3L25

Crystal structure of Zaire Ebola VP35 interferon inhibitory domain bound to 8 bp dsRNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35.

Leung, D.W., Prins, K.C., Borek, D.M., Farahbakhsh, M., Tufariello, J.M., Ramanan, P., Nix, J.C., Helgeson, L.A., Otwinowski, Z., Honzatko, R.B., Basler, C.F., Amarasinghe, G.K.

(2010) Nat Struct Mol Biol 17: 165-172

  • DOI: 10.1038/nsmb.1765
  • Primary Citation of Related Structures:  
    3L25, 3L26, 3L27, 3L28

  • PubMed Abstract: 

    • Ebola viral protein 35 (VP35), encoded by the highly pathogenic Ebola virus, facilitates host immune evasion by antagonizing antiviral signaling pathways, including those initiated by RIG-I-like receptors. Here we report the crystal structure of the ...

    Ebola viral protein 35 (VP35), encoded by the highly pathogenic Ebola virus, facilitates host immune evasion by antagonizing antiviral signaling pathways, including those initiated by RIG-I-like receptors. Here we report the crystal structure of the Ebola VP35 interferon inhibitory domain (IID) bound to short double-stranded RNA (dsRNA), which together with in vivo results reveals how VP35-dsRNA interactions contribute to immune evasion. Conserved basic residues in VP35 IID recognize the dsRNA backbone, whereas the dsRNA blunt ends are 'end-capped' by a pocket of hydrophobic residues that mimic RIG-I-like receptor recognition of blunt-end dsRNA. Residues critical for RNA binding are also important for interferon inhibition in vivo but not for viral polymerase cofactor function of VP35. These results suggest that simultaneous recognition of dsRNA backbone and blunt ends provides a mechanism by which Ebola VP35 antagonizes host dsRNA sensors and immune responses.

    Related Citations: 
    • Preliminary X-ray studies of the Ebola VP35 IFN inhibitory domain bound to double stranded RNA
      Leung, D.W., Prins, K.C., Borek, D.M., Farahbakhsh, M., Tufariello, J.M., Ramanan, P., Nix, J.C., Helgeson, L.A., Otwinowski, Z., Honzatko, R.B., Basler, C.F., Amarasinghe, G.K.
      () To be published --: --
    Organizational Affiliation: 

    Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase cofactor VP35A, B, D, E129Ebola virus - Mayinga, Zaire, 1976Mutation(s): 0 
Gene Names: VP35
Find proteins for Q05127 (Zaire ebolavirus (strain Mayinga-76))
Explore Q05127 
Go to UniProtKB:  Q05127
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*CP*AP*UP*GP*CP*G)-3')C, F8N/A
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GOL
    Query on GOL
    Download Ideal Coordinates CCD File 
    A
    		GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N    		 Ligand Interaction
    FMT
    Query on FMT
    Download Ideal Coordinates CCD File 
    A, B, C, D, E, F
    		FORMIC ACID
    C H2 O2
    BDAGIHXWWSANSR-UHFFFAOYSA-N    		 Ligand Interaction
    CL
    Query on CL
    Download Ideal Coordinates CCD File 
    A, B, D, E
    		CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M    		 Ligand Interaction
    MG
    Query on MG
    Download Ideal Coordinates CCD File 
    A
    		MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N    		 Ligand Interaction
    NA
    Query on NA
    Download Ideal Coordinates CCD File 
    A, B, C, D, F
    		SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.207 
    • R-Value Work: 0.169 
    • R-Value Observed: 0.171 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 78.947α = 90
    b = 84.571β = 90
    c = 89.316γ = 90
    Software Package:
    Software NamePurpose
    HKL-3000data collection
    PHASERphasing
    REFMACrefinement
    HKL-3000data reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2010-01-26
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance