2R6P

Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed with dengue 2 virus.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 24.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins.

Lok, S.M.Kostyuchenko, V.Nybakken, G.E.Holdaway, H.A.Battisti, A.J.Sukupolvi-Petty, S.Sedlak, D.Fremont, D.H.Chipman, P.R.Roehrig, J.T.Diamond, M.S.Kuhn, R.J.Rossmann, M.G.

(2008) Nat Struct Mol Biol 15: 312-317

  • DOI: 10.1038/nsmb.1382
  • Primary Citation of Related Structures:  
    2R6P, 2R69, 2R29

  • PubMed Abstract: 
  • The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding fragment (Fab) complexed with domain III of the viral envelope glycoprotein, E, showed that the epitope would be partially occluded in the known structure of the mature dengue virus ...

    The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding fragment (Fab) complexed with domain III of the viral envelope glycoprotein, E, showed that the epitope would be partially occluded in the known structure of the mature dengue virus. Nevertheless, antibody could bind to the virus at 37 degrees C, suggesting that the virus is in dynamic motion making hidden epitopes briefly available. A cryo-electron microscope image reconstruction of the virus:Fab complex showed large changes in the organization of the E protein that exposed the epitopes on two of the three E molecules in each of the 60 icosahedral asymmetric units of the virus. The changes in the structure of the viral surface are presumably responsible for inhibiting attachment to cells.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major envelope protein EA, B, C390Dengue virus 2 Puerto Rico/PR159-S1/1969Mutation(s): 0 
Gene Names: E protein
UniProt
Find proteins for Q66394 (Dengue virus 2)
Explore Q66394 
Go to UniProtKB:  Q66394
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy chain of 1A1D-2D, F216Mus musculusMutation(s): 0 
Gene Names: immunoglobulinIgh
UniProt
Find proteins for Q6PJB2 (Mus musculus)
Explore Q6PJB2 
Go to UniProtKB:  Q6PJB2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Light chain of 1A1D-2E, G206Mus musculusMutation(s): 0 
Gene Names: immunoglobulin
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 24.0 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: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Data collection, Data processing, Structure summary
  • Version 1.3: 2018-07-18
    Changes: Data collection