Fig. 1.

Sequences and structures of boxB RNA, N peptide variants selected for binding to boxB RNA (15), and their complexes used in this study. The WT complex structure is taken from NMR (10, 11). The bases A7, A8, A9, and A10 are colored in red, green, blue, and yellow, respectively; RNA backbone and other base pairs are in gray. The WT N peptide in the complex is represented as red ribbon with side chains of Lys-14, Gln-15, and Trp-18 shown. Structure of the boxB RNA pentaloop with U5-A11 closing base pair is viewed 90° from the full complex; the stacking between Trp-18 and A7 is viewed from the top of the loop.