Figure 6. Molecular images of multiplets with two or more modes of G·A

[shuxiang]

Figure 6. Molecular images of multiplets with two or more modes of G·A pairing in the complex of tetracycline with the U1052G-mutated 70S Escherichia coli ribosome.(69) Loops incorporating m–M sheared pairs are linked by different associations of G and A (highlighted within boxes) to other secondary structural units. A local representation of the linked bases is shown below each global depiction of associated secondary structures. Examples include (a) tetraplex with m+m pairing between a hairpin loop and a double-helical stem, (b) tetraplex with m+m pairing between an internal loop and a double-helical stem, (c) pentaplex with m+W pairing between a hairpin loop and a double-helical stem that is linked in turn to a junction, (d) tetraplex with m–m link pairing between an internal loop and a 5-way junction, (e) triplex with m–W pairing between a hairpin loop and a 3-way junction, and (f) pentaplex with .–M and m–W pairing within a 7-way junction. G·A pairs and secondary structural motifs are color-coded as in Figure 2. See Table S3 for respective Protein Data Bank identifiers, chain names, and residue numbers of depicted G·A-linked multiplets. Color-coding of bases and hydrogen bonds matches that in the corresponding secondary structural diagrams in Figure S8.

[shuxiang]

(a)pymol 5j7l.cif
create AA, chain DA and resi 2855-2862+1707-1712+1746-1751
select AAa, chain DA and resi 2855-2862
select AAb, chain DA and resi 1707-1712+1746-1751
select BB, chain DA and resi 2857+2860+1750+1708
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, BB and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain DA and resi 2857+2860+1750+1708
zoom AA
set cartoon_ring_transparency, 1, AA
set_color mycolor4, [255,51,51]
set_color mycolor, [255,51,153]
set_color mycolor3, [51,51,255]
set_color mycolor2, [255,178,102]
color mycolor2, AAa
color white, AAb
color mycolor4, chain DA and resi 2857+2860
color mycolor4, chain DA and resi 2860+1750
color mycolor4, chain DA and resi 1708
color white, chain DA and resi 2855+2862+2856+2861

hide everything, not BB or CC
set cartoon_ring_transparency, 0.5, all
set_color mycolor4, [255,51,51]
color mycolor4, all
zoom BB

[shuxiang]

(b)pymol 5j7l.cif
select AA, chain DA and resi 2806-2814+2886-2892+2630-2636+2782-2788
select AAa, chain DA and resi 2806-2814+2886-2892
select AAb, chain DA and resi 2630-2636+2782-2788
select BB, chain DA and resi 2890+2810+2631+2787
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
zoom AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, BB and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, resi 2890+2810+2631+2787
zoom AA
set cartoon_ring_transparency, 1, AA
set_color mycolor, [255,51,153]
set_color mycolor3, [51,51,255]
set_color mycolor2, [255,178,102]
color mycolor2, AAa
color white, AAb
set_color mycolor4, [255,51,51]
color mycolor4, resi 2890+2810
color mycolor4, resi 2810+2631
color mycolor4, resi 2787
color white, resi 2806+2811-2814+2886-2889+2892

hide everything, not BB or CC
set cartoon_ring_transparency, 0.5, all
set_color mycolor4, [255,51,51] #red
color mycolor4, all
zoom BB

[shuxiang]

(c) pymol 5j7l.cif
select AA, chain DA and resi 2592-2601+2071-2074+2435-2438+2074-2080+2240-2248+2256-2261+2279-2284+2425-2435
select AAa, chain DA and resi 2592-2601
select AAb, chain DA and resi 2071-2074+2435-2438
select AAc, chain DA and resi 2074-2080+2240-2248+2256-2261+2279-2284+2425-2435
select BB, chain DA and resi 2595+2598+2436+2073+2245
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
zoom AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, BB and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, resi 2595+2598+2436+2073+2245
zoom AA
set cartoon_ring_transparency, 1, 6-c

set_color mycolor, [51,153,255]
set_color mycolor3, [51,51,255]
set_color mycolor2, [255,178,102]
color mycolor2, AAa
color mycolor2, AAc
color white, AAb
set_color mycolor4, [255,51,51]
color mycolor4, resi 2595+2598
color mycolor4, resi 2598+2436
color mycolor4, resi 2073+2245
color white, resi 2592-2593+2600-2601+2240-2242+2078-2080+2246-2248+2256-2258+2259-2261+2279-2281

hide everything, not BB or CC
set cartoon_ring_transparency, 0.5, all
set_color mycolor4, [255,51,51] #red
color mycolor4, all
zoom BB

