Structured RNA molecules contain modular tertiary contact motifs. (A) Structure and sequence of the 11ntR from the P4–P6 domain of the Tetrahymena Group I intron; PDB: 1GID (Cate et al. 1996). Base pairs are denoted by the Leontis–Westhof notation (Leontis and Westhof 2001), and intermolecular hydrogen bonds are denoted by red lines; intermolecular stacking interactions are denoted by dotted red lines. The residues are numbered in accordance with Bonilla et al. (2017), and the loop residues of TL are numbered with superscript “TL” to distinguish them from TLR residues. (B) Structure and sequence of Vc2R in the V. cholera c-di-GMP riboswitch; PDB: 3MXH (Smith et al. 2010). Intermolecular interactions are shown as in (A), and the residues are numbered to correspond to the 11ntR. (C) The sequence of IC3R; its putative base pairs based on homology with Vc2R are shown as dotted lines (Zakrevsky et al. 2021). (D) Interactions between the GAAA tetraloop (green) and the 11ntR (blue) or Vc2R (orange). Interactions are depicted by dashed lines. Residues of the TLR are numbered and color coded as depicted in A–C.
