User:Margaux Boutet/Sandbox
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
| - | + | === Overall of DBL3x === | |
The DBL3x structure has three subdomains (using the nomenclature of ref 1). | The DBL3x structure has three subdomains (using the nomenclature of ref 1). | ||
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The third subdomain (residues 1445−1580 ; red) has two long antiparallel helices, H5 (residues 1449−1476) and H6 (residues 1499−1529), that are connected to each other by a large loop (residues 1477−1498) and that make contacts with the first and the second subdomains. The C-terminal domain of this subdomain (residues 1563−1580) forms a flat structure of small helices connected by short linker regions. Subdomain 3 contains four disulfide bonds: Cys1462-Cys1546, Cys1476-Cys1501, Cys1505-Cys1574 and Cys1486-Cys1576. Near the C terminus, the bond between Cys1486 and Cys1576 was not visible and, presumably, was disordered in the crystal. In addition, nine N-terminal residues, three C-terminal residues and loop residues 1279−1285, 1327−1337, 1387−1397 and 1486−1494 were disordered and not visible in the electron density. | The third subdomain (residues 1445−1580 ; red) has two long antiparallel helices, H5 (residues 1449−1476) and H6 (residues 1499−1529), that are connected to each other by a large loop (residues 1477−1498) and that make contacts with the first and the second subdomains. The C-terminal domain of this subdomain (residues 1563−1580) forms a flat structure of small helices connected by short linker regions. Subdomain 3 contains four disulfide bonds: Cys1462-Cys1546, Cys1476-Cys1501, Cys1505-Cys1574 and Cys1486-Cys1576. Near the C terminus, the bond between Cys1486 and Cys1576 was not visible and, presumably, was disordered in the crystal. In addition, nine N-terminal residues, three C-terminal residues and loop residues 1279−1285, 1327−1337, 1387−1397 and 1486−1494 were disordered and not visible in the electron density. | ||
| - | + | ===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). | 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. | 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. | ||
Revision as of 15:34, 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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