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PDBsum entry 2wdh
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Contents |
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235 a.a.
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207 a.a.
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208 a.a.
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151 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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99 a.a.
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119 a.a.
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125 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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84 a.a.
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100 a.a.
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70 a.a.
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79 a.a.
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99 a.a.
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25 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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Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70s ribosome.
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Authors
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R.M.Voorhees,
A.Weixlbaumer,
D.Loakes,
A.C.Kelley,
V.Ramakrishnan.
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Ref.
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Nat Struct Biol, 2009,
16,
528-533.
[DOI no: ]
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PubMed id
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Abstract
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Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located
in the large (50S) subunit of the ribosome. No high-resolution structure of the
intact ribosome has contained a complete active site including both A- and
P-site tRNAs. In addition, although past structures of the 50S subunit have
found no ordered proteins at the PTC, biochemical evidence suggests that
specific proteins are capable of interacting with the 3' ends of tRNA ligands.
Here we present structures, at 3.6-A and 3.5-A resolution respectively, of the
70S ribosome in complex with A- and P-site tRNAs that mimic pre- and
post-peptidyl-transfer states. These structures demonstrate that the PTC is very
similar between the 50S subunit and the intact ribosome. They also reveal
interactions between the ribosomal proteins L16 and L27 and the tRNA substrates,
helping to elucidate the role of these proteins in peptidyl transfer.
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Figure 1.
(a) Chemical diagram of the pre-peptidyl-transfer state of
the ribosomal active site. In this structure, both the A- and
P-site tRNAs contain an amide linkage between residue A76 and
the phenylalanine amino acid. (b) Model of the ribosomal active
site in the pre-peptidyl-transfer state, including
representative 3F[o] – 2F[c] density for the A- and P-site
tRNAs in green and purple, respectively. (c) Chemical diagram of
the post-peptidyl-transfer state in which the A site contains an
amide-linked Phe-tRNA^Phe and the P site contains tRNA^fMet. (d)
Model of the post-peptidyl-transfer state within the peptidyl
transferase center, including 3F[o] – 2F[c] density for the A-
and P-site tRNAs in green and purple, respectively.
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Figure 3.
(a) Overview of protein L27 in relation to the A- and P-site
tRNAs (in green and purple, respectively). The protein (dark
blue) contains a globular domain and an N-terminal extension
that localizes between the 3' ends of the ribosomal tRNAs. (b)
Predicted interactions of protein L27 with the ribosomal
substrates and 23S RNA (light blue). The modeled interactions
were observed in both structures containing occupied A sites,
though the post-peptidyl-transfer structure is displayed here as
it contained moderately better electron density for L27. A
representative 3F[o] – 2F[c] electron density map is displayed
in blue. (c) Overview of protein L16 in relation to the
ribosomal substrates. The protein is located adjacent to the
elbow of the A-site tRNA. (d) Interactions between the conserved
residues Arg51 and Arg56 of protein L16 (dark blue) with the
backbone of the A-site tRNA (green). Representative 3F[o] –
2F[c] density, as determined in the pre-peptidyl-transfer
structure, is displayed in green for the region of the A-site
tRNA predicted to interact with L16.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
Nat Struct Biol
(2009,
16,
528-533)
copyright 2009.
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