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

Nature Structural & Molecular Biology volume 15, pages 932–938 (2008)Cite this article

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.

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Figure 1: Views of the overall structure of the DBL3x domain.
Figure 2: The CSA electron density.
Figure 3: The lysine residues of DBL3x are important for binding to CSA.
Figure 4: The electrostatic potential surface in the vicinity of the CSA binding site.

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Protein Data Bank

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GenBank/EMBL/DDBJ

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Acknowledgements

We thank A. Diouf and C.A. Long (Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases) for screening monoclonal antibodies, J.F. Andersen for helping with ITC, S. Madala for giving assistance with flow cytometry, H.-P. Su for advising on molecular biology, J.M. Moore for helping with initial protein purification and J.D. Smith (Seattle Biomedical Research Institute) for giving us the A4 genomic DNA. X-ray data were collected at the SBC-CAT and SER-CAT beamlines at the Advanced Photon Source supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract W-31-109-Eng-38. This work was supported by the Intramural Research Program of the US National Institutes of Health, National Institute of Allergy and Infectious Diseases and by grant AI45086 for work performed in the laboratory of D.C. Gowda.

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Authors and Affiliations

  1. Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, 20852, Maryland, USA

    Kavita Singh, Apostolos G Gittis, Phuc Nguyen & David N Garboczi

  2. Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, 500 University Drive, H171, Hershey, 17033, Pennsylvania, USA

    D Channe Gowda

  3. Malaria Vaccine Development Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5640 Fishers Lane, Rockville, 20852, Maryland, USA

    Louis H Miller

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  1. Kavita Singh
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  2. Apostolos G Gittis
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  3. Phuc Nguyen
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  4. D Channe Gowda
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  6. David N Garboczi
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Contributions

K.S. and L.H.M. initiated the project; K.S. and P.N. expressed the proteins and produced crystals; K.S., P.N. and A.G.G. collected X-ray data; K.S., A.G.G. and D.N.G. processed the X-ray data and solved the DBL3x structure; D.C.G. prepared desulfated, digested and size-fractionated CSA; K.S. and A.G.G. built models and refined structures for more than 20 X-ray data sets from crystals with carbohydrate; K.S., A.G.G., L.H.M. and D.N.G. wrote the manuscript. All authors edited the manuscript.

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Correspondence to Kavita Singh or David N Garboczi.

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Singh, K., Gittis, A., Nguyen, P. et al. Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A. Nat Struct Mol Biol 15, 932–938 (2008). https://doi.org/10.1038/nsmb.1479

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