Location within model of AMA1 crystal structure of 10 predicted HLA-A and HLA-B epitopes. Spatial distribution of CD8 epitopes on the 3 D model structure of AMA1. The structure of PfAMA1 Domain I and II (1Z40) was fitted on the structure of PvAMA1 Domain I, II and III (1wk8), using Swiss Pdb-Viewer software http://www.expasy.org/spdbv/. Domain I and II of the PfAMA1 structure (light grey regions) and Domain III of PvAMA (dark grey region) are visible. Panels A & C show front view (largely conserved), B & D show back view (more polymorphic). Confirmed CD8 epitopes (E6, E8, E9, E12, E14) are orange in panels A & B, non-confirmed epitopes (E5, E7, E10, E11, E13) are yellow, while overlapping confirmed epitopes and non-confirmed epitopes are also in orange. Residues that are conserved among malaria species are shown in red and those that are polymorphic are shown in blue. Light grey (PfAMA) and dark grey (PvAMA1) are residues that differ between these species. Arrows point to individual epitopes. Overlapping epitopes may be indicated by multiple arrows. Confirmed epitopes E1 to E4 (see text) are not shown, as the part of the protein where these epitopes reside is not present in this crystal structure model.