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 2.0 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: https://doi.org/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 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.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon-induced protein with tetratricopeptide repeats 1
A, B
465Homo sapiensMutation(s): 0 
Gene Names: IFIT1G10P1IFI56IFNAI1ISG56
UniProt & NIH Common Fund Data Resources
Find proteins for P09914 (Homo sapiens)
Explore P09914 
Go to UniProtKB:  P09914
PHAROS:  P09914
GTEx:  ENSG00000185745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09914
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon-induced protein with tetratricopeptide repeats 3
C, D
44Homo sapiensMutation(s): 0 
Gene Names: IFIT3CIG-49IFI60IFIT4ISG60
UniProt & NIH Common Fund Data Resources
Find proteins for O14879 (Homo sapiens)
Explore O14879 
Go to UniProtKB:  O14879
PHAROS:  O14879
GTEx:  ENSG00000119917 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14879
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R((M7G)*P*AP*UP*AP*GP*GP*CP*GP*GP*CP*G)-3')
E, F
11Equine encephalosis virus
Sequence Annotations
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  • Reference Sequence
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  (Full details and data files)

  • 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
  • Version 2.0: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary