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Questions and answers > DSSR-NAR paper
Figure 5 -- analysis of the SAM-I riboswitch (2gis)
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xiangjun:
--- Quote ---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.
--- End quote ---
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 ---# Step #1 -- reorient SAM-I riboswitch into the most extended viewpdb_frag A 1:94 A 301 2gis.pdb 2gis-nts.pdbrotate_mol 2gis-nts.pdb temprotate_mol -r=2gis.rot temp 2gis-ok.pdbx3dna-dssr -i=2gis-ok.pdb --prefix=2gis-ok -o=2gis-ok.out # To get the result illustrated in panel B, load '2gis-ok-2ndstrs.ct'# or '2gis-ok-2ndstrs.dbn' into VARNA to draw the linear secondary# structure diagram, exported as .svg for annotation in Inkscape. # Step #2 -- get the cartoon-block representation, with fitted helicesx3dna-dssr -i=2gis-ok.pdb --helical-axis -o=temp\mv dssr-helicalAxes.pdb 2gis-ok-helices.pdbx3dna-dssr -i=2gis-ok.pdb --block-file -o=2gis-ok-blocks.r3d # Step #3 -- simplified representation of the [4,0,3,0] 4-way# and [1,0,2,0,0] 5-way junctions in 3D# note the '--raw-xyz' option: it keeps the original coordinatesx3dna-dssr -i=2gis-ok.pdb --raw-xyz --simple-junction -o=temp\mv dssr-simplifiedJcts.pdb 2gis-ok-jctx.pdbex_str -1 2gis-ok-jctx.pdb 2gis-ok-jct.pdb # 4-way junctionex_str -2 2gis-ok-jctx.pdb 2gis-ok-jct2.pdb # 5-way junction # see file: 2gis-ok-jct.pmlpymol -qkc 2gis-ok-jct.pmlconvert -trim +repage -border 10 -bordercolor white 2gis-ok-jct-pymol.png 2gis-ok-jct.png # see file: 2gis-ok-full.pml (cartoon-block with the schematic# junctions overlaid) -- panel Apymol -qkc 2gis-ok-full.pmlconvert -trim +repage -border 10 -bordercolor white 2gis-ok-full-pymol.png 2gis-ok-full.png # Step #4 -- pair U64-A85 stablized by base-stacking interactionspdb_frag A 63:65 A 82:86 2gis-ok.pdb 2gis-ok-UA.pdbx3dna-dssr -i=2gis-ok-UA.pdb --block-file -o=2gis-ok-UA-blocks.r3d# see file: 2gis-ok-UA.pmlpymol -qkc 2gis-ok-UA.pmlconvert -trim +repage -border 10 -bordercolor white 2gis-ok-UA-pymol.png 2gis-ok-UA.png # Step #5 -- the U64-A85 isolated pair is linchpin-like (panel C)x3dna-dssr -i=2gis-ok-UA.pdb --frame=A.64:wc+edge -o=2gis-stacks.pdbx3dna-dssr -i=2gis-stacks.pdb --block-file -o=2gis-stacks-blocks.r3d# see file: 2gis-stacks.pmlpymol -qkc 2gis-stacks.pmlconvert -trim +repage -border 10 -bordercolor white 2gis-stacks-pymol.png 2gis-stacks.png x3dna-dssr -i=4p5j-ok-linchpin.pdb --frame=A.74:wc+edge -o=4p5j-stacks.pdbx3dna-dssr -i=4p5j-stacks.pdb --block-file -o=4p5j-stacks-blocks.r3d# see file: 4p5j-stacks.pmlpymol -qkc 4p5j-stacks.pmlconvert -trim +repage -border 10 -bordercolor white 4p5j-stacks-pymol.png 4p5j-stacks.png
Here are the images generated from the above script:
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
