Figure 5 -- analysis of the SAM-I riboswitch (2gis)

[xiangjun]

Figure 5: DSSR pinpoints a linchpin-like U64–A85 pair that is shared by a four-way and a five-way junction loop in the S-adenosyl methionine I riboswitch (PDB id: 2gis (45)). (A) DSSR identifies two junction loops (right): a [4,0,3,0] four-way junction loop (red) and a [1,0,2,0,0] five-way junction loop (blue), which share a common side, i.e., the isolated U64–A85 pair (left). (B) The linear secondary structure diagram, annotated with DSSR-derived dot-bracket notation, depicts the pathways of the two junction loops. The four-way loop runs from C8 (*), follows the red arrows to the right, and returns along the outer G86→C8 arc. The five-way loop starts at G23 (*), moves to the right following the blue arrows along two arcs (C25→G68 and C69→G82), and returns to the start along three arcs (A85→U64, C65→G28, C29→G23). Note that the shared U64–A85 arc is traversed twice, from left to right along the four-way junction loop, and right to left along the five-way junction loop. (C) The U64–A85 pair is stabilized by base-stacking interactions in a way strikingly similar to the G2–C74 linchpin pair in the viral tRNA mimic (see Figure 3), and may also be regarded as a ‘linchpin’. These two images take advantage of unique visualization features within 3DNA/DSSR, including the capability to orient different molecules in a common frame (here, the frames of the linchpin pairs with the minor-groove edges facing the viewer) and to represent bases as color-coded rectangular blocks.

Here is the tarball (fig5-SAM-I-2gis.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 SAM-I riboswitch into the most extended view
2. pdb_frag A 1:94 A 301 2gis.pdb 2gis-nts.pdb
3. rotate_mol 2gis-nts.pdb temp
4. rotate_mol -r=2gis.rot temp 2gis-ok.pdb
5. x3dna-dssr -i=2gis-ok.pdb --prefix=2gis-ok -o=2gis-ok.out
6.  
7. # To get the result illustrated in panel B, load '2gis-ok-2ndstrs.ct'
8. # or '2gis-ok-2ndstrs.dbn' into VARNA to draw the linear secondary
9. # structure diagram, exported as .svg for annotation in Inkscape.
10.  
11. # Step #2 -- get the cartoon-block representation, with fitted helices
12. x3dna-dssr -i=2gis-ok.pdb --helical-axis -o=temp
13. \mv dssr-helicalAxes.pdb 2gis-ok-helices.pdb
14. x3dna-dssr -i=2gis-ok.pdb --block-file -o=2gis-ok-blocks.r3d
15.  
16. # Step #3 -- simplified representation of the [4,0,3,0] 4-way
17. #            and [1,0,2,0,0] 5-way junctions in 3D
18. #   note the '--raw-xyz' option: it keeps the original coordinates
19. x3dna-dssr -i=2gis-ok.pdb --raw-xyz --simple-junction -o=temp
20. \mv dssr-simplifiedJcts.pdb 2gis-ok-jctx.pdb
21. ex_str -1 2gis-ok-jctx.pdb 2gis-ok-jct.pdb  # 4-way junction
22. ex_str -2 2gis-ok-jctx.pdb 2gis-ok-jct2.pdb # 5-way junction
23.  
24. # see file: 2gis-ok-jct.pml
25. pymol -qkc 2gis-ok-jct.pml
26. convert -trim +repage -border 10 -bordercolor white 2gis-ok-jct-pymol.png 2gis-ok-jct.png
27.  
28. # see file: 2gis-ok-full.pml (cartoon-block with the schematic
29. #                            junctions overlaid) -- panel A
30. pymol -qkc 2gis-ok-full.pml
31. convert -trim +repage -border 10 -bordercolor white 2gis-ok-full-pymol.png 2gis-ok-full.png
32.  
33. # Step #4 -- pair U64-A85 stablized by base-stacking interactions
34. pdb_frag A 63:65 A 82:86 2gis-ok.pdb 2gis-ok-UA.pdb
35. x3dna-dssr -i=2gis-ok-UA.pdb --block-file -o=2gis-ok-UA-blocks.r3d
36. # see file: 2gis-ok-UA.pml
37. pymol -qkc 2gis-ok-UA.pml
38. convert -trim +repage -border 10 -bordercolor white 2gis-ok-UA-pymol.png 2gis-ok-UA.png
39.  
40. # Step #5 -- the U64-A85 isolated pair is linchpin-like (panel C)
41. x3dna-dssr -i=2gis-ok-UA.pdb --frame=A.64:wc+edge -o=2gis-stacks.pdb
42. x3dna-dssr -i=2gis-stacks.pdb --block-file -o=2gis-stacks-blocks.r3d
43. # see file: 2gis-stacks.pml
44. pymol -qkc 2gis-stacks.pml
45. convert -trim +repage -border 10 -bordercolor white 2gis-stacks-pymol.png 2gis-stacks.png
46.  
47. x3dna-dssr -i=4p5j-ok-linchpin.pdb --frame=A.74:wc+edge -o=4p5j-stacks.pdb
48. x3dna-dssr -i=4p5j-stacks.pdb --block-file -o=4p5j-stacks-blocks.r3d
49. # see file: 4p5j-stacks.pml
50. pymol -qkc 4p5j-stacks.pml
51. convert -trim +repage -border 10 -bordercolor white 4p5j-stacks-pymol.png 4p5j-stacks.png

Here are the images generated from the above script: