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- EMDB-26027: Cryo-EM structure of RIG-I bound to the internal sites of p3SLR30... -

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Basic information

Entry
Database: EMDB / ID: EMD-26027
TitleCryo-EM structure of RIG-I bound to the internal sites of p3SLR30 (+ATP)
Map dataCryo-EM structure of protein-RNA complex 6
Sample
  • Complex: Complex of RIG-I with p3SLR30
    • Protein or peptide: Antiviral innate immune response receptor RIG-I
    • RNA: p3SLR30
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
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 / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / cellular response to exogenous dsRNA ...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 / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / cellular response to exogenous dsRNA / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / 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: 3.2 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)1R01AI131518 United States
CitationJournal: Mol Cell / Year: 2022
Title: The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands.
Authors: Wenshuai Wang / Anna Marie Pyle /
Abstract: RIG-I is an essential innate immune receptor for detecting and responding to infection by RNA viruses. RIG-I specifically recognizes the unique molecular features of viral RNA molecules and ...RIG-I is an essential innate immune receptor for detecting and responding to infection by RNA viruses. RIG-I specifically recognizes the unique molecular features of viral RNA molecules and selectively distinguishes them from closely related RNAs abundant in host cells. The physical basis for this exquisite selectivity is revealed through a series of high-resolution cryo-EM structures of RIG-I in complex with host and viral RNA ligands. These studies demonstrate that RIG-I actively samples double-stranded RNAs in the cytoplasm and distinguishes them by adopting two different types of protein folds. Upon binding viral RNA, RIG-I adopts a high-affinity conformation that is conducive to signaling, while host RNA induces an autoinhibited conformation that stimulates RNA release. By coupling protein folding with RNA binding selectivity, RIG-I distinguishes RNA molecules that differ by as little as one phosphate group, thereby explaining the molecular basis for selective antiviral sensing and the induction of autoimmunity upon RIG-I dysregulation.
History
DepositionJan 22, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26027.png

Downloads & links

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Map

FileDownload / File: emd_26027.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of protein-RNA complex 6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 192 pix.
= 201.6 Å		1.05 Å/pix.
x 192 pix.
= 201.6 Å		1.05 Å/pix.
x 192 pix.
= 201.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.082806595 - 0.15132655
Average (Standard dev.)-0.00002476094 (±0.004216305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 201.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of RIG-I with p3SLR30

EntireName: Complex of RIG-I with p3SLR30
Components
  • Complex: Complex of RIG-I with p3SLR30
    • Protein or peptide: Antiviral innate immune response receptor RIG-I
    • RNA: p3SLR30
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of RIG-I with p3SLR30

SupramoleculeName: Complex of RIG-I 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: 106.740555 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 EKGIKDVETE DLEDKMETSD IQIFYQEDPE CQNLSENSCP PSEVSDTNLY SP FKPRNYQ LELALPAMKG KNTIICAPTG CGKTFVSLLI CEHHLKKFPQ GQKGKVVFFA NQIPVYEQQK SVFSKYFERH GYR VTGISG ATAENVPVEQ IVENNDIIIL TPQILVNNLK KGTIPSLSIF TLMIFDECHN TSKQHPYNMI MFNYLDQKLG GSSG PLPQV IGLTASVGVG DAKNTDEALD YICKLCASLD ASVIATVKHN LEELEQVVYK PQKFFRKVES RISDKFKYII AQLMR DTES LAKRICKDLE NLSQIQNREF GTQKYEQWIV TVQKACMVFQ MPDKDEESRI CKALFLYTSH LRKYNDALII SEHARM KDA LDYLKDFFSN VRAAGFDEIE QDLTQRFEEK LQELESVSRD PSNENPKLED LCFILQEEYH LNPETITILF VKTRALV DA LKNWIEGNPK LSFLKPGILT GRGKTNQNTG MTLPAQKCIL DAFKASGDHN ILIATSVADE GIDIAQCNLV ILYEYVGN V IKMIQTRGRG RARGSKCFLL TSNAGVIEKE QINMYKEKMM NDSILRLQTW DEAVFREKIL HIQTHEKFIR DSQEKPKPV PDKENKKLLC RKCKALACYT ADVRVIEECH YTVLGDAFKE CFVSRPHPKP KQFSSFEKRA KIFCARQNCS HDWGIHVKYK TFEIPVIKI ESFVVEDIAT GVQTLYSKWK DFHFEKIPFD PAEMSK

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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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / 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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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 K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 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: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 366751
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5e3h


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Overall B value: 82
Output model

PDB-7to2:
Cryo-EM structure of RIG-I bound to the internal sites of p3SLR30 (+ATP)

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