Secondary structure representation of the pseudosymmetrical region (SymR) and the tt_A1P1 construct of the protoribosome plotted over the Thermus thermophilus secondary structure of Domain V from the LSU. Secondary structure was derived from crystallographic structure data (Petrov et al. 2013, 2014a). Filled circles mark ribonucleotides that comprise the six regions of RNA/RNA interactions that have been proposed to be the driving force behind the hybridization of the P- and A-regions (Supplemental Table S1; Rivas and Fox 2020). (A) Secondary structure representation for the original proposal of the SymR (Agmon et al. 2005). P-region comprises 89 ribonucleotides and A-region is equally made from 89 for a total of 178. No proposal was originally made for the possible sequences that should be used at the tips of H75, H89, and H91 nor for the connection at the end of H80 and the beginning of H74. Hence, they are represented by gray arrows. (B) Secondary structure representation of the protoribosome construct tt_A1P1 (Bose et al. 2021, 2022). It starts with G2058 (red font) instead of A2058 due to experimental protocol requirements. P-region comprises 71 ribonucleotides while A-region is made from 64 for a total of 135. Sequence 5′-CUUCGG-3′ was used to close helixes 74, 89, and 90 (red font). C2463 and A2518 in proposed region 2 were left out in the tt_A1P1 construct (Supplemental Table S1).
