5E3H

Structural Basis for RNA Recognition and Activation of RIG-I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of RNA recognition and activation by innate immune receptor RIG-I.

Jiang, F.Ramanathan, A.Miller, M.T.Tang, G.Q.Gale, M.Patel, S.S.Marcotrigiano, J.

(2011) Nature 479: 423-427

  • DOI: 10.1038/nature10537
  • Primary Citation of Related Structures:  
    5E3H

  • PubMed Abstract: 
  • Retinoic-acid-inducible gene-I (RIG-I; also known as DDX58) is a cytoplasmic pathogen recognition receptor that recognizes pathogen-associated molecular pattern (PAMP) motifs to differentiate between viral and cellular RNAs. RIG-I is activated by blunt-ended double-stranded (ds)RNA with or without a 5'-triphosphate (ppp), by single-stranded RNA marked by a 5'-ppp and by polyuridine sequences ...

    Retinoic-acid-inducible gene-I (RIG-I; also known as DDX58) is a cytoplasmic pathogen recognition receptor that recognizes pathogen-associated molecular pattern (PAMP) motifs to differentiate between viral and cellular RNAs. RIG-I is activated by blunt-ended double-stranded (ds)RNA with or without a 5'-triphosphate (ppp), by single-stranded RNA marked by a 5'-ppp and by polyuridine sequences. Upon binding to such PAMP motifs, RIG-I initiates a signalling cascade that induces innate immune defences and inflammatory cytokines to establish an antiviral state. The RIG-I pathway is highly regulated and aberrant signalling leads to apoptosis, altered cell differentiation, inflammation, autoimmune diseases and cancer. The helicase and repressor domains (RD) of RIG-I recognize dsRNA and 5'-ppp RNA to activate the two amino-terminal caspase recruitment domains (CARDs) for signalling. Here, to understand the synergy between the helicase and the RD for RNA binding, and the contribution of ATP hydrolysis to RIG-I activation, we determined the structure of human RIG-I helicase-RD in complex with dsRNA and an ATP analogue. The helicase-RD organizes into a ring around dsRNA, capping one end, while contacting both strands using previously uncharacterized motifs to recognize dsRNA. Small-angle X-ray scattering, limited proteolysis and differential scanning fluorimetry indicate that RIG-I is in an extended and flexible conformation that compacts upon binding RNA. These results provide a detailed view of the role of helicase in dsRNA recognition, the synergy between the RD and the helicase for RNA binding and the organization of full-length RIG-I bound to dsRNA, and provide evidence of a conformational change upon RNA binding. The RIG-I helicase-RD structure is consistent with dsRNA translocation without unwinding and cooperative binding to RNA. The structure yields unprecedented insight into innate immunity and has a broader impact on other areas of biology, including RNA interference and DNA repair, which utilize homologous helicase domains within DICER and FANCM.


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, 679 Hoes Lane West, Piscataway, New Jersey 08854, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX58 A695Homo sapiensMutation(s): 0 
Gene Names: DDX58
EC: 3.6.4.13
Find proteins for O95786 (Homo sapiens)
Explore O95786 
Go to UniProtKB:  O95786
NIH Common Fund Data Resources
PHAROS:  O95786
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*U)-3')B, C14synthetic construct
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP

    Download Ideal Coordinates CCD File 
    A
    ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    A
    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    BEF
    Query on BEF

    Download Ideal Coordinates CCD File 
    A
    BERYLLIUM TRIFLUORIDE ION
    Be F3
    OGIAHMCCNXDTIE-UHFFFAOYSA-K
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    A
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    A
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.268 
    • R-Value Work: 0.234 
    • R-Value Observed: 0.236 
    • Space Group: P 65 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 176.03α = 90
    b = 176.03β = 90
    c = 108.071γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    MOSFLMdata reduction
    SCALAdata scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

    Revision History  (Full details and data files)

    • Version 1.0: 2015-11-18
      Type: Initial release
    • Version 1.1: 2017-08-09
      Changes: Derived calculations
    • Version 1.2: 2019-12-04
      Changes: Author supporting evidence