4X42

Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


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Literature

Structural and biophysical analysis of sero-specific immune responses using epitope grafted Dengue ED3 mutants.

Kulkarni, M.R.Islam, M.M.Numoto, N.Elahi, M.Mahib, M.R.Ito, N.Kuroda, Y.

(2015) Biochim.Biophys.Acta 1854: 1438-1443

  • DOI: 10.1016/j.bbapap.2015.07.004

  • PubMed Abstract: 
  • Dengue fever is a re-emerging tropical disease and its severe form is caused by cross-reactivity between its four serotypes (DEN1, DEN2, DEN3 and DEN4). The third domain of the viral envelope protein (ED3) contains the two major putative epitopes and ...

    Dengue fever is a re-emerging tropical disease and its severe form is caused by cross-reactivity between its four serotypes (DEN1, DEN2, DEN3 and DEN4). The third domain of the viral envelope protein (ED3) contains the two major putative epitopes and is a highly suitable model protein for examining the molecular determinants of a virus' sero-specificity. Here we examine d the sero-specificity and cross-reactivity of the immune response against DEN3 and DEN4 ED3 using six epitope grafted ED3 variants where the surface-exposed epitope residues from DEN3 ED3 were switched to those of DEN4 ED3 and vice versa. We prepared anti-DEN3 and anti-DEN4 ED3 serum by immunizing Swiss albino mice and measured their reactivities against all six grafted mutants. As expected, both sera exhibited strong reactivity against its own serotype's ED3, and little cross-reactivity against their counterpart serotype's ED3s. E2 played a major role in the sero-specificity of anti-DEN3 serum, whereas E1 was important for DEN4 ED3's sero-specificity. Next, the reactivity patterns corroborated our working hypothesis that sero-specificity could be transferred by grafting the surface exposed epitope residues from one serotype to the other. To analyze the above results from a structural viewpoint, we determined the crystal structure of a DEN4 ED3 variant, where E2 was grafted from DEN3 ED3, at 2.78Å resolution and modeled the structures of the five remaining grafted variants by assuming that the overall backbone remained unchanged. The examination of the electrostatic and molecular surfaces of the variants suggested some further rationale for the sero-specificity of the immune responses.


    Organizational Affiliation

    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope protein E
A, B, C, D, E, F
107Dengue virus type 4 (strain Dominica/814669/1981)Mutation(s): 4 
Find proteins for P09866 (Dengue virus type 4 (strain Dominica/814669/1981))
Go to UniProtKB:  P09866
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.234 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 124.585α = 90.00
b = 124.585β = 90.00
c = 86.132γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data processing
REFMACrefinement
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release