Figure 2. Atomic fits to the small subunit and bound cofactors of the pseudoknot-engaged ribosome.

In the centre the small subunit is viewed in a similar orientation to that of Fig. 1, with the large subunit removed computationally. The subunit, tRNA, eEF2 and pseudoknot are coloured as in Fig. 1. The yeast atomic model for the small subunit¹⁵ has been fitted to the subunit itself (blue ribbons), the structure of eEF2 (ref. 18) to the corresponding density (yellow coil), and the tRNA stalled within the complex likewise (yellow ribbon). A stereo view of the central image is provided in Supplementary Fig. 2. Left and right: close-up views, rotated as indicated to afford a detailed picture of the structural changes associated with the engaged pseudoknot (left) and the stalled tRNA (right). Left: a view from the solvent face of the 80S_PK small subunit (yellow), with the 80S_Apo structure (green mesh) superimposed. Movements of the subunit in the 80S_PK ribosome up and towards the pseudoknot structure relative to the 80S_Apo ribosome can be seen. Here the atomic fits (blue ribbon) are to the 80S_Apo structure. From this fitting the movements can be associated with the eukaryotic equivalents of the prokaryotic helicase. Although the positioning of the pseudoknot itself is clear, the mRNA passing through the entrance channel is too thin to be distinguished at the current resolution. Right: a comparison of the 80S_PK (top left) and the 80S_SL (top right) tRNAs (density in green; fitted atomic models in yellow). At the bottom a superposition of the two models is shown, showing the bending of the 80S_PK tRNA.