1OK8

Crystal structure of the dengue 2 virus envelope glycoprotein in the postfusion conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Dengue Virus Envelope Protein After Membrane Fusion

Modis, Y.Ogata, S.Clements, D.Harrison, S.C.

(2004) Nature 427: 313

  • DOI: 10.1038/nature02165

  • PubMed Abstract: 
  • Dengue virus enters a host cell when the viral envelope glycoprotein, E, binds to a receptor and responds by conformational rearrangement to the reduced pH of an endosome. The conformational change induces fusion of viral and host-cell membranes. A t ...

    Dengue virus enters a host cell when the viral envelope glycoprotein, E, binds to a receptor and responds by conformational rearrangement to the reduced pH of an endosome. The conformational change induces fusion of viral and host-cell membranes. A three-dimensional structure of the soluble E ectodomain (sE) in its trimeric, postfusion state reveals striking differences from the dimeric, prefusion form. The elongated trimer bears three 'fusion loops' at one end, to insert into the host-cell membrane. Their structure allows us to model directly how these fusion loops interact with a lipid bilayer. The protein folds back on itself, directing its carboxy terminus towards the fusion loops. We propose a fusion mechanism driven by essentially irreversible conformational changes in E and facilitated by fusion-loop insertion into the outer bilayer leaflet. Specific features of the folded-back structure suggest strategies for inhibiting flavivirus entry.


    Related Citations: 
    • A Ligand-Binding Pocket in the Dengue Virus Envelope Glycoprotein
      Modis, Y.,Ogata, S.,Clements, D.,Harrison, S.C.
      (2003) Proc.Natl.Acad.Sci.USA. 100: 6986


    Organizational Affiliation

    Howard Hughes Medical Institute, Children's Hospital and Harvard Medical School, 320 Longwood Avenue, Boston, Massachusetts 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAJOR ENVELOPE PROTEIN E
A
394Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969)Mutation(s): 0 
Find proteins for P12823 (Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969))
Go to UniProtKB:  P12823
Small Molecules
Ligands 2 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
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.151α = 90.00
b = 76.151β = 90.00
c = 130.775γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-29
    Type: Initial release
  • Version 1.1: 2012-01-25
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance