Supplementary Figure 3 -- four base triplets in the tRNA mimic (4p5j)

[xiangjun]

Figure S3: The four base triplets and associated hydrogen bonds (dashed lines) detected by DSSR in the viral tRNA mimic (PDB id: 4p5j) from turnip yellow mosaic virus. (A) GUC (G10,U11,C49) lies at the elbow of the L-shaped tertiary structure, with G10 and U11 forming a GpU dinucleotide platform. (B) CGU (C58,G72,U73) includes another GpU (G72 and U73) platform, with a single base-base hydrogen bond. (C) CGA (C59,G71,A75) forms a type I A-minor motif. (D) CGC (C61,G68,C77) contains a loop nucleotide (C61) from the hairpin-type pseudoknot. The last three triplets (B-D) are located at the 3'-end of the structure around the hairpin-type pseudoknot.

Starting from "4p5j.pdb" downloaded from RCSB PDB, here is the complete script to get each of the four base-triplet images in png format.

Code: Bash

1. x3dna-dssr -i=4p5j.pdb -o=4p5j.out --prefix=4p5j
2.  
3. ex_str -1 4p5j-multiplets.pdb 4p5j-m1.pdb
4. x3dna-dssr -i=4p5j-m1.pdb -o=4p5j-m1.pml --hbfile-pymol
5. pymol -qkc 4p5j-m1.pml
6. convert -trim +repage -border 10 -bordercolor white 4p5j-m1-pymol.png 4p5j-m1.png
7.  
8. ex_str -2 4p5j-multiplets.pdb 4p5j-m2.pdb
9. x3dna-dssr -i=4p5j-m2.pdb -o=4p5j-m2.pml --hbfile-pymol
10. pymol -qkc 4p5j-m2.pml
11. convert -trim +repage -border 10 -bordercolor white 4p5j-m2-pymol.png 4p5j-m2.png
12.  
13. ex_str -3 4p5j-multiplets.pdb 4p5j-m3.pdb
14. x3dna-dssr -i=4p5j-m3.pdb -o=4p5j-m3.pml --hbfile-pymol
15. pymol -qkc 4p5j-m3.pml
16. convert -trim +repage -border 10 -bordercolor white 4p5j-m3-pymol.png 4p5j-m3.png
17.  
18. ex_str -4 4p5j-multiplets.pdb 4p5j-m4.pdb
19. x3dna-dssr -i=4p5j-m4.pdb -o=4p5j-m4.pml --hbfile-pymol
20. pymol -qkc 4p5j-m4.pml
21. convert -trim +repage -border 10 -bordercolor white 4p5j-m4-pymol.png 4p5j-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 "4p5j-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 from ImageMagick 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-fig3-4p5j-multiplets.tar.gz

Here is a sample image generated with the above script: