Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases

Lang, Dorothy M.; Zemla, A. T.; Zhou, C. L. Ecale

The segment of conserved structure adjacent to each motif was determined from the StralSV maps. For each of the queries and each of the motifs, the location at which structure conservation of most species became discontinuous was noted. We defined the boundaries of a homomorph as the position at which the structural segment shared by all representatives in a set became discontinuous in more than two species. In all structure maps, the conserved segments that we identified based on StralSV R2R correspondences are colored light blue. We defined the homomorph of each motif as the segment consisting of the conserved motif plus the adjacent structurally conserved segments. The length of each homomorph varied somewhat depending on the query. For each query species, the start and end of the homomorphic segment of each motif were recorded, and a 20 Â 20 matrix for each motif was generated to compile the data from each query (data not shown). This matrix was used to identify the minimum start and maximum end of each homomorph, and these values are summarized in Supplementary Table S1 . These values are plotted in Figure 1 , which illustrates the maximal expanse of the homomorphic segments that include each of the polymerase motifs. All of the tertiary structures were illustrated using the Cn3D program (10) .