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Contents |
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234 a.a.
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206 a.a.
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208 a.a.
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150 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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98 a.a.
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119 a.a.
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124 a.a.
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118 a.a.
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60 a.a.
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88 a.a.
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83 a.a.
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104 a.a.
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73 a.a.
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87 a.a.
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99 a.a.
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24 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Ribosome
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Title:
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Structure of the thermus thermophilus 30s ribosomal subunit in complex with a messenger RNA fragment and cognate transfer RNA anticodon stem-loop bound at the a site
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Structure:
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16s ribosomal RNA. Chain: a. P-site messenger RNA fragment. Chain: x. Engineered: yes. Anticodon stem-loop of phenylalanine transfer RNA. Chain: y. Engineered: yes. A-site messenger RNA fragment.
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Source:
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Thermus thermophilus. Organism_taxid: 274. Synthetic: yes. Organism_taxid: 274
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Biol. unit:
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24mer (from
)
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Resolution:
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3.31Å
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R-factor:
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0.231
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R-free:
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0.286
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Authors:
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J.M.Ogle,D.E.Brodersen,W.M.Clemons Jr.,M.J.Tarry,A.P.Carter, V.Ramakrishnan
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Key ref:
|
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J.M.Ogle
et al.
(2001).
Recognition of cognate transfer RNA by the 30S ribosomal subunit.
Science,
292,
897-902.
PubMed id:
DOI:
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Date:
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28-Mar-01
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Release date:
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04-May-01
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PROCHECK
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Headers
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References
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P80371
(RS2_THET8) -
Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
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|
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Seq:
Struc:
|
|
|
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256 a.a.
234 a.a.
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P80372
(RS3_THET8) -
Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
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239 a.a.
206 a.a.
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|
|
|
|
|
|
|
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|
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P80373
(RS4_THET8) -
Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
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|
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Seq:
Struc:
|
|
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209 a.a.
208 a.a.
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Q5SHQ5
(RS5_THET8) -
Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
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|
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Seq:
Struc:
|
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162 a.a.
150 a.a.
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Q5SLP8
(RS6_THET8) -
Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
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|
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Seq:
Struc:
|
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|
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101 a.a.
101 a.a.
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P17291
(RS7_THET8) -
Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
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Seq:
Struc:
|
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|
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156 a.a.
155 a.a.
|
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P0DOY9
(RS8_THET8) -
Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
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|
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Seq:
Struc:
|
|
|
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138 a.a.
138 a.a.
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|
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P80374
(RS9_THET8) -
Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
128 a.a.
127 a.a.*
|
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Q5SHN7
(RS10_THET8) -
Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
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|
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Seq:
Struc:
|
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105 a.a.
98 a.a.
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P80376
(RS11_THET8) -
Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
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Seq:
Struc:
|
|
|
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129 a.a.
119 a.a.
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Q5SHN3
(RS12_THET8) -
Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
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Seq:
Struc:
|
|
|
|
132 a.a.
124 a.a.
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|
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P80377
(RS13_THET8) -
Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
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Seq:
Struc:
|
|
|
|
126 a.a.
118 a.a.
|
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|
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P0DOY6
(RS14Z_THET8) -
Small ribosomal subunit protein uS14 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
61 a.a.
60 a.a.
|
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|
|
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|
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|
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Q5SJ76
(RS15_THET8) -
Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
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89 a.a.
88 a.a.
|
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|
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|
|
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|
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Q5SJH3
(RS16_THET8) -
Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
88 a.a.
83 a.a.
|
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|
|
|
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|
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|
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|
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P0DOY7
(RS17_THET8) -
Small ribosomal subunit protein uS17 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
105 a.a.
104 a.a.*
|
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|
|
|
|
|
|
|
|
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|
|
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|
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Q5SLQ0
(RS18_THET8) -
Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
88 a.a.
73 a.a.*
|
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|
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|
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Q5SHP2
(RS19_THET8) -
Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
93 a.a.
