3G7T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1128/JVI.02574-08
  • Primary Citation of Related Structures:  
    3G7T

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein400dengue virus type 1Mutation(s): 0 
Gene Names: E
Membrane Entity: Yes 
UniProt
Find proteins for Q689G3 (dengue virus type 1)
Explore Q689G3 
Go to UniProtKB:  Q689G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ689G3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.65α = 90
b = 75.65β = 90
c = 292.802γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2014-04-23
    Changes: Other
  • Version 1.4: 2017-11-01
    Changes: Refinement description
  • Version 1.5: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description