5A1Z

Cryo-EM structure of Dengue virus serotype 2 strain PVP94-07 complexed with human antibody 2D22 Fab at 37 degrees C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 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

Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers.

Fibriansah, G.Ibarra, K.D.Ng, T.S.Smith, S.A.Tan, J.L.Lim, X.N.Ooi, J.S.Kostyuchenko, V.A.Wang, J.de Silva, A.M.Harris, E.Crowe, J.E.Lok, S.M.

(2015) Science 349: 88-91

  • DOI: https://doi.org/10.1126/science.aaa8651
  • Primary Citation of Related Structures:  
    4UIF, 4UIH, 5A1Z

  • PubMed Abstract: 

    There are four closely-related dengue virus (DENV) serotypes. Infection with one serotype generates antibodies that may cross-react and enhance infection with other serotypes in a secondary infection. We demonstrated that DENV serotype 2 (DENV2)-specific human monoclonal antibody (HMAb) 2D22 is therapeutic in a mouse model of antibody-enhanced severe dengue disease. We determined the cryo-electron microscopy (cryo-EM) structures of HMAb 2D22 complexed with two different DENV2 strains. HMAb 2D22 binds across viral envelope (E) proteins in the dimeric structure, which probably blocks the E protein reorganization required for virus fusion. HMAb 2D22 "locks" two-thirds of or all dimers on the virus surface, depending on the strain, but neutralizes these DENV2 strains with equal potency. The epitope defined by HMAb 2D22 is a potential target for vaccines and therapeutics.


  • Organizational Affiliation

    Program in Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, Singapore. Centre for BioImaging Sciences, National University of Singapore, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENVELOPE PROTEIN
A, C, E
495dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for E0WXJ2 (dengue virus type 2)
Explore E0WXJ2 
Go to UniProtKB:  E0WXJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0WXJ2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MEMBRANE GLYCOPROTEIN
B, D, F
72dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for E0WXJ2 (dengue virus type 2)
Explore E0WXJ2 
Go to UniProtKB:  E0WXJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0WXJ2
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
G, I, K
128Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
H, J, L
115Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN1
RECONSTRUCTIONEMAN2
RECONSTRUCTIONMPSA

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Other
  • Version 1.2: 2017-08-23
    Changes: Data collection
  • Version 1.3: 2018-02-07
    Changes: Database references