4HOR

Crystal Structure of Full-Length Human IFIT5 with 5`-triphosphate Oligocytidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for viral 5'-PPP-RNA recognition by human IFIT proteins.

Abbas, Y.M.Pichlmair, A.Gorna, M.W.Superti-Furga, G.Nagar, B.

(2013) Nature 494: 60-64

  • DOI: 10.1038/nature11783
  • Primary Citation of Related Structures:  
    4HOS, 4HOT, 4HOU, 4HOQ, 4HOR

  • PubMed Abstract: 
  • Interferon-induced proteins with tetratricopeptide repeats (IFITs) are innate immune effector molecules that are thought to confer antiviral defence through disruption of protein-protein interactions in the host translation-initiation machinery. However, it was recently discovered that IFITs can directly recognize viral RNA bearing a 5'-triphosphate group (PPP-RNA), which is a molecular signature that distinguishes it from host RNA ...

    Interferon-induced proteins with tetratricopeptide repeats (IFITs) are innate immune effector molecules that are thought to confer antiviral defence through disruption of protein-protein interactions in the host translation-initiation machinery. However, it was recently discovered that IFITs can directly recognize viral RNA bearing a 5'-triphosphate group (PPP-RNA), which is a molecular signature that distinguishes it from host RNA. Here we report crystal structures of human IFIT5, its complex with PPP-RNAs, and an amino-terminal fragment of IFIT1. The structures reveal a new helical domain that houses a positively charged cavity designed to specifically engage only single-stranded PPP-RNA, thus distinguishing it from the canonical cytosolic sensor of double-stranded viral PPP-RNA, retinoic acid-inducible gene I (RIG-I, also known as DDX58). Mutational analysis, proteolysis and gel-shift assays reveal that PPP-RNA is bound in a non-sequence-specific manner and requires a 5'-overhang of approximately three nucleotides. Abrogation of PPP-RNA binding in IFIT1 and IFIT5 was found to cause a defect in the antiviral response by human embryonic kidney cells. These results demonstrate the mechanism by which IFIT proteins selectively recognize viral RNA, and lend insight into their downstream effector function.


    Organizational Affiliation

    Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon-induced protein with tetratricopeptide repeats 5 A482Homo sapiensMutation(s): 0 
Gene Names: IFIT5IFIT5/ISG58ISG58RI58
Find proteins for Q13325 (Homo sapiens)
Explore Q13325 
Go to UniProtKB:  Q13325
NIH Common Fund Data Resources
PHAROS:  Q13325
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*(CTP)P*CP*CP*CP*C)-3')X5N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.86 Å
    • R-Value Free: 0.201 
    • R-Value Work: 0.164 
    • R-Value Observed: 0.167 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 54.588α = 90
    b = 84.903β = 106.92
    c = 61.47γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    PHASERphasing
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2013-01-23
      Type: Initial release
    • Version 1.1: 2013-02-06
      Changes: Database references
    • Version 1.2: 2013-02-27
      Changes: Database references