Figure 3 -- analysis of the tRNA mimic (4p5j)

[xiangjun]

Figure 3: DSSR reveals the striking global similarity and distinct local variations between the tRNA mimic from turnip yellow mosaic virus (PDB id: 4p5j (34)) and yeast tRNA^Phe. (A) The viral tRNA mimic assumes an overall L-shaped tertiary structure (center) composed of two helices (gray lines). DSSR uncovers a [0,0,3,0,1] five-way junction loop (right) enabled by the hairpin-type pseudoknot at the 3′-end of the molecule and the G2–C74 linchpin pair. This critical linchpin is unique to the tRNA mimic, where it is stabilized by extensive base-stacking interactions (upper-left). The lower-left inset emphasizes the intricate interactions between the D- and T-loops in the mimic, including the three base pairs (within dashed ellipses) and the unique base triplet at the elbow (Supplementary Figure S3A). (B) The linear secondary structure diagram generated with the DSSR-derived dot-bracket notation shows the sequential location of the bases comprising the linchpin pair, the five-way junction loop (red), the G10–C49 pair at the elbow, and the hairpin-type pseudoknot. Note that the dashed arcs connecting the so-called first-order pseudoknotted pairs (indicated by matched []) do not cross each other along the linear sequence. The numbering of residues used here follows that in the PDB file, which is offset by two nucleotides from that given in the original publication (e.g., the G2–C74 linchpin is termed G4–C76 there).

Here is the tarball (fig3-tRNA-mimic-4p5j.tar.gz) with the script and all related data files.
The content of the full script (named tasks) is shown below. Please see also notes for "Figure 2 -- analysis of the yeast phenylalanine tRNA (1ehz)".

Code: Bash

1. # Step #1 -- reorient viral tRNA mimic into the classic "L" shape
2. x3dna-dssr -i=4p5j.pdb -o=4p5j.out --more --prefix=4p5j
3. # To get the result illustrated in panel B, load '4p5j-2ndstrs.ct' or
4. # '4p5j-2ndstrs.dbn' into VARNA to draw the linear secondary structure
5. # diagram, which is exported as .svg for annotation in Inkscape.
6. pdb_frag A 1:84 4p5j.pdb 4p5j-nts.pdb
7. # extract the two helical axes from 4p5j.out to file: 4p5j.rot1
8. # then reorient the structure into the "L" shape: 4p5j.rot2
9. rotate_mol -t=4p5j.rot1 4p5j-nts.pdb 4p5j-rot1.pdb
10. rotate_mol -r=4p5j.rot2 4p5j-rot1.pdb 4p5j-ok.pdb
11.  
12. # Step #2 -- get the cartoon-block representation with the two
13. #            ls-fitted helical axes.
14. x3dna-dssr -i=4p5j-ok.pdb --helical-axis -o=temp
15. \mv dssr-helicalAxes.pdb 4p5j-ok-helices.pdb
16. x3dna-dssr -i=4p5j-ok.pdb --block-file -o=4p5j-ok-blocks.r3d
17.  
18. # Step #3 -- simplified representation of the [0,0,3,0,1] 5-way junction in 3D
19. #         -- note the --raw-xyz option: it keeps the original coordinates
20. x3dna-dssr -i=4p5j-ok.pdb --raw-xyz --simple-junction -o=temp
21. \mv dssr-simplifiedJcts.pdb 4p5j-ok-jct.pdb
22. #  see file: 4p5j-ok-jct.pml
23. pymol -qkc 4p5j-ok-jct.pml
24. convert -trim +repage -border 10 -bordercolor white 4p5j-ok-jct-pymol.png 4p5j-ok-jct.png
25. # see file: 4p5j-ok-full.pml (cartoon-block with the schematic junction overlaid)
26. pymol -qkc 4p5j-ok-full.pml
27. convert -trim +repage -border 10 -bordercolor white 4p5j-ok-full-pymol.png 4p5j-ok-full.png
28.  
29. # Step #4 -- get the linchpin interactions
30. pdb_frag A 1:2 A 40:42 A 13 A 73:75 4p5j-ok.pdb 4p5j-ok-linchpin.pdb
31. x3dna-dssr -i=4p5j-ok-linchpin.pdb --block-file -o=4p5j-ok-linchpin-blocks.r3d
32. pymol -qkc 4p5j-ok-linchpin.pml
33. convert -trim +repage -border 10 -bordercolor white 4p5j-ok-linchpin-pymol.png 4p5j-ok-linchpin.png
34.  
35. # Step #5 -- get the kissing loop interactions
36. pdb_frag A 8:12 A 48:54 4p5j-ok.pdb 4p5j-ok-loops.pdb
37. x3dna-dssr -i=4p5j-ok-loops.pdb --block-file -o=4p5j-ok-loops-blocks.r3d
38. pymol -qkc 4p5j-ok-loops.pml
39. convert -trim +repage -border 10 -bordercolor white 4p5j-ok-loops-pymol.png 4p5j-ok-loops.png

Here are the images generated from the above script: