4AL8

Structure of Dengue virus DIII in complex with Fab 2H12

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structural Analysis of a Dengue Cross-Reactive Antibody Complexed with Envelope Domain III Reveals the Molecular Basis of Cross-Reactivity.

Midgley, C.M., Flanagan, A., Tran, H.B., Dejnirattisai, W., Chawansuntati, K., Jumnainsong, A., Wongwiwat, W., Duangchinda, T., Mongkolsapaya, J., Grimes, J.M., Screaton, G.R.

(2012) J.Immunol. 188: 4971

  • DOI: 10.4049/jimmunol.1200227
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Dengue virus infections are still increasing at an alarming rate in tropical and subtropical countries, underlying the need for a dengue vaccine. Although it is relatively easy to generate Ab responses to dengue virus, low avidity or low concentratio ...

    Dengue virus infections are still increasing at an alarming rate in tropical and subtropical countries, underlying the need for a dengue vaccine. Although it is relatively easy to generate Ab responses to dengue virus, low avidity or low concentrations of Ab may enhance infection of FcR-bearing cells with clinical impact, posing a challenge to vaccine production. In this article, we report the characterization of a mAb, 2H12, which is cross-reactive to all four serotypes in the dengue virus group. Crystal structures of 2H12-Fab in complex with domain III of the envelope protein from three dengue serotypes have been determined. 2H12 binds to the highly conserved AB loop of domain III of the envelope protein that is poorly accessible in the mature virion. 2H12 neutralization varied between dengue serotypes and strains; in particular, dengue serotype 2 was not neutralized. Because the 2H12-binding epitope was conserved, this variation in neutralization highlights differences between dengue serotypes and suggests that significant conformational changes in the virus must take place for Ab binding. Surprisingly, 2H12 facilitated little or no enhancement of infection. These data provide a structural basis for understanding Ab neutralization and enhancement of infection, which is crucial for the development of future dengue vaccines.

    Organizational Affiliation: 

    Department of Medicine, Hammersmith Hospital Campus, Imperial College London, London W12 0NN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENVELOPE PROTEIN
C
101Dengue virus type 1 (strain Nauru/West Pac/1974)Mutation(s): 0 
Find proteins for P17763 (Dengue virus type 1 (strain Nauru/West Pac/1974))
Go to UniProtKB:  P17763
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB 2H12 HEAVY CHAIN
H
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FAB 2H12 LIGHT CHAIN
L
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
H, L
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: 1.66 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.401α = 93.32
b = 60.603β = 102.10
c = 62.833γ = 101.51
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
SCALAdata scaling
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release