4YFS

Structure of the synthetic Duffy Binding Protein (DBP) antigen DEKnull relevant for malaria vaccine design

  • Classification: Erythrocyte binding protein
  • Organism(s): Plasmodium vivax Sal-1
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-02-25 Released: 2015-03-11 
  • Deposition Author(s): Chen, E., Tolia, N.H.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Edward Mallinckrodt Jr. Foundation, Burroughs Wellcome Fund, Schlesinger Graduate Fellowship

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Analysis of the Synthetic Duffy Binding Protein (DBP) Antigen DEKnull Relevant for Plasmodium vivax Malaria Vaccine Design.

Chen, E.Salinas, N.D.Ntumngia, F.B.Adams, J.H.Tolia, N.H.

(2015) PLoS Negl Trop Dis 9: e0003644-e0003644

  • DOI: 10.1371/journal.pntd.0003644
  • Primary Citation of Related Structures:  
    4YFS

  • PubMed Abstract: 
  • The Plasmodium vivax vaccine candidate Duffy Binding Protein (DBP) is a protein necessary for P. vivax invasion of reticulocytes. The polymorphic nature of DBP induces strain-specific immune responses that pose unique challenges for vaccine development. DEKnull is a synthetic DBP based antigen that has been engineered through mutation to enhance induction of blocking inhibitory antibodies ...

    The Plasmodium vivax vaccine candidate Duffy Binding Protein (DBP) is a protein necessary for P. vivax invasion of reticulocytes. The polymorphic nature of DBP induces strain-specific immune responses that pose unique challenges for vaccine development. DEKnull is a synthetic DBP based antigen that has been engineered through mutation to enhance induction of blocking inhibitory antibodies. We determined the x-ray crystal structure of DEKnull to identify if any conformational changes had occurred upon mutation. Computational and experimental analyses assessed immunogenicity differences between DBP and DEKnull epitopes. Functional binding assays with monoclonal antibodies were used to interrogate the available epitopes in DEKnull. We demonstrate that DEKnull is structurally similar to the parental Sal1 DBP. The DEKnull mutations do not cause peptide backbone shifts within the polymorphic loop, or at either the DBP dimerization interface or DARC receptor binding pockets, two important structurally conserved protective epitope motifs. All B-cell epitopes, except for the mutated DEK motif, are conserved between DEKnull and DBP. The DEKnull protein retains binding to conformationally dependent inhibitory antibodies. DEKnull is an iterative improvement of DBP as a vaccine candidate. DEKnull has reduced immunogenicity to polymorphic regions responsible for strain-specific immunity while retaining conserved protein folds necessary for induction of strain-transcending blocking inhibitory antibodies.


    Organizational Affiliation

    Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine, Saint Louis, Missouri, United States of America; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Duffy receptorA326Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVDR
UniProt
Find proteins for P22290 (Plasmodium vivax (strain Salvador I))
Explore P22290 
Go to UniProtKB:  P22290
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.63α = 90
b = 37.35β = 108.77
c = 78.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-25 
  • Released Date: 2015-03-11 
  • Deposition Author(s): Chen, E., Tolia, N.H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI080792
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI064478
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesT32 AI007171
Edward Mallinckrodt Jr. FoundationUnited States--
Burroughs Wellcome FundUnited States--
Schlesinger Graduate FellowshipUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.3: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence