|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
111 a.a.*
|
|
|
|
|
|
|
|
|
|
|
176 a.a.*
|
|
|
|
|
|
|
|
|
|
|
161 a.a.
|
|
|
|
|
|
|
|
|
|
|
157 a.a.
|
|
|
|
|
|
|
|
|
|
|
97 a.a.
|
|
|
|
|
|
|
|
|
|
|
128 a.a.
|
|
|
|
|
|
|
|
|
|
|
136 a.a.
|
|
|
|
|
|
|
|
|
|
|
89 a.a.*
|
|
|
|
|
|
|
|
|
|
|
70 a.a.*
|
|
|
|
|
|
|
|
|
|
|
103 a.a.*
|
|
|
|
|
|
|
|
|
|
|
77 a.a.*
|
|
|
|
|
|
|
|
|
|
|
26 a.a.*
|
|
|
|
|
|
|
|
|
|
|
88 a.a.
|
|
|
|
|
|
|
|
|
|
|
84 a.a.
|
|
|
|
|
|
|
|
|
|
|
50 a.a.
|
|
|
|
|
|
|
|
|
|
|
73 a.a.
|
|
|
|
|
|
|
|
|
|
|
95 a.a.
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
* C-alpha coords only
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Ribosome
|
|
|
Title:
|
|
Structure of functionally activated small ribosomal subunit at 3.3 a resolution
|
|
Structure:
|
|
16s ribosomal RNA. Chain: a. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.
|
|
Source:
|
|
Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
|
|
Biol. unit:
|
|
20mer (from
)
|
|
Resolution:
|
|
|
3.30Å
|
R-factor:
|
0.304
|
R-free:
|
0.305
|
|
|
Authors:
|
|
F.Schluenzen,A.Tocilj,R.Zarivach,J.Harms,M.Gluehmann,D.Janell, A.Bashan,H.Bartels,I.Agmon,F.Franceschi,A.Yonath
|
Key ref:
|
|
F.Schluenzen
et al.
(2000).
Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.
Cell,
102,
615-623.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
09-Aug-00
|
Release date:
|
04-Sep-00
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P80373
(RS4_THET8) -
Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
209 a.a.
161 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Q5SHQ5
(RS5_THET8) -
Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
162 a.a.
157 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Q5SLP8
(RS6_THET8) -
Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
101 a.a.
97 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P17291
(RS7_THET8) -
Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
156 a.a.
128 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P0DOY9
(RS8_THET8) -
Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
138 a.a.
136 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Q5SJ76
(RS15_THET8) -
Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
89 a.a.
88 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
No UniProt id for this chain
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Q5SLQ0
(RS18_THET8) -
Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
|
|
|
|
Seq:
Struc:
|
|
|
|
88 a.a.
50 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
Chains D, E, F, G, H, O, R, S:
E.C.?
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Cell
102:615-623
(2000)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.
|
|
F.Schluenzen,
A.Tocilj,
R.Zarivach,
J.Harms,
M.Gluehmann,
D.Janell,
A.Bashan,
H.Bartels,
I.Agmon,
F.Franceschi,
A.Yonath.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The small ribosomal subunit performs the decoding of genetic information during
translation. The structure of that from Thermus thermophilus shows that the
decoding center, which positions mRNA and three tRNAs, is constructed entirely
of RNA. The entrance to the mRNA channel will encircle the message when a
latch-like contact closes and contributes to processivity and fidelity. Extended
RNA helical elements that run longitudinally through the body transmit
structural changes, correlating events at the particle's far end with the cycle
of mRNA translocation at the decoding region. 96% of the nucleotides were traced
and the main fold of all proteins was determined. The latter are either
peripheral or appear to serve as linkers. Some may assist the directionality of
translocation.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 1.
Figure 1. The Small Subunit and Its Electron Density
Map(Left and center) A stereo representation of the full model
described in this paper. RNA is shown in gold, using a ribbon
backbone and simple lines for base pairs. The differently
colored helical segments and loops are the proteins. The
major subdivisions are labeled: H, head; B, body; S, shoulder;
P, platform; N, nose; F, foot.In all figures, the head is at the
top of the drawing and the foot at the bottom.These portions of
Figure 1 Figure 2 Figure 3 were made with Ribbons (
[12]).(Right) Segments showing RNA (top and middle pannels) and
proteins (bottom) of the MIRAS map at 3.3 Å resolution,
with the model superimposed. Made with O ([32]).
|
|
Figure 3.
Figure 3. The Presumed mRNA Path(Left) A surface
representation of the subunit, viewed from the side of the 50S
subunit. The latch is circled in cyan and the decoding center in
red. The mRNA would enter the path in the approximate direction
shown by the dark-blue arrow, pass through the aperture defined
by the latch, and along the channel in the near face of the
subunit. The brown curved arrows show the suggested global
cooperative movements of the platform and the head, which
facilitate the mRNA entrance, progression, and exit.(Right)
Enlarged image of the decoding center region, showing the
positions of tRNA anticodon stem loops and mRNA codons, using
the superposition of tRNA and mRNA from the model of Cate et
al., 1999, as described in the text. The uppermost bulge of H44
is shown in olive, two codons of mRNA in blue, and the anticodon
bases of the tRNA molecules in green (A site), magenta (P site)
and gray (E site). The right side of the figure was made with
DINO ([47]). The contour level is 1.1 standard deviations.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from Cell Press:
Cell
(2000,
102,
615-623)
copyright 2000.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
S.O.Dahms,
M.Kuester,
C.Streb,
C.Roth,
N.Sträter,
and
M.E.Than
(2013).
Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.
|
| |
Acta Crystallogr D Biol Crystallogr,
69,
284-297.
|
|
|
|
|
|
|
W.A.Hendrickson
(2013).
Evolution of diffraction methods for solving crystal structures.
|
| |
Acta Crystallogr A,
69,
51-59.
|
|
|
|
|
|
|
F.A.Rey,
and
W.I.Sundquist
(2011).
Macromolecular assemblages.
|
| |
Curr Opin Struct Biol,
21,
221-222.
|
|
|
|
|
|
|
J.Zheng,
C.Wei,
L.Zhao,
L.Liu,
W.Leng,
W.Li,
and
Q.Jin
(2011).
Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin.
|
| |
BMC Genomics,
12,
40.
|
|
|
|
|
|
|
K.Fujii,
M.T.Young,
and
K.D.Harris
(2011).
Exploiting powder X-ray diffraction for direct structure determination in structural biology: The P2X4 receptor trafficking motif YEQGL.
|
| |
J Struct Biol,
174,
461-467.
|
|
|
|
|
|
|
M.Valle
(2011).
Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome.
|
| |
Eur Biophys J,
40,
589-597.
|
|
|
|
|
|
|
Q.Xie,
J.Lin,
Y.Qin,
J.Zhou,
and
W.Bu
(2011).
Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction.
|
| |
Protein Cell,
2,
161-170.
|
|
|
|
|
|
|
A.H.Antonioli,
J.C.Cochrane,
S.V.Lipchock,
and
S.A.Strobel
(2010).
Plasticity of the RNA kink turn structural motif.
|
| |
RNA,
16,
762-768.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Ohman,
T.Oman,
and
M.Oliveberg
(2010).
Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P(54-55).
|
| |
Protein Sci,
19,
183-189.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.M.Burmann,
X.Luo,
P.Rösch,
M.C.Wahl,
and
M.E.Gottesman
(2010).
Fine tuning of the E. coli NusB:NusE complex affinity to BoxA RNA is required for processive antitermination.
|
| |
Nucleic Acids Res,
38,
314-326.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Nanamiya,
and
F.Kawamura
(2010).
Towards an elucidation of the roles of the ribosome during different growth phases in Bacillus subtilis.
|
| |
Biosci Biotechnol Biochem,
74,
451-461.
|
|
|
|
|
|
|
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.Frank
(2010).
The Ribosome Comes Alive.
|
| |
Isr J Chem,
50,
95-98.
|
|
|
|
|
|
|
J.P.Armache,
A.Jarasch,
A.M.Anger,
E.Villa,
T.Becker,
S.Bhushan,
F.Jossinet,
M.Habeck,
G.Dindar,
S.Franckenberg,
V.Marquez,
T.Mielke,
M.Thomm,
O.Berninghausen,
B.Beatrix,
J.Söding,
E.Westhof,
D.N.Wilson,
and
R.Beckmann
(2010).
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
|
| |
Proc Natl Acad Sci U S A,
107,
19754-19759.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.P.Armache,
A.Jarasch,
A.M.Anger,
E.Villa,
T.Becker,
S.Bhushan,
F.Jossinet,
M.Habeck,
G.Dindar,
S.Franckenberg,
V.Marquez,
T.Mielke,
M.Thomm,
O.Berninghausen,
B.Beatrix,
J.Söding,
E.Westhof,
D.N.Wilson,
and
R.Beckmann
(2010).
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
|
| |
Proc Natl Acad Sci U S A,
107,
19748-19753.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Falb,
I.Amata,
F.Gabel,
B.Simon,
and
T.Carlomagno
(2010).
Structure of the K-turn U4 RNA: a combined NMR and SANS study.
|
| |
Nucleic Acids Res,
38,
6274-6285.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.V.Rodnina,
and
W.Wintermeyer
(2010).
The ribosome goes Nobel.
|
| |
Trends Biochem Sci,
35,
1-5.
|
|
|
|
|
|
|
M.Wieland,
B.Berschneider,
M.D.Erlacher,
and
J.S.Hartig
(2010).
Aptazyme-mediated regulation of 16S ribosomal RNA.
|
| |
Chem Biol,
17,
236-242.
|
|
|
|
|
|
|
P.C.Whitford,
P.Geggier,
R.B.Altman,
S.C.Blanchard,
J.N.Onuchic,
and
K.Y.Sanbonmatsu
(2010).
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.
|
| |
RNA,
16,
1196-1204.
|
|
|
|
|
|
|
Q.Zeidan,
Z.Wang,
A.De Maio,
and
G.W.Hart
(2010).
O-GlcNAc cycling enzymes associate with the translational machinery and modify core ribosomal proteins.
|
| |
Mol Biol Cell,
21,
1922-1936.
|
|
|
|
|
|
|
R.Psaila,
D.Ponti,
M.Ponzi,
F.Gigliani,
and
P.A.Battaglia
(2010).
A small sequence in domain v of the mitochondrial large ribosomal RNA restores Drosophila melanogaster pole cell determination in uv-irradiated embryos.
|
| |
Cell Mol Biol Lett,
15,
365-376.
|
|
|
|
|
|
|
S.Kimura,
and
T.Suzuki
(2010).
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA.
|
| |
Nucleic Acids Res,
38,
1341-1352.
|
|
|
|
|
|
|
Y.Wei,
and
S.Daunert
(2010).
Enabling technologies in discovery: the 2009 Nobel Prize and its implications in antibiotic design.
|
| |
Anal Bioanal Chem,
396,
1623-1626.
|
|
|
|
|
|
|
Z.Dauter,
M.Jaskolski,
and
A.Wlodawer
(2010).
Impact of synchrotron radiation on macromolecular crystallography: a personal view.
|
| |
J Synchrotron Radiat,
17,
433-444.
|
|
|
|
|
|
|
A.Yonath
(2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
|
| |
J R Soc Interface,
6,
S575-S585.
|
|
|
|
|
|
|
B.Llano-Sotelo,
R.P.Hickerson,
L.Lancaster,
H.F.Noller,
and
A.S.Mankin
(2009).
Fluorescently labeled ribosomes as a tool for analyzing antibiotic binding.
|
| |
RNA,
15,
1597-1604.
|
|
|
|
|
|
|
C.W.Carter
(2009).
E pluribus tres: the 2009 nobel prize in chemistry.
|
| |
Structure,
17,
1558-1561.
|
|
|
|
|
|
|
D.L.Bellur,
and
S.A.Woodson
(2009).
A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly.
|
| |
Nucleic Acids Res,
37,
1886-1896.
|
|
|
|
|
|
|
D.M.Hamburg,
M.J.Suh,
and
P.A.Limbach
(2009).
Limited proteolysis analysis of the ribosome is affected by subunit association.
|
| |
Biopolymers,
91,
410-422.
|
|
|
|
|
|
|
E.Zimmerman,
and
A.Yonath
(2009).
Biological implications of the ribosome's stunning stereochemistry.
|
| |
Chembiochem,
10,
63-72.
|
|
|
|
|
|
|
G.Y.Soung,
J.L.Miller,
H.Koc,
and
E.C.Koc
(2009).
Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes.
|
| |
J Proteome Res,
8,
3390-3402.
|
|
|
|
|
|
|
H.S.Zaher,
and
R.Green
(2009).
Fidelity at the molecular level: lessons from protein synthesis.
|
| |
Cell,
136,
746-762.
|
|
|
|
|
|
|
J.R.Williamson,
V.Ramakrishnan,
T.Steitz,
and
A.Yonath
(2009).
The ribosome at atomic resolution.
|
| |
Cell,
139,
1041-1043.
|
|
|
|
|
|
|
J.Sethuraman,
A.Majer,
N.C.Friedrich,
D.R.Edgell,
and
G.Hausner
(2009).
Genes within genes: multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene encoded within an rnl group I intron of Ophiostoma and related taxa.
|
| |
Mol Biol Evol,
26,
2299-2315.
|
|
|
|
|
|
|
P.B.Moore
(2009).
The ribosome returned.
|
| |
J Biol,
8,
8.
|
|
|
|
|
|
|
P.Babitzke,
C.S.Baker,
and
T.Romeo
(2009).
Regulation of translation initiation by RNA binding proteins.
|
| |
Annu Rev Microbiol,
63,
27-44.
|
|
|
|
|
|
|
P.Ramaswamy,
and
S.A.Woodson
(2009).
S16 throws a conformational switch during assembly of 30S 5' domain.
|
| |
Nat Struct Mol Biol,
16,
438-445.
|
|
|
|
|
|
|
P.Ramaswamy,
and
S.A.Woodson
(2009).
Global stabilization of rRNA structure by ribosomal proteins S4, S17, and S20.
|
| |
J Mol Biol,
392,
666-677.
|
|
|
|
|
|
|
S.Shoji,
S.E.Walker,
and
K.Fredrick
(2009).
Ribosomal translocation: one step closer to the molecular mechanism.
|
| |
ACS Chem Biol,
4,
93.
|
|
|
|
|
|
|
S.T.Gregory,
and
A.E.Dahlberg
(2009).
Genetic and structural analysis of base substitutions in the central pseudoknot of Thermus thermophilus 16S ribosomal RNA.
|
| |
RNA,
15,
215-223.
|
|
|
|
|
|
|
T.J.McLellan,
E.S.Marr,
L.M.Wondrack,
T.A.Subashi,
P.A.Aeed,
S.Han,
Z.Xu,
I.K.Wang,
and
B.A.Maguire
(2009).
A systematic study of 50S ribosomal subunit purification enabling robust crystallization.
|
| |
Acta Crystallogr D Biol Crystallogr,
65,
1270-1282.
|
|
|
|
|
|
|
T.Y.Wu,
C.C.Hsieh,
J.J.Hong,
C.Y.Chen,
and
Y.S.Tsai
(2009).
IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico.
|
| |
BMC Bioinformatics,
10,
160.
|
|
|
|
|
|
|
W.Huggins,
S.K.Ghosh,
and
P.Wollenzien
(2009).
Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome.
|
| |
BMC Struct Biol,
9,
49.
|
|
|
|
|
|
|
Y.Xie,
A.V.Dix,
and
Y.Tor
(2009).
FRET enabled real time detection of RNA-small molecule binding.
|
| |
J Am Chem Soc,
131,
17605-17614.
|
|
|
|
|
|
|
A.A.Saraiya,
T.N.Lamichhane,
C.S.Chow,
J.SantaLucia,
and
P.R.Cunningham
(2008).
Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA.
|
| |
J Mol Biol,
376,
645-657.
|
|
|
|
|
|
|
A.B.Taylor,
B.Meyer,
B.Z.Leal,
P.Kötter,
V.Schirf,
B.Demeler,
P.J.Hart,
K.D.Entian,
and
J.Wöhnert
(2008).
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
|
| |
Nucleic Acids Res,
36,
1542-1554.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Bashan,
and
A.Yonath
(2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
|
| |
J Mol Struct,
890,
289-294.
|
|
|
|
|
|
|
A.Simonetti,
S.Marzi,
A.G.Myasnikov,
A.Fabbretti,
M.Yusupov,
C.O.Gualerzi,
and
B.P.Klaholz
(2008).
Structure of the 30S translation initiation complex.
|
| |
Nature,
455,
416-420.
|
|
|
|
|
|
|
A.V.Pisarev,
V.G.Kolupaeva,
M.M.Yusupov,
C.U.Hellen,
and
T.V.Pestova
(2008).
Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes.
|
| |
EMBO J,
27,
1609-1621.
|
|
|
|
|
|
|
A.Yan,
Y.Wang,
A.Kloczkowski,
and
R.L.Jernigan
(2008).
Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome.
|
| |
J Chem Theory Comput,
4,
1757-1767.
|
|
|
|
|
|
|
C.Voisset,
J.Y.Thuret,
D.Tribouillard-Tanvier,
S.J.Saupe,
and
M.Blondel
(2008).
Tools for the study of ribosome-borne protein folding activity.
|
| |
Biotechnol J,
3,
1033-1040.
|
|
|
|
|
|
|
H.David-Eden,
and
Y.Mandel-Gutfreund
(2008).
Revealing unique properties of the ribosome using a network based analysis.
|
| |
Nucleic Acids Res,
36,
4641-4652.
|
|
|
|
|
|
|
J.E.Brock,
S.Pourshahian,
J.Giliberti,
P.A.Limbach,
and
G.R.Janssen
(2008).
Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG.
|
| |
RNA,
14,
2159-2169.
|
|
|
|
|
|
|
J.R.Williamson
(2008).
Cooperativity in macromolecular assembly.
|
| |
Nat Chem Biol,
4,
458-465.
|
|
|
|
|
|
|
J.S.Richardson,
B.Schneider,
L.W.Murray,
G.J.Kapral,
R.M.Immormino,
J.J.Headd,
D.C.Richardson,
D.Ham,
E.Hershkovits,
L.D.Williams,
K.S.Keating,
A.M.Pyle,
D.Micallef,
J.Westbrook,
and
H.M.Berman
(2008).
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
|
| |
RNA,
14,
465-481.
|
|
|
|
|
|
|
L.Garcia-Ortega,
J.Stephen,
and
S.Joseph
(2008).
Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation.
|
| |
Mol Cell,
32,
292-299.
|
|
|
|
|
|
|
M.Hainrichson,
I.Nudelman,
and
T.Baasov
(2008).
Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases.
|
| |
Org Biomol Chem,
6,
227-239.
|
|
|
|
|
|
|
P.Aliprandi,
C.Sizun,
J.Perez,
F.Mareuil,
S.Caputo,
J.L.Leroy,
B.Odaert,
S.Laalami,
M.Uzan,
and
F.Bontems
(2008).
S1 ribosomal protein functions in translation initiation and ribonuclease RegB activation are mediated by similar RNA-protein interactions: an NMR and SAXS analysis.
|
| |
J Biol Chem,
283,
13289-13301.
|
|
|
|
|
|
|
P.Chandramouli,
M.Topf,
J.F.Ménétret,
N.Eswar,
J.J.Cannone,
R.R.Gutell,
A.Sali,
and
C.W.Akey
(2008).
Structure of the mammalian 80S ribosome at 8.7 A resolution.
|
| |
Structure,
16,
535-548.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.Das,
S.Loss,
J.Li,
D.S.Waugh,
S.Tarasov,
P.T.Wingfield,
R.A.Byrd,
and
A.S.Altieri
(2008).
Structural biophysics of the NusB:NusE antitermination complex.
|
| |
J Mol Biol,
376,
705-720.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Rakauskaite,
and
J.D.Dinman
(2008).
rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance.
|
| |
Nucleic Acids Res,
36,
1497-1507.
|
|
|
|
|
|
|
S.N.Hobbie,
C.M.Bruell,
S.Akshay,
S.K.Kalapala,
D.Shcherbakov,
and
E.C.Böttger
(2008).
Mitochondrial deafness alleles confer misreading of the genetic code.
|
| |
Proc Natl Acad Sci U S A,
105,
3244-3249.
|
|
|
|
|
|
|
T.Yokoyama,
and
T.Suzuki
(2008).
Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments.
|
| |
Nucleic Acids Res,
36,
3539-3551.
|
|
|
|
|
|
|
X.Luo,
H.H.Hsiao,
M.Bubunenko,
G.Weber,
D.L.Court,
M.E.Gottesman,
H.Urlaub,
and
M.C.Wahl
(2008).
Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
|
| |
Mol Cell,
32,
791-802.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
X.Wang,
G.Kapral,
L.Murray,
D.Richardson,
J.Richardson,
and
J.Snoeyink
(2008).
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
|
| |
J Math Biol,
56,
253-278.
|
|
|
|
|
|
|
A.Cléry,
V.Bourguignon-Igel,
C.Allmang,
A.Krol,
and
C.Branlant
(2007).
An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the selenocysteine incorporation machinery.
|
| |
Nucleic Acids Res,
35,
1868-1884.
|
|
|
|
|
|
|
A.Cléry,
V.Senty-Ségault,
F.Leclerc,
H.A.Raué,
and
C.Branlant
(2007).
Analysis of sequence and structural features that identify the B/C motif of U3 small nucleolar RNA as the recognition site for the Snu13p-Rrp9p protein pair.
|
| |
Mol Cell Biol,
27,
1191-1206.
|
|
|
|
|
|
|
A.Korostelev,
and
H.F.Noller
(2007).
The ribosome in focus: new structures bring new insights.
|
| |
Trends Biochem Sci,
32,
434-441.
|
|
|
|
|
|
|
A.V.Karnaukhov,
E.V.Karnaukhova,
and
J.R.Williamson
(2007).
Numerical Matrices Method for nonlinear system identification and description of dynamics of biochemical reaction networks.
|
| |
Biophys J,
92,
3459-3473.
|
|
|
|
|
|
|
C.V.Robinson,
A.Sali,
and
W.Baumeister
(2007).
The molecular sociology of the cell.
|
| |
Nature,
450,
973-982.
|
|
|
|
|
|
|
F.Franceschi
(2007).
Back to the future: the ribosome as an antibiotic target.
|
| |
Future Microbiol,
2,
571-574.
|
|
|
|
|
|
|
H.R.Jonker,
S.Ilin,
S.K.Grimm,
J.Wöhnert,
and
H.Schwalbe
(2007).
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
|
| |
Nucleic Acids Res,
35,
441-454.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
K.Kitahara,
A.Kajiura,
N.S.Sato,
and
T.Suzuki
(2007).
Functional genetic selection of Helix 66 in Escherichia coli 23S rRNA identified the eukaryotic-binding sequence for ribosomal protein L2.
|
| |
Nucleic Acids Res,
35,
4018-4029.
|
|
|
|
|
|
|
K.Lagesen,
P.Hallin,
E.A.Rødland,
H.H.Staerfeldt,
T.Rognes,
and
D.W.Ussery
(2007).
RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
|
| |
Nucleic Acids Res,
35,
3100-3108.
|
|
|
|
|
|
|
L.A.Passmore,
T.M.Schmeing,
D.Maag,
D.J.Applefield,
M.G.Acker,
M.A.Algire,
J.R.Lorsch,
and
V.Ramakrishnan
(2007).
The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome.
|
| |
Mol Cell,
26,
41-50.
|
|
|
|
|
|
|
M.Kaczanowska,
and
M.Rydén-Aulin
(2007).
Ribosome biogenesis and the translation process in Escherichia coli.
|
| |
Microbiol Mol Biol Rev,
71,
477-494.
|
|
|
|
|
|
|
Q.Vicens,
A.R.Gooding,
A.Laederach,
and
T.R.Cech
(2007).
Local RNA structural changes induced by crystallization are revealed by SHAPE.
|
| |
RNA,
13,
536-548.
|
|
|
|
|
|
|
R.Przybilski,
and
C.Hammann
(2007).
The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements.
|
| |
RNA,
13,
1625-1630.
|
|
|
|
|
|
|
S.Blouin,
and
D.A.Lafontaine
(2007).
A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control.
|
| |
RNA,
13,
1256-1267.
|
|
|
|
|
|
|
S.D.Moore,
and
R.T.Sauer
(2007).
The tmRNA system for translational surveillance and ribosome rescue.
|
| |
Annu Rev Biochem,
76,
101-124.
|
|
|
|
|
|
|
S.V.Steinberg,
and
Y.I.Boutorine
(2007).
G-ribo: a new structural motif in ribosomal RNA.
|
| |
RNA,
13,
549-554.
|
|
|
|
|
|
|
S.V.Steinberg,
and
Y.I.Boutorine
(2007).
G-ribo motif favors the formation of pseudoknots in ribosomal RNA.
|
| |
RNA,
13,
1036-1042.
|
|
|
|
|
|
|
T.Kaminishi,
D.N.Wilson,
C.Takemoto,
J.M.Harms,
M.Kawazoe,
F.Schluenzen,
K.Hanawa-Suetsugu,
M.Shirouzu,
P.Fucini,
and
S.Yokoyama
(2007).
A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.
|
| |
Structure,
15,
289-297.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
V.Lisi,
and
F.Major
(2007).
A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships.
|
| |
RNA,
13,
1537-1545.
|
|
|
|
|
|
|
W.E.Running,
S.Ravipaty,
J.A.Karty,
and
J.P.Reilly
(2007).
A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus.
|
| |
J Proteome Res,
6,
337-347.
|
|
|
|
|
|
|
A.Liljas
(2006).
On the complementarity of methods in structural biology.
|
| |
Acta Crystallogr D Biol Crystallogr,
62,
941-945.
|
|
|
|
|
|
|
A.Pulk,
U.Maiväli,
and
J.Remme
(2006).
Identification of nucleotides in E. coli 16S rRNA essential for ribosome subunit association.
|
| |
RNA,
12,
790-796.
|
|
|
|
|
|
|
C.A.Townsend,
J.M.Crawford,
and
T.Bililign
(2006).
New images evoke FAScinating questions.
|
| |
Chem Biol,
13,
349-351.
|
|
|
|
|
|
|
C.Y.Lee
(2006).
Mass fractal dimension of the ribosome and implication of its dynamic characteristics.
|
| |
Phys Rev E Stat Nonlin Soft Matter Phys,
73,
042901.
|
|
|
|
|
|
|
E.C.Böttger
(2006).
The ribosome as a drug target.
|
| |
Trends Biotechnol,
24,
145-147.
|
|
|
|
|
|
|
F.Schluenzen,
C.Takemoto,
D.N.Wilson,
T.Kaminishi,
J.M.Harms,
K.Hanawa-Suetsugu,
W.Szaflarski,
M.Kawazoe,
M.Shirouzu,
M.Shirouzo,
K.H.Nierhaus,
S.Yokoyama,
and
P.Fucini
(2006).
The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation.
|
| |
Nat Struct Mol Biol,
13,
871-878.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.Papadopoulos,
S.Grudinin,
D.L.Kalpaxis,
and
T.Choli-Papadopoulou
(2006).
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis.
|
| |
Eur Biophys J,
35,
675-683.
|
|
|
|
|
|
|
G.Rosenbaum,
R.W.Alkire,
G.Evans,
F.J.Rotella,
K.Lazarski,
R.G.Zhang,
S.L.Ginell,
N.Duke,
I.Naday,
J.Lazarz,
M.J.Molitsky,
L.Keefe,
J.Gonczy,
L.Rock,
R.Sanishvili,
M.A.Walsh,
E.Westbrook,
and
A.Joachimiak
(2006).
The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.
|
| |
J Synchrotron Radiat,
13,
30-45.
|
|
|
|
|
|
|
G.Yusupova,
L.Jenner,
B.Rees,
D.Moras,
and
M.Yusupov
(2006).
Structural basis for messenger RNA movement on the ribosome.
|
| |
Nature,
444,
391-394.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.Yoneyama,
and
R.Katsumata
(2006).
Antibiotic resistance in bacteria and its future for novel antibiotic development.
|
| |
Biosci Biotechnol Biochem,
70,
1060-1075.
|
|
|
|
|
|
|
J.Dresios,
P.Panopoulos,
and
D.Synetos
(2006).
Eukaryotic ribosomal proteins lacking a eubacterial counterpart: important players in ribosomal function.
|
| |
Mol Microbiol,
59,
1651-1663.
|
|
|
|
|
|
|
J.J.Gillespie,
J.S.Johnston,
J.J.Cannone,
and
R.R.Gutell
(2006).
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.
|
| |
Insect Mol Biol,
15,
657-686.
|
|
|
|
|
|
|
J.M.Chandonia,
S.H.Kim,
and
S.E.Brenner
(2006).
Target selection and deselection at the Berkeley Structural Genomics Center.
|
| |
Proteins,
62,
356-370.
|
|
|
|
|
|
|
K.Koga,
A.Ikegami,
K.Nakasone,
R.Murayama,
G.Akanuma,
Y.Natori,
H.Nanamiya,
and
F.Kawamura
(2006).
Construction of Bacillus subtilis strains carrying the transcriptional bgaB fusion with the promoter region of each rrn operon and their differential transcription during spore development.
|
| |
J Gen Appl Microbiol,
52,
119-124.
|
|
|
|
|
|
|
K.Mitra,
and
J.Frank
(2006).
