6FLB

3H5 Fab bound to EDIII of DenV 2 Xtal form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Characterization of a potent and highly unusual minimally enhancing antibody directed against dengue virus.

Renner, M.Flanagan, A.Dejnirattisai, W.Puttikhunt, C.Kasinrerk, W.Supasa, P.Wongwiwat, W.Chawansuntati, K.Duangchinda, T.Cowper, A.Midgley, C.M.Malasit, P.Huiskonen, J.T.Mongkolsapaya, J.Screaton, G.R.Grimes, J.M.

(2018) Nat. Immunol. 19: 1248-1256

  • DOI: 10.1038/s41590-018-0227-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dengue virus is a major pathogen, and severe infections can lead to life-threatening dengue hemorrhagic fever. Dengue virus exists as four serotypes, and dengue hemorrhagic fever is often associated with secondary heterologous infections. Antibody-de ...

    Dengue virus is a major pathogen, and severe infections can lead to life-threatening dengue hemorrhagic fever. Dengue virus exists as four serotypes, and dengue hemorrhagic fever is often associated with secondary heterologous infections. Antibody-dependent enhancement (ADE) may drive higher viral loads in these secondary infections and is purported to result from antibodies that recognize dengue virus but fail to fully neutralize it. Here we characterize two antibodies, 2C8 and 3H5, that bind to the envelope protein. Antibody 3H5 is highly unusual as it not only is potently neutralizing but also promotes little if any ADE, whereas antibody 2C8 has strong capacity to promote ADE. We show that 3H5 shows resilient binding in endosomal pH conditions and neutralizes at low occupancy. Immunocomplexes of 3H5 and dengue virus do not efficiently interact with Fcγ receptors, which we propose is due to the binding mode of 3H5 and constitutes the primary mechanism of how ADE is avoided.


    Organizational Affiliation

    Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. juthathip.mongkolsapaya@well.ox.ac.uk.,Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. gavin.screaton@medsci.ox.ac.uk.,Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. juthathip.mongkolsapaya@well.ox.ac.uk.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. jonathan@strubi.ox.ac.uk.,Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, Chiang Mai University, Chiang Mai, Thailand.,Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Science Division, Diamond Light Source Ltd, Didcot, UK. jonathan@strubi.ox.ac.uk.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Domain III of Dengue virus 2
G
100Dengue virus 2Mutation(s): 0 
Find proteins for W5RZ25 (Dengue virus 2)
Go to UniProtKB:  W5RZ25
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of 3H5 Fab
H
227N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Light chain of 3H5 Fab
L
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
G
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
L
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.492α = 90.00
b = 131.573β = 90.00
c = 139.442γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom204703/Z/16/Z
Wellcome TrustUnited Kingdom075491/Z/04

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references