PMC

Group II intron folding assembly pathway. (a) The schematic for group II intron assembly. The D1_iso, D1_full, D2, D3 and D5 are shown in yellow, gray, cyan, green and red. (b) Interface between D1_full (gray), D2 (cyan) and D3 (green) in the full-length intron. D2 interacts with D1_full through coaxial stacking and tetraloop-receptor interactions. D3 interacts with D1 and D2 through A-minor interaction, base stacking and ribose zipper.

Crystallographic B-factor distribution in D1_iso. (a) Density plot of B-factors in D1_iso. The B-factor value (non-normalized) is color-coded by a blue-to-red spectrum. The same spectrum is also used in (b) and (c). (b) Secondary structure color-coded by average B-factor for each residue in D1_iso. The residues that are not modeled are colored in gray. (c) D1_iso tertiary structure color-coded by atomic B-factors. d1₁, d1₂, d1₃ and ω-ω′ interaction are indicated by red, orange, magenta and yellow boxes.

D1 structure in the presence and absence of downstream domains. (a) Two views of D1_iso (yellow) rotated by 90°. The 5′ half (5′H) and the 3′ half (3′H) of the clam-like D1 are shaded in blue and pink. (b) Surface representation of D1_iso (yellow) and D1_full (gray). The red lines indicate the outline of the cleft between the 5′H and the 3′H of the clam-like D1. (c) The structure of the full-length intron. D1 (D1_full), D2, D3, D4 and D5 are colored in gray, blue, green, wheat and red.

Box plot showing difference average B-factors between the junction residues (denoted as ΔB_junction, on y-axis) and specific motifs taken from D1_iso, D1_full and from all RNA entries in PDB (x-axis). “Overall” means ΔB_junction is the difference between junction residues and all residues in a specific structure. “Stem”, “hairpin” and “bulge” means the ΔB_junction is the difference between junction residues and stem, hairpin and bulge residues in a specific structure. The red dashed line indicates zero ΔB_junction value. For the D1_iso and D1_full group, the thick band indicates a single value. For groups from “PDB”, the thick band indicates the median, the box indicates the upper and lower quantiles, the vertical line indicates the variability, and the individual dots represent outliers.

Difference pseudo-torsion angle (Δ(η,θ)) between D1_iso and D1_full. (a) Schematic of difference pseudo-torsion angle calculation. The definition of RNA pseudo-torsion angles are shown on the left, and the procedure of calculating the difference pseudo-torsion angles and the combined difference pseudo-torsion angle is presented as a flow chart. (b) Plot showing Δ(η,θ) values (y-axis) for residues in D1_iso (x-axis). The deep green and the light green color indicate two Δ(η,θ) class with large and small values. Because of chain breaks, only residues 7-81, 85-99, 109-137, 141-205, 210-265 are involved in the analysis. (c) Secondary structure showing residues with large Δ(η,θ) (green). (d) Tertiary structure showing residues with large Δ(η,θ) (green). The 5′H and the 3′H are shaded in blue and pink.