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- EMDB-63260: LGP2:dsRNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63260
TitleLGP2:dsRNA complex
Map dataA primary map.
Sample
  • Complex: Complex of LGP2 and dsRNA
    • Complex: LGP2
      • Protein or peptide: ATP-dependent RNA helicase DHX58
    • Complex: dsRNA
      • RNA: RNA
      • RNA: RNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsInnate 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
ATP-dependent RNA helicase DHX58
Similarity search - Component
Biological speciesHomo sapiens (human) / uncultured archaeon (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsKurihara N / Isayama Y / Nureki O / Kato K
Funding support Japan, 1 items
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, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63260.png

Downloads & links

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Map

FileDownload / File: emd_63260.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA primary map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.38760453 - 0.48537245
Average (Standard dev.)0.0002490785 (±0.010178894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63260_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A half map B.

Fileemd_63260_half_map_1.map
AnnotationA half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A half map A.

Fileemd_63260_half_map_2.map
AnnotationA half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of LGP2 and dsRNA

EntireName: Complex of LGP2 and dsRNA
Components
  • Complex: Complex of LGP2 and dsRNA
    • Complex: LGP2
      • Protein or peptide: ATP-dependent RNA helicase DHX58
    • Complex: dsRNA
      • RNA: RNA
      • RNA: RNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of LGP2 and dsRNA

SupramoleculeName: Complex of LGP2 and dsRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: LGP2

SupramoleculeName: LGP2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: dsRNA

SupramoleculeName: dsRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: uncultured archaeon (environmental samples)

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Macromolecule #1: ATP-dependent RNA helicase DHX58

MacromoleculeName: ATP-dependent RNA helicase DHX58 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.72682 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MELRSYQWEV IMPALEGKNI IIWLPTGAGK TRAAAYVAKR HLETVDGAKV VVLVNRVHLV TQHGEEFRRM LDGRWTVTTL SGDMGPRAG FGHLARCHDL LICTAELLQM ALTSPEEEEH VELTVFSLIV VDECHHTHKD TVYNVIMSQY LELKLQRAQP L PQVLGLTA ...String:
MELRSYQWEV IMPALEGKNI IIWLPTGAGK TRAAAYVAKR HLETVDGAKV VVLVNRVHLV TQHGEEFRRM LDGRWTVTTL SGDMGPRAG FGHLARCHDL LICTAELLQM ALTSPEEEEH VELTVFSLIV VDECHHTHKD TVYNVIMSQY LELKLQRAQP L PQVLGLTA SPGTGGASKL DGAINHVLQL CANLDTWCIM SPQNCCPQLQ EHSQQPCKQY NLSHRRSQDP FGDLLKKLMD QI HDHLEMP ELSRKFGTQM YEQQVVKLSE AAALAGLQEQ RVYALHLRRY NDALLIHDTV RAVDALAALQ DFYHREHVTK TQI LCAERR LLALFDDRKN ELAHLATHGP ENPKLEMLEK ILQRQFSSSN SPRGIIFTRT RQSAHSLLLW LQQQQGLQTV DIRA QLLIG AGNSSQSTHM TQRDQQEVIR KFQDGTLNLL VATSVAEEGL DIPHCNVVVR YGLLTNEISM VQARGRARAD QSVYA FVAT EGSRELKREL INEALETLME QAVAAVQKMD QAEYQAKIRD LQQAALTKRA AQAAQRENQR QQFPVEHVQL LCINCM VAV GHGSDLRKVE GTHHVNVNPN FSNYYNVSRD PVVINKVFKD WKPGGVISCR NCGEVWGLQM IYKSVKLPVL KVRSMLL ET PQGRIQAKKW SRVPFSVPDF DFLQHCAENL SDLSLD

UniProtKB: ATP-dependent RNA helicase DHX58

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: uncultured archaeon (environmental samples)
Molecular weightTheoretical: 4.035343 KDa
SequenceString:
(GTP)ACUGACUGA GA

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Macromolecule #3: RNA

MacromoleculeName: RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: uncultured archaeon (environmental samples)
Molecular weightTheoretical: 3.749256 KDa
SequenceString:
UCUCAGUCAG UC

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.83 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50094
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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