Figure 3

[xiangjun]

Figure 3. Sample molecular images illustrating selected RNA structural features enabled by the DSSR-Jmol integration. (A) Structure of yeast phenylalanine tRNA (PDB id: 1ehz) in step diagram with bases labeled, highlighting (in red) the [2,1,5,0] four-way junction loop in 3D. (B) Structure of the Pistol self-cleaving ribozyme (PDB id: 5ktj), showcasing (in red) the vertical helix in space-filling representation. The helix is composed of six short stems stabilized via coaxial stacking interactions. (C) Structure of the xpt-pbuX guanine riboswitch in complex with hypoxanthine (PDB id: 4fe5) in ‘base blocks’ representation. The three-way junction loop encompassing the metabolite (in space-filling representation) is color-coded by base identity: A, red; C, yellow; G, green; U, cyan. The loop-loop interaction (a kissing-loop motif) at the top is highlighted in red. (D) Structure of the yeast GAL4 protein-DNA complex (PDB id: 1d66) in Jmol cartoon representation. DNA is color-coded by DSSR stems, and protein is in translucent brown. The DNA helix is broken into two stems due to a non-Watson-Crick pair (G11 with C28 in gray) in the middle. (E) Structure of the Thermus thermophilus 30S ribosomal subunit in complex with the antibiotics (PDB id: 1fjg) using a step diagram. The 16S ribosomal RNA is color-coded in spectrum with the 5'-end in blue and the 3'-end in red.

Figure 3A (Jmol script: 1ehz.scr):

Code: [Select]

load =1ehz/dssr
select nucleic; display nucleic
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
set fontSize 4
background white; color grey
select nucleic and leadAtom; spacefill 1.5
label %[group1]; set labeloffset 0 0; color labels yellow
select junctions; color red
select selected and *.P; label %n%r; color label black; set labeloffset 0 0; set labelfront;
select @{_M.dssr.nts.select("where is_modified")} and *.P; color label blue
Figure 3B (Jmol script: 5ktj.scr):

Code: [Select]

load =5ktj/dssr
cartoon only
select nts; display nts
set cartoonsteps off
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select within(dssr, "helices..2"); color red; cpk
rotate best; rotate z -90; rotate y 90
Figure 3C (Jmol script: 4ef5.scr):

Code: [Select]

load =4fe5/dssr
select nts; display nts
rotate best; rotate z 90; rotate y 50
cartoon only
set cartoonsteps off
set cartoonblocks on
set antialiasdisplay on
background white; color grey
select within(dssr, "junctions..1"); color nucleic
select within(dssr, "junctions..2"); color red
select HPA; cpk; color cpk
Figure 3D (Jmol script: 1d66.scr):

Code: [Select]

load =1d66/dssr
cartoon only
set cartoonsteps off
set cartoonblocks off
set antialiasdisplay on
background white; color grey
color property DSSR stems
select protein; color TRANSLUCENT 0.9 brown
Figure 3E (Jmol script: 1fjg.scr):

Code: [Select]

load 1fjg.pdb
calculate structure dssr
cartoon only
select nts; display nts
rotate best
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color monomer