Supplementary Figure 4: Structure comparisons of the group IIA intron in the LtrA-bound state with that in the LtrA-depleted state and the group IIB intron.
From: Structure of a group II intron in complex with its reverse transcriptase
(a) Comparison of group IIA intron structure in LtrA-bound state (color coding of RNA domains are according to Fig. 1b) and IEP-depleted state (dark slate gray) shows a RMSD value of 2.4 Å. Regions corresponding to helices Id1 and Id3ii encompassing EBS2 and EBS1, respectively, are enlarged on upper left and right corners. (b) Comparison between tertiary structures of individual domains of the group IIA intron (this study) and group IIB intron (PDB ID: 4R0D). Domains of the group IIA intron are color coded and labeled as in Fig. 2, whereas that of the group IIB intron are shown as light grey color. Differences are displayed for each domain between the two introns. The β-β' interaction site, which is unique to group IIA intron, is boxed in red in the upper left panel. (c) Difference in relative positions of RNA helices of domain I, Id(iv) and domain IV with respect to domain V (red) between the group IIA and group IIB introns. The relative movements in group IIA intron helices are indicated by black arrows. RNA helices from group IIA and group IIB introns are shown in matching colors, except that the IIB intron helices are shown as semitransparent tubes. (d) Fourier shell correlation between atomic coordinates with the corresponding EM densities. RNP, intron-LtrA complex; and DV, domain V of the intron RNA.
