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PDBsum entry 2qnh
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234 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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116 a.a.
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124 a.a.
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125 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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81 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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Interactions and dynamics of the shine dalgarno helix in the 70s ribosome.
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Authors
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A.Korostelev,
S.Trakhanov,
H.Asahara,
M.Laurberg,
L.Lancaster,
H.F.Noller.
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Ref.
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Proc Natl Acad Sci U S A, 2007,
104,
16840-16843.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of an initiation-like 70S ribosome complex containing an
8-bp Shine-Dalgarno (SD) helix was determined at 3.8-A resolution.
Translation-libration-screw analysis showed that the inherent anisotropic
motions of the SD helix were biased along its helical axis, suggesting that
during the first step of translocation, the SD helix moves along its helical
screw axis. Contacts between the SD helix and the ribosome were primarily
through interactions with helices 23a, 26, and 28 of 16S rRNA. Contact with the
neck (helix 28) of the 30S subunit near its hinge point suggests that formation
of the SD helix could affect positioning of the head of the 30S subunit for
optimal interaction with initiator tRNA. The bulged U723 in helix 23a interacts
with the minor groove of the SD helix at the C1539.G-10 base pair, explaining
its selective conservation in bacteria and archaea.
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Figure 1.
Fig. 1. Structure and dynamics of the SD helix. (a) (Upper)
Nucleotide sequences and base pairing between mRNA and 16S rRNA
in the initiation-like 70S ribosome complex. SD sequence,
initiator codon, and anti-SD sequences are shown in bold; shaded
nucleotides are disordered in the refined x-ray structure.
(Lower) Stereoview of the fit of the SD helix to a composite
omit density map calculated with  [A]-weighted (2F[o] –
F[c]) coefficients contoured at 1.2 . (b) Stereoview of the
nonintersecting screw axes (blue) for the SD helix (yellow). The
length of each axis is proportional to its respective
mean-square displacement value. The primary screw axis is
indicated by a rotational arrow. (c) Thermal ellipsoid
representation of the librational motions of the SD helix around
the dominant screw axis coinciding with the SD helical axis.
Atomic displacement parameters for the SD helix calculated from
the TLS model are colored according to the magnitude of the
displacements, increasing from blue (smallest) to red (largest).
The view is from the upstream end of the helix.
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Figure 3.
Fig. 3. Interactions of the SD helix with the ribosome. (a)
Location of the SD helix (yellow) relative to the structure of
16S rRNA in the 70S ribosome initiation-like complex. Helices
23a, 26, and 28, which contact the SD helix, are rendered in
dark blue ribbon representations, and the SD helix is shown in
yellow. (b) Interactions of the SD helix with helices 23a, 26,
and 28 of 16S rRNA. The P-site tRNA is shown in orange. (c)
Secondary structure of T. thermophilus 16S rRNA, showing in bold
the anti-SD region at the 3' end and structural features
(helices 23a, 26, and 28) that interact with the SD helix.
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