Supplementary Figure 5 -- characterizing junction loops in twister ribozyme

[xiangjun]

Figure S5: Ribbon representations of the junction loop in the env22 twister ribozyme (PDB id: 4rge). The ribbons are defined in terms of the C1′ and P atoms of the nucleotides that make up the junction loop. Inclusion of pseudoknots in the analysis of the structure reveals a [4,2,2,0,1,3,0,0,1,1] ten-way junction and a ribbon that follows a super-coiled pathway, with a linking number of three (blue, top row). Upon pseudoknot removal, only a [2,1,3] three-way junction and a ribbon with a simple relaxed circular configuration remain (green, bottom row). The overlap of the two junction loops in the middle row clearly shows that the over-simplified three-way junction spans only a small portion of the ten-way loop. The ribbons are shown in three projections: down the x-axis (left column), the y-axis (middle column), and the z-axis (right column). The images were kindly generated by Dr. Nicolas Clauvelin using the approach described in ref. 49.

Note:

• I provided Dr. Nicolas Clauvelin these two files: twister-pknot-jct.pdb for the ten-way junction, and a simplified version twister-nested-jct.pdb for the pseudoknots-removed three-way junction.
• Dr. Nicolas Clauvelin generated the ribbon diagrams of the pseudo-knotted/free junction loops and their overlaid version, each in three projections for a total of 9 files.
• The nine png images were combined using InkScape, and annotated, to get the final illustration.
• For completeness, here is the tarball file containing all the data files: supp-fig5-twister-4rge.tar.gz