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PDBsum entry 3d5d
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Contents |
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271 a.a.
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204 a.a.
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202 a.a.
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181 a.a.
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159 a.a.
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145 a.a.
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32 a.a.
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137 a.a.
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122 a.a.
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146 a.a.
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136 a.a.
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117 a.a.
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98 a.a.
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137 a.a.
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117 a.a.
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101 a.a.
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112 a.a.
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92 a.a.
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100 a.a.
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188 a.a.
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76 a.a.
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88 a.a.
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72 a.a.
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59 a.a.
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30 a.a.
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52 a.a.
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44 a.a.
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48 a.a.
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63 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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Structural basis for translation termination on the 70s ribosome.
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Authors
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M.Laurberg,
H.Asahara,
A.Korostelev,
J.Zhu,
S.Trakhanov,
H.F.Noller.
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Ref.
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Nature, 2008,
454,
852-857.
[DOI no: ]
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PubMed id
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Abstract
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At termination of protein synthesis, type I release factors promote hydrolysis
of the peptidyl-transfer RNA linkage in response to recognition of a stop codon.
Here we describe the crystal structure of the Thermus thermophilus 70S ribosome
in complex with the release factor RF1, tRNA and a messenger RNA containing a
UAA stop codon, at 3.2 A resolution. The stop codon is recognized in a pocket
formed by conserved elements of RF1, including its PxT recognition motif, and
16S ribosomal RNA. The codon and the 30S subunit A site undergo an induced fit
that results in stabilization of a conformation of RF1 that promotes its
interaction with the peptidyl transferase centre. Unexpectedly, the main-chain
amide group of Gln 230 in the universally conserved GGQ motif of the factor is
positioned to contribute directly to peptidyl-tRNA hydrolysis.
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Figure 3.
Figure 3: Interactions of the GGQ region of RF1 in the PTC.
a, Stereo view of  [A]-weighted
3F[obs]–2F[calc] electron density for RF1 (yellow), P-site
tRNA (orange) and 23S rRNA (grey) contoured at 1.7 .
b, Position of Gln 230. c, Model for product stabilization by
hydrogen bonding between the main-chain amide of Gln 230 and the
3'-OH of A76 of the P-site tRNA. d, Superposition of a
peptidyl-transferase transition-state analogue (TSA, orange)
complexed with the 50S subunit (grey)^25 on the structure of the
termination complex (this work). The main-chain amide of Gln 230
is positioned to hydrogen bond with the oxyanion of the TSA. e,
Model for transition-state stabilization.
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Figure 4.
Figure 4: Stereo view of the RF1 binding pocket for 23S rRNA
nucleotide A2602. 23S rRNA is shown in grey, P-site tRNA in
orange and RF1 in yellow.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2008,
454,
852-857)
copyright 2008.
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