3L28

Crystal structure of Zaire Ebola VP35 interferon inhibitory domain K339A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

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 mutants that display diminished dsRNA binding and immune suppression.
      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 VP35ABCDEF129Ebola virus - Mayinga, Zaire, 1976Mutation(s): 1 
Gene Names: VP35
Find proteins for Q05127 (Zaire ebolavirus (strain Mayinga-76))
Explore Q05127 
Go to UniProtKB:  Q05127
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
B, C, D, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,D,E,FL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.381α = 90
b = 91.88β = 99.6
c = 102.595γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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