Figure 3

Structural model of TGBp3. The first panel shows a model in the ribbon representation colored according to the secondary structure elements. The second panel shows a model colored according to the predicted local deviation from the real structure, as calculated by METAMQAPII. Blue indicates low predicted deviation of C-α atoms down to 0 Å, red indicates unreliable regions with deviation > 5 Å, green to orange indicate intermediate values. The third panel shows a protein in the surface representation, colored according to the distribution of the electrostatic surface potential calculated with ABPS (see Methods). Blue indicates positively charged regions, red indicates negatively charged regions. The fourth and fifth panels show models in the surface representation, colored according to sequence similarity, calculated from multiple sequence alignments of PepMV sequences using ConSurf. All four models are in the same orientation, except the last one, which has been rotated horizontally. All figures have been drawn using PyMOL [44].