Fig. 7: The pk-1 and pk-2 interactions form the core of the raiA motif.
From: Scaffold-enabled high-resolution cryo-EM structure determination of RNA
A The P3 loop (red) of raiA forms an extended pseudoknot with the pk-Loop (green) (pk-1). The pseudoknot consists of 7 consecutive cis-W:W base pairs. B pk-2 forms between the pk-Loop (green) and the junction between P4 and P1c (J4-1c) (cyan). This pseudoknot is not as extensive as pk-1 and forms 2 cis-W:W base pairs. C The sequence of pk-1 and pk-2 contained within the pk-Loop is only separated by a single nucleotide (G84). G84 base stacks with first nucleotide of the P3 Loop (A33) to further stabilize the pk-1/pk-2 structure.
