6WY1

Crystal structure of an engineered thermostable dengue virus 2 envelope protein dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.319 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies.

Kudlacek, S.T.Metz, S.Thiono, D.Payne, A.M.Phan, T.T.N.Tian, S.Forsberg, L.J.Maguire, J.Seim, I.Zhang, S.Tripathy, A.Harrison, J.Nicely, N.I.Soman, S.McCracken, M.K.Gromowski, G.D.Jarman, R.G.Premkumar, L.de Silva, A.M.Kuhlman, B.

(2021) Sci Adv 7: eabg4084-eabg4084

  • DOI: https://doi.org/10.1126/sciadv.abg4084
  • Primary Citation of Related Structures:  
    6WY1

  • PubMed Abstract: 

    Dengue virus (DENV) is a worldwide health burden, and a safe vaccine is needed. Neutralizing antibodies bind to quaternary epitopes on DENV envelope (E) protein homodimers. However, recombinantly expressed soluble E proteins are monomers under vaccination conditions and do not present these quaternary epitopes, partly explaining their limited success as vaccine antigens. Using molecular modeling, we found DENV2 E protein mutations that induce dimerization at low concentrations (<100 pM) and enhance production yield by more than 50-fold. Cross-dimer epitope antibodies bind to the stabilized dimers, and a crystal structure resembles the wild-type (WT) E protein bound to a dimer epitope antibody. Mice immunized with the stabilized dimers developed antibodies that bind to E dimers and not monomers and elicited higher levels of DENV2-neutralizing antibodies compared to mice immunized with WT E antigen. Our findings demonstrate the feasibility of using structure-based design to produce subunit vaccines for dengue and other flaviviruses.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dengue 2 soluble recombinant envelope408dengue virus type 2Mutation(s): 5 
UniProt
Find proteins for P29990 (Dengue virus type 2 (strain Thailand/16681/1984))
Explore P29990 
Go to UniProtKB:  P29990
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29990
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.319 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.8α = 90
b = 125.8β = 90
c = 142.637γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH1820035
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5 F31 AI145408-02

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary