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- EMDB-40347: Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30 -

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Basic information

Entry
Database: EMDB / ID: EMD-40347
TitleCryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30
Map data
Sample
  • Complex: Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30
    • Protein or peptide: Antiviral innate immune response receptor RIG-I
    • RNA: p3SLR30
  • Ligand: ZINC ION
Keywordsribonucleoprotein complex / RNA sensor / RIG-I like receptor / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation ...regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / RSV-host interactions / response to exogenous dsRNA / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / bicellular tight junction / positive regulation of defense response to virus by host / antiviral innate immune response / positive regulation of interferon-beta production / regulation of cell migration / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / double-stranded RNA binding / Ovarian tumor domain proteases / actin cytoskeleton / TRAF3-dependent IRF activation pathway / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
RIG-I, CARD domain repeat 2 / 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 ...RIG-I, CARD domain repeat 2 / 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 / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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
Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang W / Pyle AM
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI131518 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30
Authors: Wang W / Pyle AM
History
DepositionApr 6, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40347.png

Downloads & links

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Map

FileDownload / File: emd_40347.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 192 pix.
= 205.056 Å		1.07 Å/pix.
x 192 pix.
= 205.056 Å		1.07 Å/pix.
x 192 pix.
= 205.056 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.27201837 - 0.37192735
Average (Standard dev.)-0.000015738024 (±0.0072741797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 205.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40347_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_40347_half_map_1.map
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Histogram

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Half map: #2

Fileemd_40347_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30

EntireName: Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30
Components
  • Complex: Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30
    • Protein or peptide: Antiviral innate immune response receptor RIG-I
    • RNA: p3SLR30
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30

SupramoleculeName: Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Antiviral innate immune response receptor RIG-I

MacromoleculeName: Antiviral innate immune response receptor RIG-I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 101.823195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTEQRRSLQ AFQDYIRKTL DPTYILSYMA PWFREEEVQY IQAEKNNKGP MEAATLFLKF LLELQEEGWF RGFLDALDHA GYSGLYEAI ESWDFKKIEK LEEYRLLLKR LQPEFKTRII PTDIISDLSE CLINQECEEI LQICSTKGMM AGAEKLVECL L RSDKENWP ...String:
MTTEQRRSLQ AFQDYIRKTL DPTYILSYMA PWFREEEVQY IQAEKNNKGP MEAATLFLKF LLELQEEGWF RGFLDALDHA GYSGLYEAI ESWDFKKIEK LEEYRLLLKR LQPEFKTRII PTDIISDLSE CLINQECEEI LQICSTKGMM AGAEKLVECL L RSDKENWP KTLKLALEKE RNKFSELWIV GSGSGSGSGS GSGSFKPRNY QLELALPAMK GKNTIICAPT GCGKTFVSLL IC EHHLKKF PQGQKGKVVF FANQIPVYEQ QKSVFSKYFE RHGYRVTGIS GATAENVPVE QIVENNDIII LTPQILVNNL KKG TIPSLS IFTLMIFDEC HNTSKQHPYN MIMFNYLDQK LGGSSGPLPQ VIGLTASVGV GDAKNTDEAL DYICKLCASL DASV IATVK HNLEELEQVV YKPQKFFRKV ESRISDKFKY IIAQLMRDTE SLAKRICKDL ENLSQIQNRE FGTQKYEQWI VTVQK ACMV FQMPDKDEES RICKALFLYT SHLRKYNDAL IISEHARMKD ALDYLKDFFS NVRAAGFDEI EQDLTQRFEE KLQELE SVS RDPSNENPKL EDLCFILQEE YHLNPETITI LFVKTRALVD ALKNWIEGNP KLSFLKPGIL TGRGKTNQNT GMTLPAQ KC ILDAFKASGD HNILIATSVA DEGIDIAQCN LVILYEYVGN VIKMIQTRGR GRARGSKCFL LTSNAGVIEK EQINMYKE K MMNDSILRLQ TWDEAVFREK ILHIQTHEKF IRDSQEKPKP VPDKENKKLL CRKCKALACY TADVRVIEEC HYTVLGDAF KECFVSRPHP KPKQFSSFEK RAKIFCARQN CSHDWGIHVK YKTFEIPVIK IESFVVEDIA TGVQTLYSKW KDFHFEKIPF DPAEMSK

UniProtKB: Antiviral innate immune response receptor RIG-I

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Macromolecule #2: p3SLR30

MacromoleculeName: p3SLR30 / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.709156 KDa
SequenceString:
(GTP)GAUCGAUCG AUCGAUCGGC AUCGAUCGGC UUCGGCCGAU CGAUGCCGAU CGAUCGAUCG AUCC

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 952234
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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