87 a.a.
|
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 |
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| |
|
DOI no:
|
Science
292:897-902
(2001)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Recognition of cognate transfer RNA by the 30S ribosomal subunit.
|
|
J.M.Ogle,
D.E.Brodersen,
W.M.Clemons,
M.J.Tarry,
A.P.Carter,
V.Ramakrishnan.
|
|
|
|
|
| |
ABSTRACT
|
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|
| |
|
|
Crystal structures of the 30S ribosomal subunit in complex with messenger RNA
and cognate transfer RNA in the A site, both in the presence and absence of the
antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms
resolution. Cognate transfer RNA (tRNA) binding induces global domain movements
of the 30S subunit and changes in the conformation of the universally conserved
and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact
intimately with the minor groove of the first two base pairs between the codon
and anticodon, thus sensing Watson-Crick base-pairing geometry and
discriminating against near-cognate tRNA. The third, or "wobble,"
position of the codon is free to accommodate certain noncanonical base pairs. By
partially inducing these structural changes, paromomycin facilitates binding of
near-cognate tRNAs.
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| |
Selected figure(s)
|
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| |
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|
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Figure 2.
Fig. 2. Complex of the 30S subunit with mRNA from a U[6]
hexanucleotide and a cognate tRNA-ASL. (A) Overview of the
complex. The 50S interface side of the 30S subunit is facing the
reader, and important elements have been given standard colors
that are used throughout the figures, namely, ASL at the A site
(gold), codon from the U[6] hexanucleotide at the A site
(purple), 3' end of 16S RNA that mimics mRNA at the P site
(green), P site tRNA mimic introduced by helix 6 from a
neighboring molecule (dark blue), and protein S12 (tan). (B)
Stereo view showing details of the A and P sites, colored as in
(A), with, in addition, helix 44 (cyan, right), helix 34 (blue,
left), 530 loop (green, left), and paromomycin (yellow sticks,
within helix 44). The hydrogen bonds responsible for the
codon-anticodon interaction at both the A and P sites are shown
as red lines.
|
|
Figure 3.
Fig. 3. Stereo views showing interactions of the ribosome with
the codon-anticodon base pairs. The tightness of the
interactions is shown by the semitransparent van der Waals
surface. (A) In the first position, A1493 binds in the minor
groove of the A36-U1 base pair. (B) In the second position, G530
and A1492 (both brown) act in concert to monitor the A35-U2 base
pair. (C) The third (wobble) position, showing the G34-U3 base
pair. C1054 stacks against G36 of the ASL. U3 interacts with
G530, and indirectly through a Mg2+ ion (magenta) with C518 and
residue Pro48 (E. coli Pro44) from protein S12 (gray). The base
pair seems closer to Watson-Crick geometry. (D) The third
position in the presence of paromomycin, with the expected GU
wobble pair. The interactions with the ribosome are similar to
those in (C).
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| |
The above figures are
reprinted
by permission from the AAAs:
Science
(2001,
292,
897-902)
copyright 2001.
|
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| |
Figures were
selected
by an automated process.
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 |
 |
 |
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Literature references that cite this PDB file's key reference
|
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| |
PubMed id
|
|
Reference
|
|
|
|
|
|
M.Selmer,
Y.G.Gao,
A.Weixlbaumer,
and
V.Ramakrishnan
(2012).
Ribosome engineering to promote new crystal forms.
|
| |
Acta Crystallogr D Biol Crystallogr,
68,
578-583.
|
|
|
|
|
|
|
N.Demeshkina,
L.Jenner,
E.Westhof,
M.Yusupov,
and
G.Yusupova
(2012).
A new understanding of the decoding principle on the ribosome.
|
| |
Nature,
484,
256-259.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.B.Mentewab,
M.J.Jacobsen,
and
R.A.Flowers
(2011).
Incomplete homogenization of 18 S ribosomal DNA coding regions in Arabidopsis thaliana.
|
| |
BMC Res Notes,
4,
93.
|
|
|
|
|
|
|
B.P.Klaholz
(2011).
Molecular recognition and catalysis in translation termination complexes.
|
| |
Trends Biochem Sci,
36,
282-292.
|
|
|
|
|
|
|
C.Y.Liu,
M.T.Qureshi,
and
T.H.Lee
(2011).
Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
|
| |
Biophys J,
100,
2201-2208.
|
|
|
|
|
|
|
G.D.Wright
(2011).
Molecular mechanisms of antibiotic resistance.
|
| |
Chem Commun (Camb),
47,
4055-4061.
|
|
|
|
|
|
|
M.Ouberai,
F.El Garch,
A.Bussiere,
M.Riou,
D.Alsteens,
L.Lins,
I.Baussanne,
Y.F.Dufrêne,
R.Brasseur,
J.L.Decout,
and
M.P.Mingeot-Leclercq
(2011).
