3CPZ

Crystal structure of VAR2CSA DBL3x domain in the presence of dodecasaccharide of CSA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.299 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A.

Singh, K.Gittis, A.G.Nguyen, P.Gowda, D.C.Miller, L.H.Garboczi, D.N.

(2008) Nat Struct Mol Biol 15: 932-938

  • DOI: https://doi.org/10.1038/nsmb.1479
  • Primary Citation of Related Structures:  
    3CML, 3CPZ

  • PubMed Abstract: 

    Plasmodium falciparum-infected erythrocytes bind to chondroitin sulfate A (CSA) in the placenta via the VAR2CSA protein, a member of the P. falciparum erythrocyte membrane protein-1 family, leading to life-threatening malaria in pregnant women with severe effects on their fetuses and newborns. Here we describe the structure of the CSA binding DBL3x domain, a Duffy binding-like (DBL) domain of VAR2CSA. By forming a complex of DBL3x with CSA oligosaccharides and determining its structure, we have identified the CSA binding site to be a cluster of conserved positively charged residues on subdomain 2 and subdomain 3. Mutation or chemical modification of lysine residues at the site markedly diminished CSA binding to DBL3x. The location of the CSA binding site is an important step forward in the molecular understanding of pregnancy-associated malaria and offers a new target for vaccine development.


  • Organizational Affiliation

    Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, Maryland 20852, USA. ksingh@niaid.nih.gov


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Erythrocyte membrane protein 1362Plasmodium falciparumMutation(s): 0 
Gene Names: var
UniProt
Find proteins for Q6UDW7 (Plasmodium falciparum)
Explore Q6UDW7 
Go to UniProtKB:  Q6UDW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UDW7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.299 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.52α = 90
b = 86.76β = 90
c = 101.57γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Refinement description