6R2S

The structure of Plasmodium vivax Duffy binding protein (PvDBP) bound to human antibody DB9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for inhibition of Plasmodium vivax invasion by a broadly neutralizing vaccine-induced human antibody.

Rawlinson, T.A.Barber, N.M.Mohring, F.Cho, J.S.Kosaisavee, V.Gerard, S.F.Alanine, D.G.W.Labbe, G.M.Elias, S.C.Silk, S.E.Quinkert, D.Jin, J.Marshall, J.M.Payne, R.O.Minassian, A.M.Russell, B.Renia, L.Nosten, F.H.Moon, R.W.Higgins, M.K.Draper, S.J.

(2019) Nat Microbiol 4: 1497-1507

  • DOI: 10.1038/s41564-019-0462-1

  • PubMed Abstract: 
  • The most widespread form of malaria is caused by Plasmodium vivax. To replicate, this parasite must invade immature red blood cells through a process requiring interaction of the P. vivax Duffy binding protein (PvDBP) with its human receptor, the Duf ...

    The most widespread form of malaria is caused by Plasmodium vivax. To replicate, this parasite must invade immature red blood cells through a process requiring interaction of the P. vivax Duffy binding protein (PvDBP) with its human receptor, the Duffy antigen receptor for chemokines. Naturally acquired antibodies that inhibit this interaction associate with clinical immunity, suggesting PvDBP as a leading candidate for inclusion in a vaccine to prevent malaria due to P. vivax. Here, we isolated a panel of monoclonal antibodies from human volunteers immunized in a clinical vaccine trial of PvDBP. We screened their ability to prevent PvDBP from binding to the Duffy antigen receptor for chemokines, and their capacity to block red blood cell invasion by a transgenic Plasmodium knowlesi parasite genetically modified to express PvDBP and to prevent reticulocyte invasion by multiple clinical isolates of P. vivax. This identified a broadly neutralizing human monoclonal antibody that inhibited invasion of all tested strains of P. vivax. Finally, we determined the structure of a complex of this antibody bound to PvDBP, indicating the molecular basis for inhibition. These findings will guide future vaccine design strategies and open up possibilities for testing the prophylactic use of such an antibody.


    Organizational Affiliation

    Singapore Immunology Network, A*STAR, Singapore, Singapore.,Department of Biochemistry, University of Oxford, Oxford, UK. matthew.higgins@bioch.ox.ac.uk.,Jenner Institute, University of Oxford, Oxford, UK.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Department of Biochemistry, University of Oxford, Oxford, UK.,Faculty of Public Health, Mahidol University, Bangkok, Thailand.,Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Shoklo Malaria Research Unit, Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Jenner Institute, University of Oxford, Oxford, UK. simon.draper@ndm.ox.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antibody DB9 light chain
A
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody DB9 heavy chain
B
278N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Duffy receptor
C
300Plasmodium vivax (strain Salvador I)Mutation(s): 0 
Gene Names: PVDR
Find proteins for P22290 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  P22290
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 173.560α = 90.00
b = 173.560β = 90.00
c = 169.730γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome Trust101020/Z/13/Z

Revision History 

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-06-12
    Type: Data collection, Database references
  • Version 1.2: 2019-08-21
    Type: Data collection
  • Version 1.3: 2019-09-04
    Type: Data collection, Database references