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. Author manuscript; available in PMC: 2020 May 25.
Published in final edited form as: Nat Struct Mol Biol. 2019 Nov 25;26(12):1132–1140. doi: 10.1038/s41594-019-0331-x

Fig. 3. Poly(A)-induced decoding center rearrangement.

Fig. 3

(A) The ribosome A-site containing the poly(A) single-stranded helix (pink), capped by stacking interactions with 18S rRNA bases (yellow), is shown fitted within the EM density map (mesh). (B) Comparison of the decoding center configurations in the poly(A)-stalled ribosome (solid model) and the ribosome trapped during decoding (PDB 5LZS; transparent model). The mRNA bases and tRNA (in the case of decoding) are omitted for clarity. (C) Superimposed models of the poly(A)-stalled ribosome and the A/T tRNA (grey) positioned as it would be during decoding (PDB 5LZS). Base 37 of the tRNA clashes with 18S rRNA base A1825, which cannot move to its ‘flipped in’ position because A3760 of 28S rRNA occupies this space. Base modifications would be present at position 37 (and 34) when the incoming tRNA is the cognate Lys-tRNALys,3, but this is not shown for clarity.