Supplementary Figure 9 -- comparison of diloops

[xiangjun]

Figure S9: Images of 15 diloops (GGUC, CARG, CUUG, CUAG, and UUKA) identified by DSSR in the NR3A-dataset. The diloops can be categorized into five groups by base sequence: GGUC, where the second position G is flipped away from the closing pair; CARG, where the second position A is extruded into the minor-groove side of the closing pair; CUUG, which shows structural variations in the three crystallographic examples and differences from their NMR solution counterpart (PDB id: 1rng, Figure 6C); CUAG, where all four cases occur in Cas9 complexes either without (PDB id: 4oo8) or with (PDB ids: 4un3 and 4un5) a protospacer adjacent motif; and UUKA, where the two cases are quite distinct.

The file 'all-diloops.txt' contains a collection of all diloops identified by DSSR in the non-redundant dataset of RNA crystal structures solved at 3.0 Å or better resolution (referred to as the NR3A-dataset in the paper, release 1.89 on 5 December 2014). The corresponding file 'all-diloops.pdb' contains all the 15 diloops in a MODEL/ENDMDL ensemble where each one is re-oriented with the minor-groove edge of the closing Watson-Crick base pair facing the viewer. So for the diloop from chain B of 4oo8 (a CRISPR Cas9 ternary complex), which has the following info in 'all-diloops.txt':

Code: [Select]

4oo8    2 nts=4 CUAG B.C55,B.U56,B.A57,B.G58  C3',C2',C2',C3'  anti,anti,anti,anti
the transformation option is: --frame=B.55:wc+edge. The transformed diloops (stored in 'all-diloops.pdb') now share the same view for direct comparison.

With all the diloops in proper orientation, the following scripts ("tasks") generates each diloop image in png format.