The Pseudomonas aeruginosa membranes: A target for a new amphiphilic aminoglycoside derivative?
|
| |
Biochim Biophys Acta,
1808,
1716-1727.
|
|
|
|
|
|
|
P.K.Khade,
and
S.Joseph
(2011).
Messenger RNA interactions in the decoding center control the rate of translocation.
|
| |
Nat Struct Mol Biol,
18,
1300-1302.
|
|
|
|
|
|
|
T.Cottin,
C.Pyrkotis,
C.I.Stathakis,
I.Mavridis,
I.A.Katsoulis,
P.Anastasopoulou,
G.Kythreoti,
A.L.Zografos,
V.R.Nahmias,
A.Papakyriakou,
and
D.Vourloumis
(2011).
Designed spiro-bicyclic analogues targeting the ribosomal decoding center.
|
| |
Chembiochem,
12,
71-87.
|
|
|
|
|
|
|
T.M.Schmeing,
R.M.Voorhees,
A.C.Kelley,
and
V.Ramakrishnan
(2011).
How mutations in tRNA distant from the anticodon affect the fidelity of decoding.
|
| |
Nat Struct Mol Biol,
18,
432-436.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
X.Agirrezabala,
E.Schreiner,
L.G.Trabuco,
J.Lei,
R.F.Ortiz-Meoz,
K.Schulten,
R.Green,
and
J.Frank
(2011).
Structural insights into cognate versus near-cognate discrimination during decoding.
|
| |
EMBO J,
30,
1497-1507.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Ben-Shem,
L.Jenner,
G.Yusupova,
and
M.Yusupov
(2010).
Crystal structure of the eukaryotic ribosome.
|
| |
Science,
330,
1203-1209.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.L.Ng,
K.Lang,
N.A.Meenan,
A.Sharma,
A.C.Kelley,
C.Kleanthous,
and
V.Ramakrishnan
(2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
|
| |
Nat Struct Mol Biol,
17,
1241-1246.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
G.De Pascale,
and
G.D.Wright
(2010).
Antibiotic resistance by enzyme inactivation: from mechanisms to solutions.
|
| |
Chembiochem,
11,
1325-1334.
|
|
|
|
|
|
|
H.David-Eden,
A.S.Mankin,
and
Y.Mandel-Gutfreund
(2010).
Structural signatures of antibiotic binding sites on the ribosome.
|
| |
Nucleic Acids Res,
38,
5982-5994.
|
|
|
|
|
|
|
I.Wohlgemuth,
C.Pohl,
and
M.V.Rodnina
(2010).
Optimization of speed and accuracy of decoding in translation.
|
| |
EMBO J,
29,
3701-3709.
|
|
|
|
|
|
|
J.A.Dunkle,
and
J.H.Cate
(2010).
Ribosome structure and dynamics during translocation and termination.
|
| |
Annu Rev Biophys,
39,
227-244.
|
|
|
|
|
|
|
J.Frank,
and
R.L.Gonzalez
(2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
|
| |
Annu Rev Biochem,
79,
381-412.
|
|
|
|
|
|
|
J.Sund,
M.Andér,
and
J.Aqvist
(2010).
Principles of stop-codon reading on the ribosome.
|
| |
Nature,
465,
947-950.
|
|
|
|
|
|
|
K.D.Green,
W.Chen,
J.L.Houghton,
M.Fridman,
and
S.Garneau-Tsodikova
(2010).
Exploring the substrate promiscuity of drug-modifying enzymes for the chemoenzymatic generation of N-acylated aminoglycosides.
|
| |
Chembiochem,
11,
119-126.
|
|
|
|
|
|
|
L.B.Jenner,
N.Demeshkina,
G.Yusupova,
and
M.Yusupov
(2010).
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
|
| |
Nat Struct Mol Biol,
17,
555-560.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.Jenner,
N.Demeshkina,
G.Yusupova,
and
M.Yusupov
(2010).
Structural rearrangements of the ribosome at the tRNA proofreading step.
|
| |
Nat Struct Mol Biol,
17,
1072-1078.
|
|
|
|
|
|
|
M.S.Ramirez,
and
M.E.Tolmasky
(2010).
