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Questions and answers => RNA structures (DSSR) => DSSR-NAR paper => Topic started by: xiangjun on July 06, 2015, 12:57:49 pm

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Title: Supplementary Figure 3 -- four base triplets in the tRNA mimic (4p5j)
Post by: xiangjun on July 06, 2015, 12:57:49 pm
(http://x3dna.bio.columbia.edu/dssr-nar/supp-fig3-4p5j-multiplets/4p5j-multiplets.png)
Quote
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:

Here is a sample image generated with the above script:
(http://x3dna.bio.columbia.edu/dssr-nar/supp-fig3-4p5j-multiplets/4p5j-m1.png)

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.