Comparison of experimentally derived secondary and tertiary conformations for the 86 nt SARS-CoV-2 FSE. (A) 3D structure displaying 3_6 H-type pseudoknot conformation in λ form obtained through cryo-EM (PDB ID 6XRZ). (B) Multiple cryo-EM derived structural models (PDB ID 6XRZ) display conformational flexibility in 87 nt FSE. The 5′ end consisting of a slippery site is highly flexible; however, all alternative 3D conformations adopt the same 3_6 H-type pseudoknot secondary structure conformation. (C) Arc plot and radial layout computed through DMS-MaP and SHAPEknots for 86 nt FSE 3_6 H-type pseudoknot secondary structure (D) 3_5 three-way junction and (E) 3_3 H-type pseudoknot. Slippery site, Stem I, Stem II, and Stem III are annotated in the arc plot and radial layout. The three alternative conformations depicted in C, D, and E were also observed in a previous SHAPE study (Schlick 2021a).