[shuxiang]

(d) pymol 5j7l.cif
create AA, chain DA and resi 583-589+668-671+809-813+1194-1198+1248-1257+672-674+806-808
select AAa, chain DA and resi 583-589+668-671+809-813+1194-1198+1248-1257
select AAb, chain DA and resi 672-674+806-808
select BB, chain DA and resi 585+1254+808+672
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
zoom AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, BB and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain DA and resi 585+1254+808+672
zoom AA
set cartoon_ring_transparency, 1, AA
set_color mycolor, [255,51,51]
set_color mycolor3, [51,51,255]
set_color mycolor2, [255,178,102]
color mycolor2, AAa
color mycolor2, AAb
set_color mycolor4, [255,51,51] #red
color mycolor4, chain DA and resi 585+1254
color mycolor4, chain DA and resi 1254+808
color mycolor4, chain DA and resi 672
color white, chain DA and resi 673+674+806+807+809+588+589+668+670+671+583+584+1256+1257+1248+1249+1250+812+813+1194-1198

hide everything, not BB or CC
set cartoon_ring_transparency, 0.5, all
set_color mycolor4, [255,51,51]
color mycolor4, allzoom BB

[shuxiang]

(e)pymol 5j7l.cif
create AA, chain DA and resi 696-702+730-736+760-764+1628-1638
select AAa, chain DA and resi 696-702+730-736+760-764
select AAb, chain DA and resi 1628-1638
select BB, chain DA and resi 699+733+1633
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
zoom AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, BB and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain DA and resi 699+733+1633
zoom AA
set cartoon_ring_transparency, 1, AA
set_color mycolor, [255,51,255]
set_color mycolor3, [51,51,255]
set_color mycolor2, [255,178,102]
color mycolor2, AAa
color mycolor2, AAb
set_color mycolor4, [255,51,51] #red
color mycolor4, chain DA and resi 699+733
color mycolor4, chain DA and resi 699+733
color mycolor4, chain DA and resi 699+1633
color white, chain DA and resi 1628-1630+1636-1638+700-702+730-732+735+736+760+761+698+763

hide everything, not BB or CC
set cartoon_ring_transparency, 0.5, all
set_color mycolor4, [255,51,51]
color mycolor4, all
zoom BB

[shuxiang]

(f)pymol 5j7l.cif
create AA, chain DA and resi 296-302+315-342
select AAa, chain DA and resi 296-302+315-342
select BB, chain DA and resi 323+319+299+338+324
bg_color white
set ray_opaque_background, off
set ray_shadows,off
hide all
show cartoon, AA
zoom AA
cartoon oval
set cartoon_oval_length, 1.0
set cartoon_oval_width, 0.2
set cartoon_ring_finder,2
set cartoon_ring_mode,3
set cartoon_ladder_mode,1
set cartoon_ring_width, 0.1
show sticks, BB
set valence, 0
set stick_radius=0.12
hide sticks, BB and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain DA and resi 323+319+299+338+324
zoom AA
set cartoon_ring_transparency, 1, AA
set_color mycolor, [255,51,255]
set_color mycolor3, [51,51,255]
set_color mycolor2, [255,178,102]
color mycolor2, AAa
set_color mycolor4, [255,51,51]
color mycolor4, chain DA and resi 338+324
color mycolor4, chain DA and resi 319+299
color mycolor4, chain DA and resi 323
color white, chain DA and resi 325-328+332-337+296-298+340+342+315-318+301+302

hide everything, not BB or CC
set cartoon_ring_transparency, 0.5, all
set_color mycolor4, [255,51,51]
zoom BB
set cartoon_oval_width, 0.0
set cartoon_oval_length, 0.0