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PDBsum entry 1lu3
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References listed in PDB file
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Key reference
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Title
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Cryo-Em reveals an active role for aminoacyl-Trna in the accommodation process.
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Authors
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M.Valle,
J.Sengupta,
N.K.Swami,
R.A.Grassucci,
N.Burkhardt,
K.H.Nierhaus,
R.K.Agrawal,
J.Frank.
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Ref.
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EMBO J, 2002,
21,
3557-3567.
[DOI no: ]
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PubMed id
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Abstract
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During the elongation cycle of protein biosynthesis, the specific amino acid
coded for by the mRNA is delivered by a complex that is comprised of the cognate
aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to
the ribosome, the anticodon end of the tRNA reaches the decoding center in the
30S subunit. Here we present the cryo- electron microscopy (EM) study of an
Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic,
kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new
conformation that appears to facilitate the initial codon-anticodon interaction.
Furthermore, the elbow region of the tRNA is seen to contact the
GTPase-associated center on the 50S subunit of the ribosome, suggesting an
active role of the tRNA in the transmission of the signal prompting the GTP
hydrolysis upon codon recognition.
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Figure 4.
Figure 4 Interaction of EF-Tu and aa-tRNA with the ribosome. (A
and B) Ribbons representation of the docked EF-Tu and aa-tRNA
within the ternary complex. (C and D) Focus on the interaction
between the  -sarcin−ricin
loop (SRL) and the effector loop within domain I of EF-Tu
(cyan). In (C) the coordinates of the whole ternary complex from
T.aquaticus with a GTP analog (Nissen et al., 1995) were used
for the fitting, while in (D) the crystal structure of EF-Tu
from E.coli bound to GDP (Song et al., 1999) was used.
Orientation of the ribosomes for (A) and (B) are shown as
thumbnails on the left. Labeling is the same as in Figure 5.
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Figure 5.
Figure 5 Interaction in the decoding center and accommodation of
the aa-tRNA. (A−C) Semi-transparent representation of the
ternary complex density from the cryo-EM map showing the fitted
tRNA (gold) and the A-site tRNA (red) with corresponding mRNA
codon (Yusupova et al., 2001). (C) A tRNA construct in which the
anticodon position, up to the kink, is adopted from (B) and the
rest of the tRNA from (A). (D−F) Interaction in the anticodon
loop of the tRNA in the decoding site. H69, helix 69 from 23S
rRNA; h44, helix 44 from 16S rRNA; h34, helix 34 from 16S rRNA;
cd, A-site codon in the mRNA; AC, anticodon loop; S12, protein
S12 in the 30S subunit.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
3557-3567)
copyright 2002.
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Secondary reference #1
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Title
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Crystal structure of intact elongation factor ef-Tu from escherichia coli in gdp conformation at 2.05 a resolution.
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Authors
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H.Song,
M.R.Parsons,
S.Rowsell,
G.Leonard,
S.E.Phillips.
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Ref.
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J Mol Biol, 1999,
285,
1245-1256.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Ribbon diagrams of EF-Tu molecules.
(a) EC-EF-Tu-GDP; (b) same view of EF-Tu-GTP from
T. aquaticus (TA-EF-Tu-GTP). The switch I region is
shown in yellow and the switch II region in green. The
rest of the polypeptide backbone is shown in purple,
royal blue and dark blue for domain 1 (residues 8-204),
domain 2 (residues 205-298) and domain 3 (299-393),
respectively. GDP or GTP molecules are shown in ball-
and-stick models, and Mg
2+
are shown as cyan spheres.
The Figure was drawn with MOLSCRIPT (Kraulis,
1991), as are Figures 4 and 5.
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Figure 5.
Figure 5. Stereo view of the interface between domain
1 and domain 3. The switch I and II regions are shown
in yellow and green, respectively. The rest of the poly-
peptide chain in domain 1 is shown in purple, and that
of the domain 3 in slate blue. Hydrogen bonds are
shown as broken lines, and water molecules as cyan
spheres. Residues involved in interactions between
domains 1 and 3 are shown as ball-and-stick. (a) EC-EF-
Tu-GDP; (b) TA-EF-Tu-GTP.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Crystal structure of the ternary complex of phe-Trnaphe, Ef-Tu, And a gtp analog.
