Structure of the trigger loop and its interface to the bridge helix. (a) Overview of the spatial relationship between the trigger loop (blue ribbon representation) and the bridge helix (green ribbon representation) based on a yeast RNAPII X-ray structure containing a folded trigger loop structure  (PDB 2E2H). Bridge helix residues E833 and T834 (yellow) and trigger loop residues A1076 and K1102 (orange) are shown as space-filling models. (b) Spatial relationship of the trigger loop base helices with the bridge helix in the kinked (PDB 1IW7) and straight (PDB 2O5J) versions of T. thermophilus RNAP. Note how the flipping out of bridge helix residues D1090 and S1091 during kinking disrupts their proximity to trigger loop residues I1260 and G1233, respectively. (c) Sequence alignments of trigger loop sequences using the same criteria as for the bridge helix alignments shown in Figure 1b. TL-N and TL-C indicate the amino-terminal and carboxy-terminal trigger loop base helices, respectively.