3G7T

Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation and its implications for membrane fusion.

Nayak, V.Dessau, M.Kucera, K.Anthony, K.Ledizet, M.Modis, Y.

(2009) J.Virol. 83: 4338-4344

  • DOI: 10.1128/JVI.02574-08

  • PubMed Abstract: 
  • Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragm ...

    Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragment E (sE) of dengue virus type 1 (DEN-1). The protein is in the postfusion conformation even though it was not exposed to a lipid membrane or detergent. At the domain I-domain III interface, 4 polar residues form a tight cluster that is absent in other flaviviral postfusion structures. Two of these residues, His-282 and His-317, are conserved in flaviviruses and are part of the "pH sensor" that triggers the fusogenic conformational change in E, at the reduced pH of the endosome. In the fusion loop, Phe-108 adopts a distinct conformation, forming additional trimer contacts and filling the bowl-shaped concavity observed at the tip of the DEN-2 sE trimer.


    Organizational Affiliation

    Department of Molecular Biophysics & Biochemistry, The Bass Center for Structural Biology, Yale University, New Haven, Connecticut 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope protein
A
400Dengue virus 1Mutation(s): 0 
Find proteins for Q689G3 (Dengue virus 1)
Go to UniProtKB:  Q689G3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.208 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 75.650α = 90.00
b = 75.650β = 90.00
c = 292.802γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
ADSCdata collection
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data scaling
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-02-10 
  • Released Date: 2009-04-21 
  • Deposition Author(s): Modis, Y.

Revision History 

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2012-03-28
    Type: Database references
  • Version 1.3: 2014-04-23
    Type: Other
  • Version 1.4: 2017-11-01
    Type: Refinement description