Aminoglycoside modifying enzymes.
|
| |
Drug Resist Updat,
13,
151-171.
|
|
|
|
|
|
|
M.V.Rodnina,
and
W.Wintermeyer
(2010).
The ribosome goes Nobel.
|
| |
Trends Biochem Sci,
35,
1-5.
|
|
|
|
|
|
|
P.Khade,
and
S.Joseph
(2010).
Functional interactions by transfer RNAs in the ribosome.
|
| |
FEBS Lett,
584,
420-426.
|
|
|
|
|
|
|
P.Shah,
and
M.A.Gilchrist
(2010).
Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.
|
| |
PLoS Genet,
6,
0.
|
|
|
|
|
|
|
R.E.Stanley,
G.Blaha,
R.L.Grodzicki,
M.D.Strickler,
and
T.A.Steitz
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X.Agirrezabala,
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Mol Cell,
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Use of 2-aminopurine as a fluorescent tool for characterizing antibiotic recognition of the bacterial rRNA A-site.
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Tetrahedron,
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Defining the molecular forces that determine the impact of neomycin on bacterial protein synthesis: importance of the 2'-amino functionality.
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RNA,
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817-823.
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PDB codes:
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D.J.Taylor,
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D.L.Taliaferro,
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RNA,
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RNA,
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L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
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Nucleic Acids Res,
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PDB codes:
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J.B.Munro,
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Mol Cell,
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Proc Natl Acad Sci U S A,
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Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity.
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ChemMedChem,
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PDB code:
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J.Kondo,
M.Hainrichson,
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Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites.
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Chembiochem,
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PDB codes:
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J.Zhou,
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Modifications of aminoglycoside antibiotics targeting RNA.
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Nat Struct Mol Biol,
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Self-assembled lamellar complexes of siRNA with lipidic aminoglycoside derivatives promote efficient siRNA delivery and interference.
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Proc Natl Acad Sci U S A,
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Proc Natl Acad Sci U S A,
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Biopolymers,
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Group I intron renders differential susceptibility of Candida albicans to Bleomycin.
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Characterization of the 16S-23S internal transcribed spacer among 34 higher plants: suitability for interspecific plastid transformation.
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Structural aspects of RbfA action during small ribosomal subunit assembly.
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Mol Cell,
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PDB codes:
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P.V.Sergiev,
A.A.Bogdanov,
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Ribosomal RNA guanine-(N2)-methyltransferases and their targets.
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Human ribosomal protein L13a is dispensable for canonical ribosome function but indispensable for efficient rRNA methylation.
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RNA,
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The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons.
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RNA,
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Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria.
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Nucleic Acids Res,
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Chem Biol Drug Des,
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S.V.Steinberg,
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RNA,
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Proc Natl Acad Sci U S A,
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Mol Cell,
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Fluorescent HIV-1 Dimerization Initiation Site: design, properties, and use for ligand discovery.
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J Am Chem Soc,
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Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
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Cell,
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PDB codes:
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A.Liljas
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On the complementarity of methods in structural biology.
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Acta Crystallogr D Biol Crystallogr,
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Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
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Nucleic Acids Res,
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Specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48S translation initiation complex.
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Genes Dev,
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Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.
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Mol Cell,
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PDB code:
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E.M.Youngman,
L.Cochella,
J.L.Brunelle,
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Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors.
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Cold Spring Harb Symp Quant Biol,
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A late-acting quality control process for mature eukaryotic rRNAs.
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Mol Cell,
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F.S.Liang,
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Proc Natl Acad Sci U S A,
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The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation.
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Nat Struct Mol Biol,
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PDB code:
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G.Hirokawa,
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Trends Biochem Sci,
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The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.
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Structural basis for messenger RNA movement on the ribosome.
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Nature,
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PDB codes:
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|
I.K.Ali,
L.Lancaster,
J.Feinberg,
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Mol Cell,
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J.J.Gillespie,
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Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements.
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Insect Mol Biol,
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J.Kondo,
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Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.
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Nucleic Acids Res,
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PDB code:
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J.Kondo,
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Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin.
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Angew Chem Int Ed Engl,
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PDB code:
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J.S.Feinberg,
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RNA,
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K.B.Gromadski,
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A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity.
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Mol Cell,
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K.P.Hofmann,
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Building functional modules from molecular interactions.
