User:Margaux Boutet/Sandbox
From Proteopedia
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| - | + | == Crystal structure of VAR2CSA DBL3x domain == | |
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| - | == Crystal structure of VAR2CSA DBL3x domain == | + | |
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VAR2CSA is a 350 kDa transmembrane protein and has been identified as the only gene overexpressed by Plasmodium falciparum infected erythrocytes selected to adhere to CSA. The resulting protein is the major receptor responsible for the adhesion of EI (infected erythrocytes) to the placenta. We were able to identify it by the antibodies present in the body of pregnant women infected with P. falciparum. Its extracellular part is composed of 6 known (epsilon) or unknown (x) domains, interspersed with Cysteine-rich Inter-Domain Regions (CIDR) and TM and ATS regions (Acidic Terminal Segment) including DBL3x. In fact, Duffy binding-like 3 X domain (DBL3X) is one of the six DBL domains of the variant surface antigen 2 CSA, belonging to the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family and involved in Pregnancy-associated Malaria. | VAR2CSA is a 350 kDa transmembrane protein and has been identified as the only gene overexpressed by Plasmodium falciparum infected erythrocytes selected to adhere to CSA. The resulting protein is the major receptor responsible for the adhesion of EI (infected erythrocytes) to the placenta. We were able to identify it by the antibodies present in the body of pregnant women infected with P. falciparum. Its extracellular part is composed of 6 known (epsilon) or unknown (x) domains, interspersed with Cysteine-rich Inter-Domain Regions (CIDR) and TM and ATS regions (Acidic Terminal Segment) including DBL3x. In fact, Duffy binding-like 3 X domain (DBL3X) is one of the six DBL domains of the variant surface antigen 2 CSA, belonging to the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family and involved in Pregnancy-associated Malaria. | ||
| + | <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> | ||
| + | This is a default text for your page '''Margaux Boutet/Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | ||
| + | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | ||
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== Function == | == Function == | ||
Revision as of 14:43, 15 January 2017
Crystal structure of VAR2CSA DBL3x domain
VAR2CSA is a 350 kDa transmembrane protein and has been identified as the only gene overexpressed by Plasmodium falciparum infected erythrocytes selected to adhere to CSA. The resulting protein is the major receptor responsible for the adhesion of EI (infected erythrocytes) to the placenta. We were able to identify it by the antibodies present in the body of pregnant women infected with P. falciparum. Its extracellular part is composed of 6 known (epsilon) or unknown (x) domains, interspersed with Cysteine-rich Inter-Domain Regions (CIDR) and TM and ATS regions (Acidic Terminal Segment) including DBL3x. In fact, Duffy binding-like 3 X domain (DBL3X) is one of the six DBL domains of the variant surface antigen 2 CSA, belonging to the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family and involved in Pregnancy-associated Malaria.
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References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
Comparaison with known DBL structures
DBL3x is compared to two other proteins that are not PfEMP1 family members: the P. falciparum erythrocyte binding antigen (EBA)-175, which has two DBL domains F1 and F2 (PDB 1ZRL), and the Plasmodium knowlesi (Pk)α-DBL protein, which has one DBL domain (PDB 2C6J). The structure of the DBL3x adds to the evidence that PfEMP1 domains have the conserved DBL protein fold. Structure-based sequence alignments of DBL3x with EBA-175 and Pkα-DBL show conserved cysteines amid a few other conserved residues. Futhermore, conserved helices have been observed in the absence of substantial sequence identity. Structural superimpositions of DBL3x and the three other DBL domains yielded r.m.s. deviations on all Cα atoms for F1, F2 and Pkα-DBL of 2.8Å, 2.7Å and 2.2Å, respectively. Overlays of the four structures based on the structural superimposition of the long helices in the third subdomain made it clear that each DBL domain has its three subdomains positioned differently. Differences in subdomain positions relative to each other probably contributed to our finding that only the Pkα-DBL structure (r.m.s. deviation 2.2Å) yielded convincing solutions when used as a model in several molecular replacement programs. Calculated phases from the best molecular replacement solutions, however, were poor, and it was necessary to improve them through multicrystal averaging (Methods).
Location of CSA binding site
Residues with side chains within 5Å of the CSA electron density are Lys1324 and Lys1327 of the second subdomain, Arg1467 of helix H5 of subdomain 3, and Arg1503, Lys1504, Lys1507 and Lys1510 of helix H6 of the third subdomain. One strong region of density is chemically consistent with a sulfate ion that seems to be coordinated by Lys1324, Arg1467 and Lys1504 (Fig. 2). The lysines of DBL3x are required for binding CSA
Mechanism
Clusters of several PfEMP1 molecules occur on protuberances, or 'knobs', which are characteristic surface features of P. falciparum–infected erythrocytes. The adhesin comprises a large extracellular N-terminal region with six DBL domains, a single transmembrane segment and a cytoplasmic acid terminal segment (ATS) at the C terminus. The first three DBL domains belong to class X, whereas the last three belong to class epsilon. Individual recombinant DBL domains from VAR2CSA that have been shown to bind CSA are colored in orange. The DBL3x domain, illustrated as an enlargement in ribbon form, is a highly alpha-helical protein (PDB 3CML). The subdomains 1, 2 and 3 are colored yellow, red and green, respectively. VAR2CSA binds to the CSA moiety of placental chondroitin sulfate proteoglycan present on the surface of the syncytiotrophoblast cells in the placenta. The CSA ligand is shown schematically as hexagons (blue), positioned over the region covering subdomains 2 and 3 identified by the two research groups as the CSA binding site.
