Fig. 1: Group II intron structural motifs.

A Secondary structure map of the O. iheyensis I1 group II intron. Domains are abbreviated as D1 to D5. Secondary structure elements of D1 described in the text are depicted with respective labels and colors corresponding to all subsequent subpanels. Tertiary interactions and active site motifs are depicted in Roman letters. B Same map highlighting key RNA helices and geometric descriptors used in the text, i.e., ‘angles A-D’ and ‘gate distance’. C D1 crystal structure (PDB id 4Y1O) in which each subdomain discussed in the text is represented with a distinctive color, as in panel A. The position of the hinge 1 and 2 residues is indicated. D Same structure as in (C), where the helical axes of ‘core D1c’ (orange) and D1d1 (violet), used to calculate ‘angle A’, are indicated by the black lines. E Same structure as in (C), where the helical axes of ‘core D1c’ (orange), ‘peripheral D1c’ (light green) and i₁-i₂ (dark green), used to calculate ‘angle B’ and ‘angle C’, respectively, are indicated by the black lines. F Same structure as in (C), where the helical axes of D1d1 (violet) and i₁-i₂ (dark green), used to calculate ‘angle D’, are indicated by the black lines. G Superposition of “closed” D1 (PDB id 4Y1O, colored as in panel C) and “catalytic” D1 (PDB id 4FAQ, light yellow). H Same representation as in (G), rotated by 90° with respect to the right subpanel G, and showing here the steric clash between the “closed” D1 structure and D5. I) Zoom into the hinge 1 residues from “closed” D1 (PDB id 4Y1O, orange) and “catalytic” D1 (PDB id 4FAQ, light yellow). J Highlight into the steric clash (red label) between A72 (orange, “closed” state) and nucleotides of the Z-anchor motif (yellow, “catalytic open” state). Z-anchor nucleotides are flexible in the “closed” state. In this latter state, the first nucleotides flanking the Z-anchor and visible in the structure are C102 (light green) and G108 (grey).