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Trends Biochem Sci,
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Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations.
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Biopolymers,
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L.Brandi,
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A.Lazzarini,
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G.C.Winters,
M.Takahashi,
S.Shandrick,
Q.Zhao,
and
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(2003).
Piperidine glycosides targeting the ribosomal decoding site.
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Chembiochem,
4,
886-890.
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K.Takai,
and
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(2003).
Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons.
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Nucleic Acids Res,
31,
6383-6391.
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M.Galimand,
P.Courvalin,
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(2003).
Plasmid-mediated high-level resistance to aminoglycosides in Enterobacteriaceae due to 16S rRNA methylation.
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Antimicrob Agents Chemother,
47,
2565-2571.
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M.Praetorius-Ibba,
and
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(2003).
Aminoacyl-tRNA synthesis in archaea: different but not unique.
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Mol Microbiol,
48,
631-637.
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M.Valle,
A.Zavialov,
W.Li,
S.M.Stagg,
J.Sengupta,
R.C.Nielsen,
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S.C.Harvey,
M.Ehrenberg,
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(2003).
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy.
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Nat Struct Biol,
10,
899-906.
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PDB codes:
|
|
|
|
|
|
|
|
N.B.Leontis,
and
E.Westhof
(2003).
Analysis of RNA motifs.
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| |
Curr Opin Struct Biol,
13,
300-308.
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P.B.Moore,
and
T.A.Steitz
(2003).
The structural basis of large ribosomal subunit function.
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Annu Rev Biochem,
72,
813-850.
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P.Licznar,
N.Mejlhede,
M.F.Prère,
N.Wills,
R.F.Gesteland,
J.F.Atkins,
and
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(2003).
Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs.
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EMBO J,
22,
4770-4778.
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P.Pfister,
M.Risch,
D.E.Brodersen,
and
E.C.Böttger
(2003).
Role of 16S rRNA Helix 44 in Ribosomal Resistance to Hygromycin B.
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Antimicrob Agents Chemother,
47,
1496-1502.
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P.Pfister,
S.Hobbie,
Q.Vicens,
E.C.Böttger,
and
E.Westhof
(2003).
The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures.
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Chembiochem,
4,
1078-1088.
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Q.Vicens,
and
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(2003).
Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures.
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Biopolymers,
70,
42-57.
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Q.Vicens,
and
E.Westhof
(2003).
RNA as a drug target: the case of aminoglycosides.
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Chembiochem,
4,
1018-1023.
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S.B.Vakulenko,
and
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(2003).
Versatility of aminoglycosides and prospects for their future.
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Clin Microbiol Rev,
16,
430-450.
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S.C.Harvey,
C.Wang,
S.Teletchea,
and
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(2003).
Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking.
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J Comput Chem,
24,
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S.Joseph
(2003).
After the ribosome structure: how does translocation work?
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| |
RNA,
9,
160-164.
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S.R.Lynch,
R.L.Gonzalez,
and
J.D.Puglisi
(2003).
Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex.
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Structure,
11,
43-53.
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T.A.Steitz,
and
P.B.Moore
(2003).
RNA, the first macromolecular catalyst: the ribosome is a ribozyme.
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Trends Biochem Sci,
28,
411-418.
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T.M.Hansen,
P.V.Baranov,
I.P.Ivanov,
R.F.Gesteland,
and
J.F.Atkins
(2003).
Maintenance of the correct open reading frame by the ribosome.
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| |
EMBO Rep,
4,
499-504.
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|
T.M.Schmeing,
P.B.Moore,
and
T.A.Steitz
(2003).
Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit.
|
| |
RNA,
9,
1345-1352.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
T.Nishiyama,
H.Yamamoto,
N.Shibuya,
Y.Hatakeyama,
A.Hachimori,
T.Uchiumi,
and
N.Nakashima
(2003).
Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes.
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Nucleic Acids Res,
31,
2434-2442.
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Y.Okamoto-Hosoya,
S.Okamoto,
and
K.Ochi
(2003).
Development of antibiotic-overproducing strains by site-directed mutagenesis of the rpsL gene in Streptomyces lividans.
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| |
Appl Environ Microbiol,
69,
4256-4259.
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A.Ambrogelly,
D.Korencic,
and
M.Ibba
(2002).
