3I50

Crystal structure of the West Nile Virus envelope glycoprotein in complex with the E53 antibody Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody.

Cherrier, M.V.Kaufmann, B.Nybakken, G.E.Lok, S.M.Warren, J.T.Chen, B.R.Nelson, C.A.Kostyuchenko, V.A.Holdaway, H.A.Chipman, P.R.Kuhn, R.J.Diamond, M.S.Rossmann, M.G.Fremont, D.H.

(2009) Embo J. 28: 3269-3276

  • DOI: 10.1038/emboj.2009.245
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have defined the structure of the flavivirus cross-reactive ...

    Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have defined the structure of the flavivirus cross-reactive antibody E53 that engages the highly conserved fusion loop of the West Nile virus envelope glycoprotein. Using cryo-electron microscopy, we also determined that E53 Fab binds preferentially to spikes in noninfectious, immature flavivirions but is unable to bind significantly to mature virions, consistent with the limited solvent exposure of the epitope. We conclude that the neutralizing impact of E53 and likely similar fusion-loop-specific antibodies depends on its binding to the frequently observed immature component of flavivirus particles. Our results elucidate how fusion-loop antibodies, which comprise a significant fraction of the humoral response against flaviviruses, can function to control infection without appreciably recognizing mature virions. As these highly cross-reactive antibodies are often weakly neutralizing they also may contribute to antibody-dependent enhancement and flavi virus pathogenesis thereby complicating development of safe and effective vaccines.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
E
402West Nile virus (strain NY-99)Mutation(s): 0 
Gene Names: GP1
Find proteins for Q9Q6P4 (West Nile virus (strain NY-99))
Go to UniProtKB:  Q9Q6P4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
murine kappa light chain of E53 monoclonal antibody Fab
L
207N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
murine heavy chain (IgG3) of E53 monoclonal antibody Fab
H
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 146.410α = 90.00
b = 160.140β = 90.00
c = 43.880γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
ALSdata collection
PHASERphasing
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-09-25
    Type: Derived calculations