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PDBsum entry 2gyc
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222 a.a.
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119 a.a.
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227 a.a.
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209 a.a.
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198 a.a.
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177 a.a.
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167 a.a.
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149 a.a.
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139 a.a.
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142 a.a.
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122 a.a.
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140 a.a.
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131 a.a.
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114 a.a.
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113 a.a.
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114 a.a.
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115 a.a.
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106 a.a.
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92 a.a.
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99 a.a.
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94 a.a.
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84 a.a.
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60 a.a.
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56 a.a.
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29 a.a.
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52 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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Elongation arrest by secm via a cascade of ribosomal RNA rearrangements.
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Authors
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K.Mitra,
C.Schaffitzel,
F.Fabiola,
M.S.Chapman,
N.Ban,
J.Frank.
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Ref.
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Mol Cell, 2006,
22,
533-543.
[DOI no: ]
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PubMed id
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Abstract
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In E. coli, the SecM nascent polypeptide causes elongation arrest, while
interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the
large ribosomal subunit. We compared atomic models fitted by real-space
refinement into cryo-electron microscopy reconstructions of a pretranslocational
and SecM-stalled E. coli ribosome complex. A cascade of RNA rearrangements
propagates from the exit tunnel throughout the large subunit, affecting
intersubunit bridges and tRNA positions, which in turn reorient small subunit
RNA elements. Elongation arrest could result from the inhibition of mRNA.(tRNAs)
translocation, E site tRNA egress, and perhaps translation factor activation at
the GTPase-associated center. Our study suggests that the specific secondary and
tertiary arrangement of ribosomal RNA provides the basis for internal signal
transduction within the ribosome. Thus, the ribosome may itself have the ability
to regulate its progression through translation by modulating its structure and
consequently its receptivity to activation by cofactors.
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Figure 3.
Figure 3. Overview and Interconnectivity of rRNA Elements
in Relation to the Interaction Sites with the SecM Nascent
Polypeptide
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Figure 4.
Figure 4. Flowchart of SecM Nascent Polypeptide-Induced
rRNA Rearrangements in the Ribosome
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The above figures are
reprinted
by permission from Cell Press:
Mol Cell
(2006,
22,
533-543)
copyright 2006.
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Secondary reference #1
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Title
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Structure of the e. Coli protein-Conducting channel bound to a translating ribosome.
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Authors
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K.Mitra,
C.Schaffitzel,
T.Shaikh,
F.Tama,
S.Jenni,
C.L.Brooks,
N.Ban,
J.Frank.
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Ref.
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Nature, 2005,
438,
318-324.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3: Stereo views of RNA and protein elements in the
ribosome-PCC junction. Real-space refined models showing E.
coli ribosomal proteins rendered as ribbons, and rRNA regions
interacting with the PCC as thick, light-grey backbone
snake-like structures (rattlers). The PCC is coloured and
rendered as in Fig. 2d with the cryo-EM density in cyan mesh.
a-c, The ribosome-PCC junction at the polypeptide exit site
(nascent chain density semi-transparent yellow surface) is shown
in the front (a) and back (b) views. Ribosomal elements near the
polypeptide exit site and parts of the PCC in the three
connection regions are also illustrated (c), with the line of
view perpendicular to the membrane plane. Connection regions
between ribosome and PCC are circled in orange and labelled. d,
The non-translocating PCC uses its CFADs to interact with
hairpins in the mRNA (mRNA shown as semi-transparent purple
surface with non-interacting mRNA rattler regions in yellow). h,
helix.
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Figure 4.
Figure 4: The path of the nascent chain through the ribosome and
PCC. a, Stereo view of a front-to-front SecYEG[Ec] model
fitted into the translocating PCC electron microscopy density
showing prominent regions of density unaccounted for (green and
yellow asterisks). The PCC is viewed within the plane of the
membrane, with the ribosome behind the plane, and coloured and
rendered as before with the TMHs numbered. b, Stereo view of the
nascent chain (yellow rattler) fitted into the isolated
polypeptide density inside the ribosome. The front view is
shown. Schematic versions of the PCC at the polypeptide exit
site of the ribosome in views corresponding to a (in panel c)
and b (in panel d). The PCC and ribosomal elements are coloured
as before, with the nascent chain (TMH signal anchor) in green
and yellow. See text for discussion.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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Secondary reference #2
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Title
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Locking and unlocking of ribosomal motions.
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Authors
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M.Valle,
A.Zavialov,
J.Sengupta,
U.Rawat,
M.Ehrenberg,
J.Frank.
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Ref.
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Cell, 2003,
114,
123-134.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. Docking of EF-GStereo views of the fitted
EF-G·GDP structure in the cryo-EM density for
EF-G·GDPNP (semitransparent red). In (A) relative
movements between domains were allowed, while in (B) the
EF-G·GDP coordinates were used as a rigid body and only
domains I and II were docked.
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Figure 5.
Figure 5. A Pretranslocational ComplexRendering of the
cryo-EM map for 70S ribosome bearing deacylated tRNA^fMet in the
P site (green) and dipeptidyl fMet-Phe-tRNA^Phe in the A site
(magenta). The E site is occupied by deacylated tRNA (orange)
available in the solution.(A) shows the segmented map in solid,
while in (B) a semitransparent representation of the ribosomal
subunits allows the visualization of the tRNAs in A, P, and E
sites.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #3
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Title
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A model for co-Translational translocation: ribosome-Regulated nascent polypeptide translocation at the protein-Conducting channel.
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Authors
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K.Mitra,
J.Frank.
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Ref.
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FEBS Lett, 2006,
580,
3353-3360.
[DOI no: ]
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PubMed id
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Figure 3.
Fig. 3. Segregated surface characteristics of the
polypeptide exit site and alignment with segregated PCC pores.
(A) In D. radiodurans [28] and T. thermophilus [27] (inset, rRNA
in ribbon) surface characteristics of ribosomal proteins L24 are
different from those of L23/L29, as indicated by the
distribution of hydrophobic (white), hydrophilic (green),
positively (blue) and negatively (red) charged residues. The
polypeptide tunnel exit is indicated by a yellow circle. (B)
Hydrophobic L23/L29 surfaces align with Sec[1]YEG on the left,
and the hydrophilic L24 surface and rRNA h24 align with
Sec[2]YEG on the right of the exit site. View is from the
frontal opening of the ribosome–PCC.
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Figure 4.
Fig. 4. Model of polypeptide translocation through the
ribosome–PCC complex. The hydrophobic NPS/TMH is shown as a
green cylinder with the hydrophilic portion shown as a yellow
line/open circle. Grey arrows indicate inter-CFAD distance. The
view in the upper panel is as in Fig. 3B, and in the lower panel
as in Fig. 1B. See text for discussion.
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The above figures are
reproduced from the cited reference
with permission from the Federation of European Biochemical Societies
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