6C6K

Structural basis for preferential recognition of cap 0 RNA by a human IFIT1-IFIT3 protein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Human IFIT3 Modulates IFIT1 RNA Binding Specificity and Protein Stability.

Johnson, B.VanBlargan, L.A.Xu, W.White, J.P.Shan, C.Shi, P.Y.Zhang, R.Adhikari, J.Gross, M.L.Leung, D.W.Diamond, M.S.Amarasinghe, G.K.

(2018) Immunity 48: 487-499.e5

  • DOI: 10.1016/j.immuni.2018.01.014
  • Primary Citation of Related Structures:  
    6C6K

  • PubMed Abstract: 
  • Although interferon-induced proteins with tetratricopeptide repeats (IFIT proteins) inhibit infection of many viruses by recognizing their RNA, the regulatory mechanisms involved remain unclear. Here we report a crystal structure of cap 0 (m 7

    Although interferon-induced proteins with tetratricopeptide repeats (IFIT proteins) inhibit infection of many viruses by recognizing their RNA, the regulatory mechanisms involved remain unclear. Here we report a crystal structure of cap 0 (m 7 GpppN) RNA bound to human IFIT1 in complex with the C-terminal domain of human IFIT3. Structural, biochemical, and genetic studies suggest that IFIT3 binding to IFIT1 has dual regulatory functions: (1) extending the half-life of IFIT1 and thereby increasing its steady-state amounts in cells; and (2) allosterically regulating the IFIT1 RNA-binding channel, thereby enhancing the specificity of recognition for cap 0 but not cap 1 (m 7 GpppNm) or 5'-ppp RNA. Mouse Ifit3 lacks this key C-terminal domain and does not bind mouse Ifit1. The IFIT3 interaction with IFIT1 is important for restricting infection of viruses lacking 2'-O methylation in their RNA cap structures. Our experiments establish differences in the regulation of IFIT1 orthologs and define targets for modulation of human IFIT protein activity.


    Organizational Affiliation

    Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: gamarasinghe@wustl.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon-induced protein with tetratricopeptide repeats 1 AB465Homo sapiensMutation(s): 0 
Gene Names: IFIT1G10P1IFI56IFNAI1ISG56
Find proteins for P09914 (Homo sapiens)
Explore P09914 
Go to UniProtKB:  P09914
NIH Common Fund Data Resources
PHAROS:  P09914
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon-induced protein with tetratricopeptide repeats 3 CD44Homo sapiensMutation(s): 0 
Gene Names: IFIT3CIG-49IFI60IFIT4ISG60
Find proteins for O14879 (Homo sapiens)
Explore O14879 
Go to UniProtKB:  O14879
NIH Common Fund Data Resources
PHAROS:  O14879
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-R((M7G)*P*AP*UP*AP*GP*GP*CP*GP*GP*CP*G)-3')E, F11Equine encephalosis virus
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.54 Å
    • R-Value Free: 0.237 
    • R-Value Work: 0.169 
    • R-Value Observed: 0.172 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 51.957α = 79.82
    b = 80.484β = 78.81
    c = 88.054γ = 90.04
    Software Package:
    Software NamePurpose
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing
    REFMACrefinement
    PDB_EXTRACTdata extraction

    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 StatesR01 AI10497
    National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19 AI109680
    National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19 AI083019
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103422
    National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI120943
    National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI109945

    Revision History 

    • Version 1.0: 2018-04-04
      Type: Initial release
    • Version 1.1: 2019-02-20
      Changes: Author supporting evidence, Data collection
    • Version 1.2: 2019-12-18
      Changes: Author supporting evidence