1UZG

CRYSTAL STRUCTURE OF THE DENGUE TYPE 3 VIRUS ENVELOPE PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.284 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Variable Surface Epitopes in the Crystal Structure of Dengue Virus Type 3 Envelope Glycoprotein

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

(2005) J.Virol. 79: 1223

  • DOI: 10.1128/JVI.79.2.1223-1231.2005

  • PubMed Abstract: 
  • Dengue virus is an emerging global health threat. The major envelope glycoprotein, E, mediates viral attachment and entry by membrane fusion. Antibodies that bind but fail to neutralize noncognate serotypes enhance infection. We have determined the c ...

    Dengue virus is an emerging global health threat. The major envelope glycoprotein, E, mediates viral attachment and entry by membrane fusion. Antibodies that bind but fail to neutralize noncognate serotypes enhance infection. We have determined the crystal structure of a soluble fragment of the envelope glycoprotein E from dengue virus type 3. The structure closely resembles those of E proteins from dengue type 2 and tick-borne encephalitis viruses. Serotype-specific neutralization escape mutants in dengue virus E proteins are all located on a surface of domain III, which has been implicated in receptor binding. While antibodies against epitopes in domain I are nonneutralizing in dengue virus, there are neutralizing antibodies that recognize serotype-conserved epitopes in domain II. The mechanism of neutralization for these antibodies is probably inhibition of membrane fusion. Our structure shows that neighboring glycans on the viral surface are spaced widely enough (at least 32 A) that they can interact with multiple carbohydrate recognition domains on oligomeric lectins such as DC-SIGN, ensuring maximum affinity for these putative receptors.


    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

    Children's Hospital, Enders 673, 320 Longwood Ave., Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAJOR ENVELOPE PROTEIN E
A, B
392Dengue virus type 3 (strain Philippines/H87/1956)Mutation(s): 0 
Find proteins for P27915 (Dengue virus type 3 (strain Philippines/H87/1956))
Go to UniProtKB:  P27915
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
A, B
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.284 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.855α = 90.00
b = 68.631β = 90.00
c = 270.180γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
AMoREphasing
CNSphasing
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance