Structure of DBL6 epsilon domain from VAR2CSA

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.290 

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Structural Comparison of Two Cspg-Binding Dbl Domains from the Var2Csa Protein Important in Malaria During Pregnancy.

Khunrae, P.Philip, J.M.D.Bull, D.R.Higgins, M.K.

(2009) J Mol Biol 393: 202

  • DOI: https://doi.org/10.1016/j.jmb.2009.08.027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Severe malaria during pregnancy is associated with accumulation of parasite-infected erythrocytes in the placenta due to interactions between VAR2CSA protein, expressed on the surface of infected-erythrocytes, and placental chondroitin sulfate proteoglycans (CSPG). VAR2CSA contains multiple CSPG-binding domains, including DBL3X and DBL6 epsilon. Previous structural studies of DBL3X suggested CSPG to bind to a positively charged patch and sulfate-binding site on the concave surface of the domain. Here we present the structure of the DBL6 epsilon domain from VAR2CSA. This domain displays the same overall architecture and secondary structure as that of DBL3X but differs in loop structures, disulfide bond positions and surface charge distribution. In particular, despite binding to CSPG, DBL6 epsilon lacks the key features of the CSPG-binding site of DBL3X. Instead DBL6 epsilon binds to CSPG through a positively charged surface on the distal side of subdomain 2 that is exposed in intact VAR2CSA on the erythrocyte surface. Finally, unlike intact VAR2CSA, both DBL3X and DBL6 epsilon bind to various carbohydrates, with greatest affinity for ligands with high sulfation and negative charge. These studies provide further insight into the structure of DBL domains and suggest a model for the role of individual domains in CSPG binding by VAR2CSA in placental malaria.

  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80, Tennis Court Road, Cambridge CB2 1GA, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
302Plasmodium falciparum 3D7Mutation(s): 1 
Find proteins for Q8I639 (Plasmodium falciparum (isolate 3D7))
Explore Q8I639 
Go to UniProtKB:  Q8I639
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I639
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.290 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.943α = 90
b = 62.943β = 90
c = 334.269γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2014-12-03
    Changes: Data collection