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 output from the all-against-all structure comparisons was parsed to extract R2R correspondences for each query/template pair. In each comparison the full query sequence was represented. At some positions in the template sequences, gaps occurred either due to structure deviation exceeding the alignment cutoff (5 Ã… ) or because the template contained additional residues (e.g. a loop) without correspondence in the query structure. A structure map was created for each set of R2R correspondences derived from each query/template-set StralSV comparison by combining the data for each binary alignment in an Excel spreadsheet. In this article, we report the structure map using poliovirus RdRp as the primary query (Figures 2-8) , although in most cases we include structure maps with other species as query (Figures 2 and 4 -8) . Alternative query species were used when structure similarity of some of the templates was not identified with poliovirus as query (e.g. Motif G in WNV and DENV were identified based on DENV as the query). The query that contributes to non-poliovirus matches is indicated on each alignment ('q' following the species abbreviation).