Supplementary Figure 2 -- three similar base pairs in tRNA and its mimic

[xiangjun]

Figure S2: Three similarly positioned base pairs that hold the D- and T-loops of tRNA^Phe (PDB id: 1ehz, gold) and its viral mimic (PDB id: 4p5j, magenta) in place. The interacting loops in the two molecules are overlaid on the reference frame of the common elbow G–C pair, which is oriented vertically with its major-groove edge facing the viewer, roughly matching Figures 2 and 3 (A-C). Since the two elbow G–C pairs have very similar base- pair parameters, they overlap nearly perfectly. Despite large structural variations between the D-loops, the H2U16+U59 pair in tRNA (B, detailed in D) is similar to the presumably semi-protonated C8+C52 pair (forming an i-motif) in the mimic (C, detailed in E). The other two pairs near the elbow (F and G) are also strikingly alike, despite dramatically different modes of interaction. Note that DSSR identifies the C+C pair (E) with the assumed acceptor-acceptor (N3 to N3) hydrogen bond highlighted (red).

Here is the complete script -- it looks quite involved. In essence, however, the logic is quite simple. This example takes advantage of some unique features from DSSR and 3DNA. See notes below.

Code: Bash

1. # commands for tRNA: 1ehz
2. pdb_frag A 13:22 A 53:61 1ehz.pdb 1ehz-kissingLoops.pdb
3.  
4. x3dna-dssr -i=1ehz-kissingLoops.pdb -o=1ehz-DT-mEdge.pdb --frame=A.G.19:wc+edge
5. rotate_mol -r=rotDT 1ehz-DT-mEdge.pdb 1ehz-DT.pdb
6.  
7. pdb_frag A 16 A 18:19 A 55:56 A 59 1ehz-DT.pdb 1ehz-DT-3bps.pdb
8. x3dna-dssr -i=1ehz-DT-3bps.pdb -o=1ehz-DT-3bps-blocks.r3d --block-file
9.  
10. pymol -qkc 1ehz-DT-3bps.pml
11. convert -trim +repage -border 10 -bordercolor white 1ehz-DT-3bps-pymol.png 1ehz-DT-3bps.png
12.  
13. x3dna-dssr -i=1ehz.pdb -o=1ehz.out --prefix=1ehz
14.  
15. ex_str -17 1ehz-pairs.pdb 1ehz-p17.pdb
16. x3dna-dssr -i=1ehz-p17.pdb -o=1ehz-p17.pml --hbfile-pymol
17. pymol -qkc 1ehz-p17.pml
18. convert -trim +repage -border 10 -bordercolor white 1ehz-p17-pymol.png 1ehz-p17.png
19.  
20. ex_str -18 1ehz-pairs.pdb 1ehz-p18.pdb
21. x3dna-dssr -i=1ehz-p18.pdb -o=1ehz-p18.pml --hbfile-pymol
22. pymol -qkc 1ehz-p18.pml
23. convert -trim +repage -border 10 -bordercolor white 1ehz-p18-pymol.png 1ehz-p18.png
24.  
25. #------------------------------------------------------------------
26.  
27. # commands for tRNA mimic: 4p5j
28. pdb_frag A 7:14 A 46:54 4p5j.pdb 4p5j-kissingLoops.pdb
29.  
30. x3dna-dssr -i=4p5j-kissingLoops.pdb -o=4p5j-DT-mEdge.pdb --frame=A.G.10:wc+edge
31. rotate_mol -r=rotDT 4p5j-DT-mEdge.pdb 4p5j-DT.pdb
32.  
33. pdb_frag A 8:10 A 48:49 A 52 4p5j-DT.pdb 4p5j-DT-3bps.pdb
34. x3dna-dssr -i=4p5j-DT-3bps.pdb -o=4p5j-DT-3bps-blocks.r3d --block-file
35.  
36. pymol -qkc 4p5j-DT-3bps.pml
37. convert -trim +repage -border 10 -bordercolor white 4p5j-DT-3bps-pymol.png 4p5j-DT-3bps.png
38.  
39. x3dna-dssr -i=4p5j.pdb -o=4p5j.out --prefix=4p5j
40.  
41. ex_str -7 4p5j-pairs.pdb 4p5j-p7.pdb
42. x3dna-dssr -i=4p5j-p7.pdb -o=4p5j-p7.pml --hbfile-pymol
43. pymol -qkc 4p5j-p7.pml
44. convert -trim +repage -border 10 -bordercolor white 4p5j-p7-pymol.png 4p5j-p7.png
45.  
46. ex_str -8 4p5j-pairs.pdb 4p5j-p8.pdb
47. x3dna-dssr -i=4p5j-p8.pdb -o=4p5j-p8.pml --hbfile-pymol
48. pymol -qkc 4p5j-p8.pml
49. convert -trim +repage -border 10 -bordercolor white 4p5j-p8-pymol.png 4p5j-p8.png
50.  
51. #------------------------------------------------------------------
52.  
53. # combined image
54. pymol -qkc compare-DT-3bps.pml
55. convert -trim +repage -border 10 -bordercolor white compare-DT-3bps-pymol.png compare-DT-3bps.png

Note:

• The pdb_frag utility program is distribute with 3DNA. It can be used to extract fragments (here the D- and T-loops) based on chain id and residue numbers from a given PDB file.
• The --frame option is used to reorient a structure based on specific base or base-pair reference frame. For example, "--frame=A.G.19:wc+edge" sets the kissing-loops in tRNA (1ehz) to the minor-groove edge of the Watson-Crick base-pair formed by G19 on chain A (with C56). Similar functionality may be achieved with "analyze/frame_mol/rotate_mol" using 3DNA. I have integrated some of the useful features into DSSR, mostly for personal convenience.
• The DSSR --hbfile-pymol option is used to generate a .pml file with all required settings for rendering in PyMOL.
• The DSSR --block-file option creates a .r3d file with bases (or Watson-Crick base pairs) in rectangular block represention.
• 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-fig2-tRNA-vs-mimic-3bps.tar.gz

Here are the images generated from the above script: