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PDBsum entry 2e5l
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222 a.a.
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206 a.a.
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208 a.a.
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150 a.a.
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101 a.a.
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155 a.a.
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138 a.a.
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127 a.a.
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98 a.a.
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115 a.a.
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124 a.a.
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122 a.a.
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60 a.a.
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88 a.a.
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83 a.a.
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104 a.a.
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73 a.a.
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80 a.a.
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99 a.a.
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24 a.a.
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References listed in PDB file
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Key reference
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Title
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A snapshot of the 30s ribosomal subunit capturing mRNA via the shine-Dalgarno interaction.
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Authors
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T.Kaminishi,
D.N.Wilson,
C.Takemoto,
J.M.Harms,
M.Kawazoe,
F.Schluenzen,
K.Hanawa-Suetsugu,
M.Shirouzu,
P.Fucini,
S.Yokoyama.
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Ref.
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Structure, 2007,
15,
289-297.
[DOI no: ]
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PubMed id
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Abstract
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In the initiation phase of bacterial translation, the 30S ribosomal subunit
captures mRNA in preparation for binding with initiator tRNA. The purine-rich
Shine-Dalgarno (SD) sequence, in the 5' untranslated region of the mRNA, anchors
the 30S subunit near the start codon, via base pairing with an anti-SD (aSD)
sequence at the 3' terminus of 16S rRNA. Here, we present the 3.3 A crystal
structure of the Thermus thermophilus 30S subunit bound with an mRNA mimic. The
duplex formed by the SD and aSD sequences is snugly docked in a
"chamber" between the head and platform domains, demonstrating how the
30S subunit captures and stabilizes the otherwise labile SD helix. This location
of the SD helix is suitable for the placement of the start codon AUG in the
immediate vicinity of the mRNA channel, in agreement with reported crosslinks
between the second position of the start codon and G1530 of 16S rRNA.
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Figure 1.
Figure 1. Location of the SD Helix on the 30S Ribosomal
Subunit
(A–C) The rRNA and the ribosomal proteins are
colored light blue and pale pink, respectively. (A) Front
(subunit interface), side (rotated 145° counterclockwise),
and back (solvent) views of the 30S subunit, with the SD helix
accommodated in a cavity formed between the head (orange) and
platform (green) domains. Oligonucleotides (5′-GAAAGA-3′)
are colored yellow, and the 3′ end nucleotides of 16S rRNA
from A1534, which were clearly identified in the present
structure, but were disordered in previous structures, are
colored dark blue. (B) Stereo enlargement of the boxed region in
the side view of (A). RNA helices from the head (h28 and h37)
and platform (h23a and h26) domains are dark orange and dark
green, respectively. The ribosomal proteins surrounding the
cavity are colored salmon. (C) Stereo view of the SD helix
position on the 30S subunit, which is represented as a molecular
surface.
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Figure 2.
Figure 2. Stereo Representations of the SD Helix in the
Chamber on the 30S Subunit
(A) Close-up view. U723 and
G1530–A1531 are represented in magenta and cyan, respectively.
Other coloring is as in Figure 1A. The chamber defined by h26,
U723, G1530–A1531, and S2 is highlighted with a rectangle.
(B) Detailed view of the SD helix. The 2mF[o] − DF[c] map
contoured at 1.5σ shows unbiased density for the SD helix (not
included in the refinement). The U723 nucleotide (magenta) on
h23a of 16S rRNA faces the minor groove near the proximal end of
the SD helix. S18 is omitted for clarity.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2007,
15,
289-297)
copyright 2007.
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