Functional annotation of class I lysyl-tRNA synthetase phylogeny indicates a limited role for gene transfer.
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| |
J Bacteriol,
184,
4594-4600.
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A.Kuglstatter,
C.Oubridge,
and
K.Nagai
(2002).
Induced structural changes of 7SL RNA during the assembly of human signal recognition particle.
|
| |
Nat Struct Biol,
9,
740-744.
|
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|
PDB code:
|
|
|
|
|
|
|
|
A.Yonath
(2002).
The search and its outcome: high-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states.
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| |
Annu Rev Biophys Biomol Struct,
31,
257-273.
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|
D.J.Battle,
and
J.A.Doudna
(2002).
Specificity of RNA-RNA helix recognition.
|
| |
Proc Natl Acad Sci U S A,
99,
11676-11681.
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|
PDB code:
|
|
|
|
|
|
|
|
E.L.Christian,
N.M.Kaye,
and
M.E.Harris
(2002).
Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA.
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| |
EMBO J,
21,
2253-2262.
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E.Schmitt,
S.Blanquet,
and
Y.Mechulam
(2002).
The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors.
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| |
EMBO J,
21,
1821-1832.
|
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|
PDB codes:
|
|
|
|
|
|
|
|
F.J.Grundy,
W.C.Winkler,
and
T.M.Henkin
(2002).
tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome.
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| |
Proc Natl Acad Sci U S A,
99,
11121-11126.
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F.Walter,
J.Pütz,
R.Giegé,
and
E.Westhof
(2002).
Binding of tobramycin leads to conformational changes in yeast tRNA(Asp) and inhibition of aminoacylation.
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| |
EMBO J,
21,
760-768.
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G.Caetano-Anollés
(2002).
Tracing the evolution of RNA structure in ribosomes.
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Nucleic Acids Res,
30,
2575-2587.
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G.Stahl,
G.P.McCarty,
and
P.J.Farabaugh
(2002).
Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding.
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Trends Biochem Sci,
27,
178-183.
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H.Stark,
M.V.Rodnina,
H.J.Wieden,
F.Zemlin,
W.Wintermeyer,
and
M.van Heel
(2002).
Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
|
| |
Nat Struct Biol,
9,
849-854.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
I.Amarantos,
I.K.Zarkadis,
and
D.L.Kalpaxis
(2002).
The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions.
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| |
Nucleic Acids Res,
30,
2832-2843.
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J.Ma,
A.Campbell,
and
S.Karlin
(2002).
Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures.
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J Bacteriol,
184,
5733-5745.
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K.B.Simonsen,
B.K.Ayida,
D.Vourloumis,
M.Takahashi,
G.C.Winters,
S.Barluenga,
S.Qamar,
S.Shandrick,
Q.Zhao,
and
T.Hermann
(2002).
Novel paromamine derivatives exploring shallow-groove recognition of ribosomal-decoding-site RNA.
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Chembiochem,
3,
1223-1228.
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K.Fredrick,
and
H.F.Noller
(2002).
Accurate translocation of mRNA by the ribosome requires a peptidyl group or its analog on the tRNA moving into the 30S P site.
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| |
Mol Cell,
9,
1125-1131.
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L.Frolova,
A.Seit-Nebi,
and
L.Kisselev
(2002).
Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRF1.
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| |
RNA,
8,
129-136.
|
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|
|
|
|
|
M.Uno,
K.Ito,
and
Y.Nakamura
(2002).
Polypeptide release at sense and noncognate stop codons by localized charge-exchange alterations in translational release factors.
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| |
Proc Natl Acad Sci U S A,
99,
1819-1824.
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R.Mehta,
and
W.S.Champney
(2002).
30S ribosomal subunit assembly is a target for inhibition by aminoglycosides in Escherichia coli.
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| |
Antimicrob Agents Chemother,
46,
1546-1549.
|
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|
|
S.R.Connell,
C.A.Trieber,
U.Stelzl,
E.Einfeldt,
D.E.Taylor,
and
K.H.Nierhaus
(2002).
The tetracycline resistance protein Tet(o) perturbs the conformation of the ribosomal decoding centre.
|
| |
Mol Microbiol,
45,
1463-1472.
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|
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|
S.S.Phelps,
O.Jerinic,
and
S.Joseph
(2002).
Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation.
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| |
Mol Cell,
10,
799-807.
