5N09

Crystal structure of L107C/A313C covalently linked dengue 2 virus envelope glycoprotein dimer in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 A11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.304 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Covalently linked dengue virus envelope glycoprotein dimers reduce exposure of the immunodominant fusion loop epitope.

Rouvinski, A.Dejnirattisai, W.Guardado-Calvo, P.Vaney, M.C.Sharma, A.Duquerroy, S.Supasa, P.Wongwiwat, W.Haouz, A.Barba-Spaeth, G.Mongkolsapaya, J.Rey, F.A.Screaton, G.R.

(2017) Nat Commun 8: 15411-15411

  • DOI: 10.1038/ncomms15411
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A problem in the search for an efficient vaccine against dengue virus is the immunodominance of the fusion loop epitope (FLE), a segment of the envelope protein E that is buried at the interface of the E dimers coating mature viral particles. Anti-FL ...

    A problem in the search for an efficient vaccine against dengue virus is the immunodominance of the fusion loop epitope (FLE), a segment of the envelope protein E that is buried at the interface of the E dimers coating mature viral particles. Anti-FLE antibodies are broadly cross-reactive but poorly neutralizing, displaying a strong infection enhancing potential. FLE exposure takes place via dynamic 'breathing' of E dimers at the virion surface. In contrast, antibodies targeting the E dimer epitope (EDE), readily exposed at the E dimer interface over the region of the conserved fusion loop, are very potent and broadly neutralizing. We here engineer E dimers locked by inter-subunit disulfide bonds, and show by X-ray crystallography and by binding to a panel of human antibodies that these engineered dimers do not expose the FLE, while retaining the EDE exposure. These locked dimers are strong immunogen candidates for a next-generation vaccine.


    Related Citations: 
    • Recognition determinants of broadly neutralizing human antibodies against dengue viruses.
      Rouvinski, A.,Guardado-Calvo, P.,Barba-Spaeth, G.,Duquerroy, S.,Vaney, M.C.,Kikuti, C.M.,Navarro Sanchez, M.E.,Dejnirattisai, W.,Wongwiwat, W.,Haouz, A.,Girard-Blanc, C.,Petres, S.,Shepard, W.E.,Despres, P.,Arenzana-Seisdedos, F.,Dussart, P.,Mongkolsapaya, J.,Screaton, G.R.,Rey, F.A.
      (2015) Nature 520: 109


    Organizational Affiliation

    Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope Glycoprotein E
A, B
430Dengue virus 2Mutation(s): 2 
Find proteins for A0A0B4SHY9 (Dengue virus 2)
Go to UniProtKB:  A0A0B4SHY9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 - Heavy chain
H, I
283N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 - Light chain
L, M
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.304 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.902α = 90.00
b = 180.598β = 90.00
c = 205.043γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Commission FP7 ProgrammeFrance282 378FP
rench Government Investissements de Avenir programFrancer ANR-10-LABX-62-IBEID

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release