MICROSCOPYf_plane_restr0.003870

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