3UC0

Crystal structure of domain I of the envelope glycoprotein ectodomain from dengue virus serotype 4 in complex with the fab fragment of the chimpanzee monoclonal antibody 5H2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into the neutralization mechanism of a higher primate antibody against dengue virus.

Cockburn, J.J.Navarro Sanchez, M.E.Goncalvez, A.P.Zaitseva, E.Stura, E.A.Kikuti, C.M.Duquerroy, S.Dussart, P.Chernomordik, L.V.Lai, C.J.Rey, F.A.

(2012) Embo J. 31: 767-779

  • DOI: 10.1038/emboj.2011.439
  • Primary Citation of Related Structures:  3UAJ

  • PubMed Abstract: 
  • The four serotypes of dengue virus (DENV-1 to -4) cause the most important emerging viral disease. Protein E, the principal viral envelope glycoprotein, mediates fusion of the viral and endosomal membranes during virus entry and is the target of neut ...

    The four serotypes of dengue virus (DENV-1 to -4) cause the most important emerging viral disease. Protein E, the principal viral envelope glycoprotein, mediates fusion of the viral and endosomal membranes during virus entry and is the target of neutralizing antibodies. However, the epitopes of strongly neutralizing human antibodies have not been described despite their importance to vaccine development. The chimpanzee Mab 5H2 potently neutralizes DENV-4 by binding to domain I of E. The crystal structure of Fab 5H2 bound to E from DENV-4 shows that antibody binding prevents formation of the fusogenic hairpin conformation of E, which together with in-vitro assays, demonstrates that 5H2 neutralizes by blocking membrane fusion in the endosome. Furthermore, we show that human sera from patients recovering from DENV-4 infection contain antibodies that bind to the 5H2 epitope region on domain I. This study, thus, provides new information and tools for effective vaccine design to prevent dengue disease.


    Organizational Affiliation

    Département de Virologie, Institut Pasteur, Unité de Virologie Structurale, Paris, France. joseph.cockburn@cancer.org.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
envelope protein
A, B
165Dengue virus 4N/A
Find proteins for Q91AI1 (Dengue virus 4)
Go to UniProtKB:  Q91AI1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain, monoclonal antibody 5H2
H, I
236N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Light chain, monoclonal antibody 5H2
L, M
215N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, H, I, M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.937α = 90.00
b = 113.864β = 90.00
c = 169.583γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
BUSTERrefinement
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-02-15
    Type: Database references, Source and taxonomy
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy