6FLA | pdb_00006fla

3H5 Fab bound to EDIII of DenV 2 Xtal form 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.221 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.203 (Depositor) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6FLA

This is version 1.3 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: https://doi.org/10.1038/s41590-018-0227-7
  • Primary Citation Related Structures: 
    6FLA, 6FLB, 6FLC

  • 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-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
    • Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

Macromolecule Content 

  • Total Structure Weight: 119.55 kDa 
  • Atom Count: 8,142 
  • Modeled Residue Count: 1,058 
  • Deposited Residue Count: 1,089 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chainA,
D [auth H]
227Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light Chain of 3H5B,
F [auth L]
218Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Domain III of Dengue virus 2C [auth G]98dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for P14340 (Dengue virus type 2 (strain Thailand/NGS-C/1944))
Explore P14340 
Go to UniProtKB:  P14340
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14340
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Domain III of Dengue virus 2E [auth I]101dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for P29991 (Dengue virus type 2 (strain 16681-PDK53))
Explore P29991 
Go to UniProtKB:  P29991
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29991
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.221 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.203 (Depositor) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.84α = 90
b = 263.87β = 90
c = 272.83γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary