Figure 2. Molecular images of RNA secondary structural motifs incorporating each

[shuxiang]

Figure 2. Molecular images of RNA secondary structural motifs incorporating each of the dominant modes of G·A base pairing. Motifs correspond to one of the common settings of the designated pairs: (a) sheared m–M pair closing the GNRA tetraloop at the end of the P4 helix of the glmS ribozyme bound to glucosamine 6-phosphate;(35) (b) imino W–W pair at the end of an asymmetric internal loop in the Thermus thermophilus 70S ribosome in complex with the hibernation factor pY;(36) (c) m+m pair linking the G in a double-helical stem and the A in an internal loop of the complex of Thermus thermophilus ribosomal protein L1 with a fragment of the L1 RNA from Methanoccocus vannielii;(37) (d) m–m pair joining a stem and single-stranded fragment within a three-way junction of the Thermoanaerobacter tengcongenesis ydaO riboswitch bound to cyclic di-AMP;(38) (e) m+W pair connecting the D and T hairpin loops of yeast initiator tRNA;(39) (f) m–W pair linking two hairpin loops of the 5S rRNA within the structure of the hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.(40) The G·A pairs are color-coded as in Figure 1 and shown at the nucleotide level within each structural element and in a separate local depiction to the right of each example. Loops are depicted in gold and canonical base pairs at the ends of loops or within double-helical stems in white. Ribbons connect phosphorus atoms in successive nucleotides. See Table S3 for Protein Data Bank identifiers, chain names, and residue numbers of the depicted pairs and Figure S2 for simple secondary structural diagrams of the associated motifs.

[shuxiang]

Figure 2.a
pymol 2Z75.cif
select AA, chain B and resi 111-120
select AAa, chain B and resi 114-117
select BB, chain B and resi 114+117
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, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain B and resi 114+117
zoom AA
set cartoon_ring_transparency, 1, 2Z75
set_color mycolor, [51,51,255]
set_color mycolor2, [255,178,102]
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC
show spheres,BB
set sphere_scale, 0.15
hide spheres, BB and name OP2+OP1
set cartoon_ring_transparency, 0, CC

[shuxiang]

Figure 2.b
pymol 4Y4O.cif
select AA, resi 605-612 or resi 628-633
select AAa, resi 606-611 or resi 629-632
select BB, resi 611+629
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, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, resi 611+629
zoom AA
set cartoon_ring_transparency, 1, 2-b
set_color mycolor, [160,160,160]
set_color mycolor2, [255,178,102]
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC
show spheres,BB
set sphere_scale, 0.15
hide spheres, BB and name OP2+OP1
set cartoon_ring_transparency, 0, CC

[shuxiang]

Figure 2.c
pymol 2HW8.cif
select AA, chain B and resi 7-15+20-32
select AAa, chain B and resi 11-12+23-28
select BB, chain B and resi 13+28
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, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain B and resi 13+28
zoom AA
set cartoon_ring_transparency, 1, 2HW8
set_color mycolor, [255,51,153]
set_color mycolor2, [255,178,102]
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC
show spheres,BB
set sphere_scale, 0.15
hide spheres, BB and name OP2+OP1
set cartoon_ring_transparency, 0, CC

[shuxiang]

Figure 2.d
pymol 4qlm.pdb
select AA, chain A and resi 42-49+64-72+81-89
select AAa, chain A and resi 44-47+66-67+86-87
select BB, chain A and resi 68+45
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, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain A and resi 68+45
zoom AA
set cartoon_ring_transparency, 1, 2-d
set_color mycolor, [255,51,51] #m-m
set_color mycolor2, [255,178,102] #loop
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC

[shuxiang]

Figure 2.e
pymol 1yfg.pdb
select AA, chain A and resi 12-23+52-62
select AAa, chain A and resi 53-61+14-21+54-60
select BB, chain A and resi 57+20
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, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain C and resi 922+946
zoom AA
set cartoon_ring_transparency, 1, 2-e
set_color mycolor, [51,153,255]
set_color mycolor2, [255,178,102]
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC

[shuxiang]

Figure 2.f
pymol 1il2.pdb
select AA, chain C and resi 903-970
select AAa, chain C and resi 908-909+913-922+926+932-938+944-948+954-960
select BB, chain C and resi 922+946
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, AA and name OP1 or name OP2
set cartoon_ladder_mode, 0, BB
create CC, chain C and resi 922+946
zoom AA
set cartoon_ring_transparency, 1, 2-f
set_color mycolor, [255,51,255]
set_color mycolor2, [255,178,102]
color white, AA
color mycolor2, AAa
color mycolor, BB
color mycolor, CC