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Authors
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P.Nissen,
M.Kjeldgaard,
S.Thirup,
G.Polekhina,
L.Reshetnikova,
B.F.Clark,
J.Nyborg.
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Ref.
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Science, 1995,
270,
1464-1472.
[DOI no: ]
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PubMed id
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Secondary reference #3
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Title
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Visualization of elongation factor tu on the escherichia coli ribosome.
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Authors
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H.Stark,
M.V.Rodnina,
J.Rinke-Appel,
R.Brimacombe,
W.Wintermeyer,
M.Van heel.
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Ref.
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Nature, 1997,
389,
403-406.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 a, b, The 70S E.coli ribosome with the ternary
complex locked into the A site by kirromycin. Domain 1 of the
EF-Tu forms a bridge to the L7/L12 stalk on the 50S subunit and
is directly adjacent to the L11/L10 site on the large subunit.
Other details indicated follow earlier nomenclature^5. c, d, The
A/P state of the ribosome. After GTP hydrolysis the ribosome
normally (if not stalled by kirromycin) would go into the A/P
pre-translocational state carrying tRNA[f]^Met in the P site and
fMet-Phe-tRNA^Phe in the A site^5. In the A/P state the A-site
tRNA appears somewhat stretched^5 when compared to the classic
L-shape of the tRNA bound to the EF-Tu in the ternary complex.
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Figure 3.
Figure 3 The crystallographic structure of the ternary
complex (at 2.7 Å resolution) compared to the electron
microscopical reconstruction (18 Å resolution). a, The ternary
complex as revealed by X-ray crystallography10, with the
aminoacyl-tRNA shown in grey in the background in 'stick'
representation ('RASMOL'), and the EF-Tu in cartoon
representation in the foreground, rainbow colour-coded along the
length of the chain. The viewing direction is chosen to match
that of the ternary complex within the electron microscope
reconstruction shown in c. b, X-ray structure of the ternary
complex in space-fill representation ('IMAGIC'). c, Structure of
the ternary complex in the kirromycin-stalled
pre-translocational 70S ribosome extracted interactively from
the electron microscope 3D reconstruction. d, The X-ray and
electron microscopic densities superimposed. The X-ray structure
was aligned with respect to the electron microscopic
reconstruction mainly by the position of domain 2 of the EF-Tu.
Although the tRNA part of the ternary complex in the electron
microscopic reconstruction is simply a low-resolution version of
the X-ray structure, in the EF-Tu part of the complex some
differences exist with respect to the GTP-state X-ray structure
that cannot be accounted for by just the differences in
resolution between the structures.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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Secondary reference #4
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Title
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The crystal structure of elongation factor ef-Tu from thermus aquaticus in the gtp conformation.
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Authors
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M.Kjeldgaard,
P.Nissen,
S.Thirup,
J.Nyborg.
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Ref.
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Structure, 1993,
1,
35-50.
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PubMed id
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Secondary reference #5
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Title
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Helix unwinding in the effector region of elongation factor ef-Tu-Gdp.
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Authors
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G.Polekhina,
S.Thirup,
M.Kjeldgaard,
P.Nissen,
C.Lippmann,
J.Nyborg.
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Ref.
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Structure, 1996,
4,
1141-1151.
[DOI no: ]
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PubMed id
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Figure 6.
Figure 6. Comparison of the Mg2+-binding sites in T.
aquaticus EF-Tu-GDP and EF-Tu-GDPNP. (a) EF-Tu-GDP and (b)
EF-Tu-GDPNP; GDP and GDPNP are shown in ball-and-stick
representation. The atoms are coloured as in Figure 4. (Figure
produced with MOLSCRIPT [37].)
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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Headers
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