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Figure 4.
(a,b) Superposition of the trigger loops and bridge helices
in the  -amanitin
inhibited Pol II EC and the free T. thermophilus (Tth) RNA
polymerase^6. The trigger loop residue Leu1081 (S. cerevisiae
(Sc) Pol II) or its homologous residue Met1238 (Tth) forms a
wedge between the bridge helix and helix 37
in Pol II or G' in Tth. The views are from the top (a) or the
side (b), as in Figure 3b or 1e, respectively. In the -amanitin–inhibited
Pol II EC, the central bridge helix is shifted, whereas in the
bacterial holoenzyme it adopts a flipped-out conformation. (c,d)
Four possible states of the EC. Above to below, the
pretranslocation state (PDB 1I6H)^1, a potential transition
state with a modeled flipped-out bridge helix (PDB 1IW7)^17, the
-amanitin–inhibited
EC (the apparent translocation intermediate with the shifted
bridge helix, this study), and the post-translocation state (PDB
1Y1W)^2 are shown with space-filling models (c) or ribbon
diagrams (d). The bridge helix residues Ala832/Ala1089 (Pol
II/Tth) and Thr831/Thr1088 (Pol II/Tth) are highlighted in
yellow and brown, respectively. (e,f) Comparison of trigger loop
conformations. Pol II EC structures in the post-translocation
state (PDB 1Y1W)^2, with bound NTP substrate (PDB 2E2H)^4, and
in the intermediary state are superimposed. Nucleic acids and
metal A are from the translocation intermediate. The trigger
loops of the three structures are depicted in dark red (wedged,
translocation intermediate), light blue (open, 1Y1W) and yellow
(closed, 2E2H, labels in black). (f) Also depicted are the
bridge helix (green, apparent translocation intermediate) and
the NTP in the insertion site (orange, 2E2H). (g) Comparison of
bridge helix conformations in the -amanitin–inhibited
EC (green, with residues Ala832 and Thr831 highlighted in yellow
and brown, respectively), the post-translocation EC^2 (light
green) and the core Pol II EC with bound NTP^4 (beige).
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