3IXY

The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 23.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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:  
    3IXX, 3IXY, 3I50

  • 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 antibody E53 that engages the highly conserved fusion loop of the West Nile virus envelope glycoprotein ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope protein EA, B, C395Dengue virus 2Mutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q9WDA6 (Dengue virus type 2 (strain Peru/IQT2913/1996))
Explore Q9WDA6 
Go to UniProtKB:  Q9WDA6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide prD, E, F81Dengue virus 2Mutation(s): 0 
UniProt
Find proteins for P18356 (Dengue virus type 2 (strain Thailand/PUO-218/1980))
Explore P18356 
Go to UniProtKB:  P18356
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
E53 Fab Fragment (chain H)G, I221Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
E53 Fab Fragment (chain L)H, J215Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 23.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-07-18
    Changes: Data collection