4IJE

Crystal structure of the Zaire ebolavirus VP35 interferon inhibitory domain R312A/K319A/R322A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.899 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Development of RNA Aptamers Targeting Ebola Virus VP35.

Binning, J.M.Wang, T.Luthra, P.Shabman, R.S.Borek, D.M.Liu, G.Xu, W.Leung, D.W.Basler, C.F.Amarasinghe, G.K.

(2013) Biochemistry 52: 8406-8419

  • DOI: 10.1021/bi400704d
  • Primary Citation of Related Structures:  4IJF

  • PubMed Abstract: 
  • Viral protein 35 (VP35), encoded by filoviruses, is a multifunctional dsRNA binding protein that plays important roles in viral replication, innate immune evasion, and pathogenesis. The multifunctional nature of these proteins also presents opportuni ...

    Viral protein 35 (VP35), encoded by filoviruses, is a multifunctional dsRNA binding protein that plays important roles in viral replication, innate immune evasion, and pathogenesis. The multifunctional nature of these proteins also presents opportunities to develop countermeasures that target distinct functional regions. However, functional validation and the establishment of therapeutic approaches toward such multifunctional proteins, particularly for nonenzymatic targets, are often challenging. Our previous work on filoviral VP35 proteins defined conserved basic residues located within its C-terminal dsRNA binding interferon (IFN) inhibitory domain (IID) as important for VP35 mediated IFN antagonism and viral polymerase cofactor functions. In the current study, we used a combination of structural and functional data to determine regions of Ebola virus (EBOV) VP35 (eVP35) to target for aptamer selection using SELEX. Select aptamers, representing, two distinct classes, were further characterized based on their interaction properties to eVP35 IID. These results revealed that these aptamers bind to distinct regions of eVP35 IID with high affinity (10-50 nM) and specificity. These aptamers can compete with dsRNA for binding to eVP35 and disrupt the eVP35-nucleoprotein (NP) interaction. Consistent with the ability to antagonize the eVP35-NP interaction, select aptamers can inhibit the function of the EBOV polymerase complex reconstituted by the expression of select viral proteins. Taken together, our results support the identification of two aptamers that bind filoviral VP35 proteins with high affinity and specificity and have the capacity to potentially function as filoviral VP35 protein inhibitors.


    Organizational Affiliation

    Department of Pathology and Immunology, Washington University School of Medicine , St. Louis, Missouri 63110, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase cofactor VP35
A, B, C, D
129Zaire ebolavirus (strain Mayinga-76)Gene Names: VP35
Find proteins for Q05127 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  Q05127
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.899 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 81.012α = 90.00
b = 81.012β = 90.00
c = 344.410γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-3000data collection
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Refinement description