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Author Topic: Supplementary Figure 9 -- comparison of diloops  (Read 1107 times)

Offline xiangjun

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Supplementary Figure 9 -- comparison of diloops
« on: July 08, 2015, 11:55:59 am »
"comparison of 15 diloops identified by DSSR" title="comparison of 15 diloops identified by DSSR"
Quote
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
« Last Edit: August 05, 2015, 05:43:52 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.