Supplementary Figure 4 -- four multiplets in the env22 twister ribozyme (4rge)

[xiangjun]

Figure S4: The four base multiplets and associated hydrogen bonds (dashed lines) de- tected by DSSR in the env22 twister ribozyme (chain A, PDB id: 4rge). (A) Triplet UUA (U1,U33,A50) where U1 and A50 form a Hoogsteen pair (U1+A50). (B) Triplet UAA (U4,A34,A49) where U4 and A49 form a reverse Hoogsteen pair (U4–A49). (C) Quadruplet CGUA (C14,G25,U41,A42) which includes a type II A-minor motif. (D) Pen- taplet CAGUA (C13,A26,G36,U41,A43) which contains a type I A-minor motif. The two neighboring A-minor motifs (in C and D) are part of a larger structural framework involv- ing U41 and A26 (see Figure 4).

Starting from "4rge.pdb" downloaded from RCSB PDB, chain A is extracted into "4rgeA.pdb". Below is the complete script to get each of the four base-multiplet images in png format.

Code: Bash

1. x3dna-dssr -i=4rgeA.pdb -o=4rgeA.out --prefix=4rgeA
2.  
3. ex_str -1 4rgeA-multiplets.pdb 4rgeA-m1.pdb
4. x3dna-dssr -i=4rgeA-m1.pdb -o=4rgeA-m1.pml --hbfile-pymol
5. pymol -qkc 4rgeA-m1.pml
6. convert -trim +repage -border 10 -bordercolor white 4rgeA-m1-pymol.png 4rgeA-m1.png
7.  
8. ex_str -2 4rgeA-multiplets.pdb 4rgeA-m2.pdb
9. x3dna-dssr -i=4rgeA-m2.pdb -o=4rgeA-m2.pml --hbfile-pymol
10. pymol -qkc 4rgeA-m2.pml
11. convert -trim +repage -border 10 -bordercolor white 4rgeA-m2-pymol.png 4rgeA-m2.png
12.  
13. ex_str -3 4rgeA-multiplets.pdb 4rgeA-m3.pdb
14. x3dna-dssr -i=4rgeA-m3.pdb -o=4rgeA-m3.pml --hbfile-pymol
15. pymol -qkc 4rgeA-m3.pml
16. convert -trim +repage -border 10 -bordercolor white 4rgeA-m3-pymol.png 4rgeA-m3.png
17.  
18. ex_str -4 4rgeA-multiplets.pdb 4rgeA-m4.pdb
19. x3dna-dssr -i=4rgeA-m4.pdb -o=4rgeA-m4.pml --hbfile-pymol
20. pymol -qkc 4rgeA-m4.pml
21. convert -trim +repage -border 10 -bordercolor white 4rgeA-m4-pymol.png 4rgeA-m4.png

Note:

• The --prefix option makes the auxiliary files having a specified prefix instead of the default "dssr". For example, "dssr-multiplets.pdb" becomes "4rgeA-multiplets.pdb".
• The ex_str utility program is from the 3DNA distribution. It is used to extract a specific model from a MODEL/ENDMDL ensemble.
• The DSSR --hbfile-pymol option is used to generate a .pml file with all required settings for rendering in PyMOL.
• The convert  program is from ImageMagick that is used here to trim extra white boundaries.
• The multiplet-png images (here four triplets) were combined using InkScape, and annotated, to get the final illustration.
• For completeness, here is the tarball file containing all the data files and the script ("tasks"): supp-fig4-4rgeA-multiplets.tar.gz

Here is a sample image generated with the above script: