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PDBsum entry 1qzc
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RNA binding protein/RNA
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PDB id
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1qzc
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References listed in PDB file
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Key reference
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Title
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Incorporation of aminoacyl-Trna into the ribosome as seen by cryo-Electron microscopy.
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Authors
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M.Valle,
A.Zavialov,
W.Li,
S.M.Stagg,
J.Sengupta,
R.C.Nielsen,
P.Nissen,
S.C.Harvey,
M.Ehrenberg,
J.Frank.
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Ref.
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Nat Struct Biol, 2003,
10,
899-906.
[DOI no: ]
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PubMed id
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Abstract
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Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary
complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a
cryo-electron microscopy (cryo-EM) study, at a resolution of approximately 9 A,
showing that during the incorporation of the aa-tRNA into the 70S ribosome of
Escherichia coli, the flexibility of aa-tRNA allows the initial codon
recognition and its accommodation into the ribosomal A site. In addition, a
conformational change observed in the GTPase-associated center (GAC) of the
ribosomal 50S subunit may provide the mechanism by which the ribosome promotes a
relative movement of the aa-tRNA with respect to EF-Tu. This relative
rearrangement seems to facilitate codon recognition by the incoming aa-tRNA, and
to provide the codon-anticodon recognition-dependent signal for the GTPase
activity of EF-Tu. From these new findings we propose a mechanism that can
explain the sequence of events during the decoding of mRNA on the ribosome.
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Figure 2.
Figure 2. Topology of the decoding site. (a) 30S subunit
portion isolated from the 70S -fMet-tRNA^fMet -Phe-tRNA^Phe
-EF-Tu -GDP -kir complex, seen from the intersubunit space. The
architecture of the decoding site (dc) shows a density in the
region of the A-site codon (labeled with an asterisk) and a
low-density region (indicated by an arrow) within SH44. (b)
Ribbons representation of the docked atomic coordinates for
SH44, ribosomal protein S12 (S12), SH18 and the A site codon
(cd) from Ogle and co-workers21 within the density region
extracted from a.
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Figure 6.
Figure 6. Coupling of the conformational change of the GAC with
the movement of aa-tRNA. (a) Comparison of the aa-tRNA
position defined inside the cryo-EM density for the ternary
complex (green) versus the position of the aa-tRNA in the atomic
coordinates of Phe-tRNA^Phe -EF-Tu -GDPNP -kir (gray). The
ribbons representation of the GAC and the SRL serves as a frame
of reference to make it apparent that the change in the aa-tRNA
position follows the conformational change of the GAC while the
aa-tRNA maintains its position in the region of the SRL. The GAC
position shown correspond to the fitting of the atomic
coordinates in the 'closed' GAC from the 70S -fMet-tRNA^fMet
-Phe-tRNA^Phe -EF-Tu -GDP -kir complex. The ribosomal
orientation is depicted in the thumbnail. (b -d) The postulated
coupling between the movement of the GAC and the approach of the
aa-tRNA to LH69. In a hypothetical initial binding, the 'open'
GAC would interact with the aa-tRNA delivered in the ternary
complex by EF-Tu (b). The transition of the GAC to the closed
conformation (c) brings the aa-tRNA in contact with LH69. The
aa-tRNA -LH69 interaction facilitates a distortion in the
aa-tRNA (d) that reorients the anticodon arm (in the region
encircled) and allows a codon (cd)-anticodon recognition.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2003,
10,
899-906)
copyright 2003.
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Headers
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