Code: Bash

1. ex_str -1 all-diloops.pdb 2f8k-1-UUGA.pdb
2. x3dna-dssr -i=2f8k-1-UUGA.pdb -o=2f8k-1-UUGA-blocks.r3d --block-file
3. pymol -qkc 2f8k-1-UUGA.pml
4. convert -trim +repage -border 10 -bordercolor white 2f8k-1-UUGA-pymol.png 2f8k-1-UUGA.png
5.  
6. ex_str -2 all-diloops.pdb 2pjp-1-GGUC.pdb
7. x3dna-dssr -i=2pjp-1-GGUC.pdb -o=2pjp-1-GGUC-blocks.r3d --block-file
8. pymol -qkc 2pjp-1-GGUC.pml
9. convert -trim +repage -border 10 -bordercolor white 2pjp-1-GGUC-pymol.png 2pjp-1-GGUC.png
10.  
11. ex_str -3 all-diloops.pdb 2ply-1-GGUC.pdb
12. x3dna-dssr -i=2ply-1-GGUC.pdb -o=2ply-1-GGUC-blocks.r3d --block-file
13. pymol -qkc 2ply-1-GGUC.pml
14. convert -trim +repage -border 10 -bordercolor white 2ply-1-GGUC-pymol.png 2ply-1-GGUC.png
15.  
16. ex_str -4 all-diloops.pdb 2ply-2-GGUC.pdb
17. x3dna-dssr -i=2ply-2-GGUC.pdb -o=2ply-2-GGUC-blocks.r3d --block-file
18. pymol -qkc 2ply-2-GGUC.pml
19. convert -trim +repage -border 10 -bordercolor white 2ply-2-GGUC-pymol.png 2ply-2-GGUC.png
20.  
21. ex_str -5 all-diloops.pdb 2zjr-40-CAAG.pdb
22. x3dna-dssr -i=2zjr-40-CAAG.pdb -o=2zjr-40-CAAG-blocks.r3d --block-file
23. pymol -qkc 2zjr-40-CAAG.pml
24. convert -trim +repage -border 10 -bordercolor white 2zjr-40-CAAG-pymol.png 2zjr-40-CAAG.png
25.  
26. ex_str -6 all-diloops.pdb 3u5f-7-CUUG.pdb
27. x3dna-dssr -i=3u5f-7-CUUG.pdb -o=3u5f-7-CUUG-blocks.r3d --block-file
28. pymol -qkc 3u5f-7-CUUG.pml
29. convert -trim +repage -border 10 -bordercolor white 3u5f-7-CUUG-pymol.png 3u5f-7-CUUG.png
30.  
31. ex_str -7 all-diloops.pdb 3u5h-69-CUUG.pdb
32. x3dna-dssr -i=3u5h-69-CUUG.pdb -o=3u5h-69-CUUG-blocks.r3d --block-file
33. pymol -qkc 3u5h-69-CUUG.pml
34. convert -trim +repage -border 10 -bordercolor white 3u5h-69-CUUG-pymol.png 3u5h-69-CUUG.png
35.  
36. ex_str -8 all-diloops.pdb 3u5h-72-CUUG.pdb
37. x3dna-dssr -i=3u5h-72-CUUG.pdb -o=3u5h-72-CUUG-blocks.r3d --block-file
38. pymol -qkc 3u5h-72-CUUG.pml
39. convert -trim +repage -border 10 -bordercolor white 3u5h-72-CUUG-pymol.png 3u5h-72-CUUG.png
40.  
41. ex_str -9 all-diloops.pdb 4kj9-40-CAGG.pdb
42. x3dna-dssr -i=4kj9-40-CAGG.pdb -o=4kj9-40-CAGG-blocks.r3d --block-file
43. pymol -qkc 4kj9-40-CAGG.pml
44. convert -trim +repage -border 10 -bordercolor white 4kj9-40-CAGG-pymol.png 4kj9-40-CAGG.png
45.  
46. ex_str -10 all-diloops.pdb 4kj9-69-UUUA.pdb
47. x3dna-dssr -i=4kj9-69-UUUA.pdb -o=4kj9-69-UUUA-blocks.r3d --block-file
48. pymol -qkc 4kj9-69-UUUA.pml
49. convert -trim +repage -border 10 -bordercolor white 4kj9-69-UUUA-pymol.png 4kj9-69-UUUA.png
50.  
51. ex_str -11 all-diloops.pdb 4oo8-2-CUAG.pdb
52. x3dna-dssr -i=4oo8-2-CUAG.pdb -o=4oo8-2-CUAG-blocks.r3d --block-file
53. pymol -qkc 4oo8-2-CUAG.pml
54. convert -trim +repage -border 10 -bordercolor white 4oo8-2-CUAG-pymol.png 4oo8-2-CUAG.png
55.  
56. ex_str -12 all-diloops.pdb 4oo8-6-CUAG.pdb
57. x3dna-dssr -i=4oo8-6-CUAG.pdb -o=4oo8-6-CUAG-blocks.r3d --block-file
58. pymol -qkc 4oo8-6-CUAG.pml
59. convert -trim +repage -border 10 -bordercolor white 4oo8-6-CUAG-pymol.png 4oo8-6-CUAG.png
60.  
61. ex_str -13 all-diloops.pdb 4qcn-37-CAAG.pdb
62. x3dna-dssr -i=4qcn-37-CAAG.pdb -o=4qcn-37-CAAG-blocks.r3d --block-file
63. pymol -qkc 4qcn-37-CAAG.pml
64. convert -trim +repage -border 10 -bordercolor white 4qcn-37-CAAG-pymol.png 4qcn-37-CAAG.png
65.  
66. ex_str -14 all-diloops.pdb 4un3-2-CUAG.pdb
67. x3dna-dssr -i=4un3-2-CUAG.pdb -o=4un3-2-CUAG-blocks.r3d --block-file
68. pymol -qkc 4un3-2-CUAG.pml
69. convert -trim +repage -border 10 -bordercolor white 4un3-2-CUAG-pymol.png 4un3-2-CUAG.png
70.  
71. ex_str -15 all-diloops.pdb 4un5-2-CUAG.pdb
72. x3dna-dssr -i=4un5-2-CUAG.pdb -o=4un5-2-CUAG-blocks.r3d --block-file
73. pymol -qkc 4un5-2-CUAG.pml
74. convert -trim +repage -border 10 -bordercolor white 4un5-2-CUAG-pymol.png 4un5-2-CUAG.png
75.  

Note:

• For the aforementioned diloop from chain B of 4oo8, the png image is named 4oo8-2-CUAG.png (see the script above) and is shown below:
  .
• The ex_str utility program is from the 3DNA distribution. It is used to extract a specific model from a MODEL/ENDMDL ensemble.
• The --block-file option generates a .r3d file with base rectangular blocks for rendering in PyMOL.
• The convert program is from ImageMagick that is used here to trim extra white boundaries.
• The 15 diloop-png images 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-fig9-diloops.tar.gz