Fig. 7: Interactions at the P site. | Nature Communications

Fig. 7: Interactions at the P site.

From: Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity

Fig. 7

a Network of interactions at the P site in IC-DS1. The proximal part of the h44 helix is in orange. The h24 loop and parts of h45 interacting with h44 are in red. mRNA is in blue and the initiator tRNA is in yellow. Modified nucleotides are colored by atoms and labeled. Parts of the rRNA located close to the codon-anticodon duplex are in aquamarine. The same color code is used in the three views. b Close-up of the codon:anticodon interaction in IC-DS1. c Same as view a but for IC-DS2. d Same as view b but for IC-DS2. The cryo-EM map is also shown to highlight the network of water molecules located above G889. The view shows that the water network mimicks base −1, as observed in the leadered mRNA shown in view b (base −1 in pink). A zoomed view on the region above G889 nucleobase studied by molecular dynamics is shown in the right-hand corner. The view shows that the GIST predicted water oxygens (red) and hydrogen (white) densities fit with the experimentally placed water molecules (red spheres) (see also “Methods” and Supplementary figs. 15, 16).

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