Extended Data Fig. 8: Structural characteristics of λPR intermediates at 5 °C.
a. Comparison of λPR intermediates obtained by tr-Spotiton and at 5 °C. Eσ70 model of each state is shown as a transparent molecular surface, focusing on σ701.1 or duplex DNA occupying the RNAP cleft. Cryo-EM difference density (local-resolution filtered77) for σ701.1 (RPc5 °C) or for the DNA (I1d, RPo, I1d5 °C) is shown. The color-coding is shown in the legend at the upper left. The top row shows tr-Spotiton I1d and RPo (7MKD)8. The bottom row shows λPR-5 °C data (RPc5 °C and 1Id5 °C). A view of the entire structure (I1d5 °C) is shown in the lower right; the box denotes the region magnified in the other views. The orientation of the views shown is the same as the bottom view in each panel of Fig. 4. b. Each of the λPR-5 °C structures (RPc5 °C, I1c5 °C, I1d5 °C) were aligned pairwise with each of the tr-Spotiton structures (I1a, I1b, I1c, I1d) using the PyMOL align command on the RNAP structural core (α-carbons only), then the root-mean-square deviation was determined using the PyMOL rms_cur command over all matching α-carbons (the minimum number of overlapping α-carbon atoms was 3,709). The resulting rmsd values are plotted for each λPR-5 °C structure against each of the tr-Spotiton structures, showing that I1c5 °C matched most closely with I1c (orange arrow), and I1d5 °C matched most closely with I1d (red arrow).
