8A44

Plasmodium vivax Duffy binding protein region II bound the DARC ectodomain and monoclonal antibody DB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for DARC binding in reticulocyte invasion by Plasmodium vivax.

Moskovitz, R.Pholcharee, T.DonVito, S.M.Guloglu, B.Lowe, E.Mohring, F.Moon, R.W.Higgins, M.K.

(2023) Nat Commun 14: 3637-3637

  • DOI: https://doi.org/10.1038/s41467-023-39357-w
  • Primary Citation of Related Structures:  
    8A44

  • PubMed Abstract: 

    The symptoms of malaria occur during the blood stage of infection, when the parasite replicates within human red blood cells. The human malaria parasite, Plasmodium vivax, selectively invades reticulocytes in a process which requires an interaction between the ectodomain of the human DARC receptor and the Plasmodium vivax Duffy-binding protein, PvDBP. Previous studies have revealed that a small helical peptide from DARC binds to region II of PvDBP (PvDBP-RII). However, it is also known that sulphation of tyrosine residues on DARC affects its binding to PvDBP and these residues were not observed in previous structures. We therefore present the structure of PvDBP-RII bound to sulphated DARC peptide, showing that a sulphate on tyrosine 41 binds to a charged pocket on PvDBP-RII. We use molecular dynamics simulations, affinity measurements and growth-inhibition experiments in parasites to confirm the importance of this interaction. We also reveal the epitope for vaccine-elicited growth-inhibitory antibody DB1. This provides a complete understanding of the binding of PvDBP-RII to DARC and will guide the design of vaccines and therapeutics to target this essential interaction.


  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Duffy binding protein294Plasmodium vivaxMutation(s): 0 
Gene Names: dbpII
UniProt
Find proteins for A5KDR7 (Plasmodium vivax (strain Salvador I))
Explore A5KDR7 
Go to UniProtKB:  A5KDR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5KDR7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Atypical chemokine receptor 160Homo sapiensMutation(s): 3 
Gene Names: DARC
UniProt & NIH Common Fund Data Resources
Find proteins for Q16570 (Homo sapiens)
Explore Q16570 
Go to UniProtKB:  Q16570
PHAROS:  Q16570
GTEx:  ENSG00000213088 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16570
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of monoclonal antibody DB1225Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of monoclonal antibody DB1213Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.204α = 90
b = 97.949β = 90
c = 287.987γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description