Figure 3

Evolutionary conservation of the functional residues of Runx(RD) and CBFβ involved in DNA binding and dimerization. The three dimensional structures of the cnidarian and sponge proteins were modeled according to the published structure of their human counterparts (PDB #1H9D). The RD is depicted in blue, CBFβ in green and DNA in purple. The interacting residues are depicted as ball and stick models, and colored according to their conservation with their human counterparts (Yellow = identical, Orange = conservative substitution, Red = non-conservative substitution). For clarity, a similar model with the relevant residues numbered according to the Nematostella Runx RD and CBFβ proteins is provided as Additional file 8, and detailed tables comparing the residues of all the proteins discussed can be found as Additional files 3, 4, 5. A) A General view of the Nematostella RD-CBFβ-DNA complex. All of the residues in the RD involved in DNA binding are completely conserved in Nematostella. The arrow points to compensatory changes in H163 of the RD, which is replaced with C131 in Nematostella. B) A rotation of Panel A by 180°, showing a second compensatory change which involves the substitution of F153 and M106 in human with K121 and A73 in Nematostella in the RD and the replacement of Q67 and S65 with H67 and T65 in CBFβ (indicated with arrow). C-F) The CBFβ-binding faces of the RD from Nematostella (C), Hydra (D), Amphimedon queenslandica (E) and Oscarella carmella (F). In the cnidarian proteins, the majority of non-conserved residues which interact with CBFβ are located at the periphery of the interacting surfaces (C, D). A. queenslandica and particularly O. carmella indicate greater sequence divergence within this domain, with non-conservative substituions not being restricted to the periphery. G-I) the Runx-binding surfaces of CBFβ proteins from Nematostella (G), Hydra (H) and A. queenslandica (I). Most of the functional residues are conserved between all three proteins and the human variant, with most of the non-conservative subsitutions found at the periphery of the binding face.