4P1T

Crystal structure of the DBL3X-DBL4epsilon double domain from the extracellular part of VAR2CSA PfEMP1 from Plasmodium falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the DBL3X-DBL4 epsilon region of the VAR2CSA placental malaria vaccine candidate: insight into DBL domain interactions.

Gangnard, S.Lewit-Bentley, A.Dechavanne, S.Srivastava, A.Amirat, F.Bentley, G.A.Gamain, B.

(2015) Sci Rep 5: 14868-14868

  • DOI: 10.1038/srep14868
  • Primary Citation of Related Structures:  
    4P1T

  • PubMed Abstract: 
  • The human malaria parasite, Plasmodium falciparum, is able to evade spleen-mediated clearing from blood stream by sequestering in peripheral organs. This is due to the adhesive properties conferred by the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family exported by the parasite to the surface of infected erythrocytes ...

    The human malaria parasite, Plasmodium falciparum, is able to evade spleen-mediated clearing from blood stream by sequestering in peripheral organs. This is due to the adhesive properties conferred by the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family exported by the parasite to the surface of infected erythrocytes. Expression of the VAR2CSA variant of PfEMP1 leads to pregnancy-associated malaria, which occurs when infected erythrocytes massively sequester in the placenta by binding to low-sulfated Chondroitin Sulfate A (CSA) present in the intervillous spaces. VAR2CSA is a 350 kDa protein that carries six Duffy-Binding Like (DBL) domains, one Cysteine-rich Inter-Domain Regions (CIDR) and several inter-domain regions. In the present paper, we report for the first time the crystal structure at 2.9 Å of a VAR2CSA double domain, DBL3X-DBL4ε, from the FCR3 strain. DBL3X and DBL4ε share a large contact interface formed by residues that are invariant or highly conserved in VAR2CSA variants, which suggests that these two central DBL domains (DBL3X-DBL4ε) contribute significantly to the structuring of the functional VAR2CSA extracellular region. We have also examined the antigenicity of peptides corresponding to exposed loop regions of the DBL4ε structure.


    Organizational Affiliation

    Laboratory of excellence GR-Ex, Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Erythrocyte membrane protein 1A746Plasmodium falciparum FCR-3/GambiaMutation(s): 8 
Gene Names: var2csa
UniProt
Find proteins for Q6UDW7 (Plasmodium falciparum)
Explore Q6UDW7 
Go to UniProtKB:  Q6UDW7
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.794α = 90
b = 129.336β = 90
c = 64.065γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references