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|
V.Ramakrishnan
(2002).
Ribosome structure and the mechanism of translation.
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| |
Cell,
108,
557-572.
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W.A.Decatur,
and
M.J.Fournier
(2002).
rRNA modifications and ribosome function.
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| |
Trends Biochem Sci,
27,
344-351.
|
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|
A.B.Matassova,
M.V.Rodnina,
and
W.Wintermeyer
(2001).
Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome.
|
| |
RNA,
7,
1879-1885.
|
|
|
|
|
|
|
A.Bashan,
I.Agmon,
R.Zarivach,
F.Schluenzen,
J.Harms,
M.Pioletti,
H.Bartels,
M.Gluehmann,
H.Hansen,
T.Auerbach,
F.Franceschi,
and
A.Yonath
(2001).
High-resolution structures of ribosomal subunits: initiation, inhibition, and conformational variability.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
43-56.
|
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|
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|
|
C.M.Spahn,
R.Beckmann,
N.Eswar,
P.A.Penczek,
A.Sali,
G.Blobel,
and
J.Frank
(2001).
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
|
| |
Cell,
107,
373-386.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.E.Brodersen,
A.P.Carter,
W.M.Clemons,
R.J.Morgan-Warren,
F.V.Murphy,
J.M.Ogle,
M.J.Tarry,
B.T.Wimberly,
and
V.Ramakrishnan
(2001).
Atomic structures of the 30S subunit and its complexes with ligands and antibiotics.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
17-32.
|
|
|
|
|
|
|
G.Blaha,
and
K.H.Nierhaus
(2001).
Features and functions of the ribosomal E site.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
135-146.
|
|
|
|
|
|
|
G.M.Culver
(2001).
Meanderings of the mRNA through the ribosome.
|
| |
Structure,
9,
751-758.
|
|
|
|
|
|
|
G.R.Andersen,
and
J.Nyborg
(2001).
Structural studies of eukaryotic elongation factors.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
425-437.
|
|
|
|
|
|
|
G.Stahl,
S.Ben Salem,
Z.Li,
G.McCarty,
A.Raman,
M.Shah,
and
P.J.Farabaugh
(2001).
Programmed +1 translational frameshifting in the yeast Saccharomyces cerevisiae results from disruption of translational error correction.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
249-258.
|
|
|
|
|
|
|
G.Z.Yusupova,
M.M.Yusupov,
J.H.Cate,
and
H.F.Noller
(2001).
The path of messenger RNA through the ribosome.
|
| |
Cell,
106,
233-241.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.F.Noller,
M.M.Yusupov,
G.Z.Yusupova,
A.Baucom,
K.Lieberman,
L.Lancaster,
A.Dallas,
K.Fredrick,
T.N.Earnest,
and
J.H.Cate
(2001).
Structure of the ribosome at 5.5 A resolution and its interactions with functional ligands.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
57-66.
|
|
|
|
|
|
|
J.Ofengand,
A.Malhotra,
J.Remme,
N.S.Gutgsell,
M.Del Campo,
S.Jean-Charles,
L.Peil,
and
Y.Kaya
(2001).
Pseudouridines and pseudouridine synthases of the ribosome.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
147-159.
|
|
|
|
|
|
|
M.A.Bayfield,
A.E.Dahlberg,
U.Schulmeister,
S.Dorner,
and
A.Barta
(2001).
A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition.
|
| |
Proc Natl Acad Sci U S A,
98,
10096-10101.
|
|
|
|
|
|
|
S.A.Gerbi,
A.V.Borovjagin,
M.Ezrokhi,
and
T.S.Lange
(2001).
Ribosome biogenesis: role of small nucleolar RNA in maturation of eukaryotic rRNA.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
575-590.
|
|
|
|
|
|
|
T.Yasukawa,
T.Suzuki,
N.Ishii,
S.Ohta,
and
K.Watanabe
(2001).
Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease.
|
| |
EMBO J,
20,
4794-4802.
|
|
|
|
|
|
|
V.I.Lim,
and
J.F.Curran
(2001).
Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure.
|
| |
RNA,
7,
942-957.
|
|
|
|
|
|
|
W.Li,
and
D.W.Hoffman
(2001).
Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy.
|
| |
Protein Sci,
10,
2426-2438.
|
|
|
PDB code:
|
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
| |
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