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- PDB-9ktw: Cryo-EM structure of wild type RIG-I with 5'p-RNA -

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Basic information

Entry
Database: PDB / ID: 9ktw
TitleCryo-EM structure of wild type RIG-I with 5'p-RNA
Components
  • 5'p-RNA (60-MER)
  • Antiviral innate immune response receptor RIG-I
KeywordsIMMUNE SYSTEM / RNA recognition / ATP hydrolysis / RLR signaling
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 / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of granulocyte macrophage colony-stimulating factor production / Modulation of host responses by IFN-stimulated genes / 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 / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of granulocyte macrophage colony-stimulating factor production / Modulation of host responses by IFN-stimulated genes / TRAF6 mediated IRF7 activation / cellular response to exogenous dsRNA / pattern recognition receptor activity / response to exogenous dsRNA / RSV-host interactions / cytoplasmic pattern recognition receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / bicellular tight junction / positive regulation of defense response to virus by host / regulation of cell migration / positive regulation of interferon-beta production / antiviral innate immune response / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / positive regulation of interleukin-6 production / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / gene expression / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / actin cytoskeleton / double-stranded RNA binding / TRAF3-dependent IRF activation pathway / 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 / positive regulation of gene expression / ubiquitin protein ligase binding / 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 / plasma membrane / 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
RNA / RNA (> 10) / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsTan, Y.B. / Luo, D.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE AcRF Tier 1 award RT22/23 Singapore
CitationJournal: Sci Immunol / Year: 2025
Title: Local activation of mutant RIG-I by short noncoding Y-RNA in the kidney triggers lethal nephritis.
Authors: Saya Satoh / Yaw Bia Tan / Benjamin Heil / Shintaro Yamada / Verena Schütte / Celest Phang / Chaozhi Tang / Yuta Tsukamoto / Takahiro Higuchi / Takashi Fujita / Rayk Behrendt / Martin ...Authors: Saya Satoh / Yaw Bia Tan / Benjamin Heil / Shintaro Yamada / Verena Schütte / Celest Phang / Chaozhi Tang / Yuta Tsukamoto / Takahiro Higuchi / Takashi Fujita / Rayk Behrendt / Martin Schlee / Dahai Luo / Hiroki Kato /
Abstract: Detecting viral RNA by the ubiquitously expressed cytosolic receptor retinoic acid-inducible gene I (RIG-I) is critical for antiviral immune responses, including type I interferon (IFN-I) and ...Detecting viral RNA by the ubiquitously expressed cytosolic receptor retinoic acid-inducible gene I (RIG-I) is critical for antiviral immune responses, including type I interferon (IFN-I) and chemokine induction. RIG-I has evolved to sensitively recognize viral RNA but tolerate self-RNA. RIG-I mutations causing self-tolerance loss induce IFN-I and chemokines in patients, initiating autoinflammation. We observed that mice expressing the RIG-I patient variant E373A spontaneously developed lupus-like nephritis. Kidney-derived chemokines attracted monocytes through CCR2 (C-C motif chemokine receptor 2) and induced interstitial inflammation and tubular damage. This led to renal dysfunction independently of immunoglobulin G-nucleic acid complex deposition. Sequencing of RIG-I E373A-bound RNA from kidney-derived cells identified short noncoding Y-RNA. Deletion of the most enriched Y-RNA species reduced RIG-I E373A-induced IFN-I responses. Cryo-electron microscopy and molecular analyses revealed that RIG-I E373A binding to the Y-RNA stem region resulted in its activation. Thus, we demonstrate that Y-RNA activates a RIG-I gain-of-function mutant in a tissue-specific manner, causing autoinflammation culminating in lupus nephritis.
History
DepositionDec 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Antiviral innate immune response receptor RIG-I
C: 5'p-RNA (60-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0483
Polymers125,9832
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, structural determination
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Antiviral innate immune response receptor RIG-I / ATP-dependent RNA helicase DDX58 / DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / RNA sensor ...ATP-dependent RNA helicase DDX58 / DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / RNA sensor RIG-I / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


Mass: 106740.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIGI, DDX58 / Production host: Escherichia coli (E. coli) / References: UniProt: O95786, RNA helicase
#2: RNA chain 5'p-RNA (60-MER)


Mass: 19242.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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
1RIG-I WT protein with 5'p-RNACOMPLEX#1-#20MULTIPLE SOURCES
2RIG-ICOMPLEX#11RECOMBINANT
35'p-RNACOMPLEX#21SYNTHETIC
Molecular weightValue: 0.1066 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33synthetic construct (others)32630
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: 25mM HEPES, 150mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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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: 1600 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2cryoSPARCparticle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8UCSF ChimeraXmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 908633 / Details: topaz train/extract
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182187 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7TO0

7to0


Pdb chain-ID: A / Accession code: 7TO0 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026456
ELECTRON MICROSCOPYf_angle_d0.4698891
ELECTRON MICROSCOPYf_dihedral_angle_d7.141185
ELECTRON MICROSCOPYf_chiral_restr0.041025
ELECTRON MICROSCOPYf_plane_restr0.004995

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