Fig. 2: Interactions within the triple guanine (GGG) motif of the closed and open SLII conformers.
A Closed RRE SLII conformer. The SLII closed conformer is shown with the 2FoFc electron density contoured at 1.0 σ in light gray. The size of the molecule and the angle between stems IIB and IIC are indicated. B Tertiary interactions in the high-affinity Rev-binding site of the closed conformer. A schematic of base pair interactions in the three-way junction are shown (left). The filled boxes indicate the nucleotides involved in the interactions mediating non-canonical base pairs and the opening/closing of the three-way junction. The close-up view of the high-affinity Rev-binding site (the GGG motif, filled boxes) is shown (right). Note that closure of the three-way junction, and thus lengthening of stem IIB, is mediated by non-canonical G8·U35 and syn-G9·G34 base pairs. The syn-G10 base stacks on the syn-G9·G34 base pair. The syn-G9·G34 base pair interaction is shown along with chemical structures. Hydrogen bond lengths below 3.4 Å are displayed. C Open RRE SLII conformer. The SLII open conformer is shown with the 2FoFc electron density contoured at 1.0 σ in light gray. D Tertiary interactions in the high-affinity Rev-binding site of the open conformer. Schematic of base pair interactions (left) and close-up views of the high-affinity Rev-binding site (the GGG motif, right) are shown. Note that only G34 forms a non-canonical G10·syn-G34 base pair, thus opening the three-way junction. The G10·syn-G34 base pair interaction is shown along with their chemical structures. The structures and schematics are colored as in Fig. 1.