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.
|
| |
Annu Rev Biophys Biomol Struct,
35,
299-317.
|
|
|
|
|
|
|
L.Nasalean,
S.Baudrey,
N.B.Leontis,
and
L.Jaeger
(2006).
Controlling RNA self-assembly to form filaments.
|
| |
Nucleic Acids Res,
34,
1381-1392.
|
|
|
|
|
|
|
M.Buchhaupt,
B.Meyer,
P.Kötter,
and
K.D.Entian
(2006).
Genetic evidence for 18S rRNA binding and an Rps19p assembly function of yeast nucleolar protein Nep1p.
|
| |
Mol Genet Genomics,
276,
273-284.
|
|
|
|
|
|
|
M.G.Gagnon,
A.Mukhopadhyay,
and
S.V.Steinberg
(2006).
Close packing of helices 3 and 12 of 16 S rRNA is required for the normal ribosome function.
|
| |
J Biol Chem,
281,
39349-39357.
|
|
|
|
|
|
|
M.Newby Lambert,
E.Vöcker,
S.Blumberg,
S.Redemann,
A.Gajraj,
J.C.Meiners,
and
N.G.Walter
(2006).
Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy.
|
| |
Biophys J,
90,
3672-3685.
|
|
|
|
|
|
|
T.L.Sorensen,
K.E.McAuley,
R.Flaig,
and
E.M.Duke
(2006).
New light for science: synchrotron radiation in structural medicine.
|
| |
Trends Biotechnol,
24,
500-508.
|
|
|
|
|
|
|
W.J.Melchers,
J.Zoll,
M.Tessari,
D.V.Bakhmutov,
A.P.Gmyl,
V.I.Agol,
and
H.A.Heus
(2006).
A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA.
|
| |
RNA,
12,
1671-1682.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.K.Woźniak,
S.Nottrott,
E.Kühn-Hölsken,
G.F.Schröder,
H.Grubmüller,
R.Lührmann,
C.A.Seidel,
and
F.Oesterhelt
(2005).
Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements.
|
| |
RNA,
11,
1545-1554.
|
|
|
|
|
|
|
A.Matte,
G.V.Louie,
J.Sivaraman,
M.Cygler,
and
S.K.Burley
(2005).
Structure of the pseudouridine synthase RsuA from Haemophilus influenzae.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
350-354.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Yassin,
K.Fredrick,
and
A.S.Mankin
(2005).
Deleterious mutations in small subunit ribosomal RNA identify functional sites and potential targets for antibiotics.
|
| |
Proc Natl Acad Sci U S A,
102,
16620-16625.
|
|
|
|
|
|
|
A.Yonath
(2005).
Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation.
|
| |
Annu Rev Biochem,
74,
649-679.
|
|
|
|
|
|
|
B.S.Laursen,
H.P.Sørensen,
K.K.Mortensen,
and
H.U.Sperling-Petersen
(2005).
Initiation of protein synthesis in bacteria.
|
| |
Microbiol Mol Biol Rev,
69,
101-123.
|
|
|
|
|
|
|
B.S.Schuwirth,
M.A.Borovinskaya,
C.W.Hau,
W.Zhang,
A.Vila-Sanjurjo,
J.M.Holton,
and
J.H.Cate
(2005).
Structures of the bacterial ribosome at 3.5 A resolution.
|
| |
Science,
310,
827-834.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.E.Brodersen,
and
P.Nissen
(2005).
The social life of ribosomal proteins.
|
| |
FEBS J,
272,
2098-2108.
|
|
|
|
|
|
|
D.N.Wilson,
J.M.Harms,
K.H.Nierhaus,
F.Schlünzen,
and
P.Fucini
(2005).
Species-specific antibiotic-ribosome interactions: implications for drug development.
|
| |
Biol Chem,
386,
1239-1252.
|
|
|
|
|
|
|
F.Bélanger,
G.Théberge-Julien,
P.R.Cunningham,
and
L.Brakier-Gingras
(2005).
A functional relationship between helix 1 and the 900 tetraloop of 16S ribosomal RNA within the bacterial ribosome.
|
| |
RNA,
11,
906-913.
|
|
|
|
|
|
|
F.Rázga,
J.Koca,
J.Sponer,
and
N.B.Leontis
(2005).
Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.
|
| |
Biophys J,
88,
3466-3485.
|
|
|
|
|
|
|
H.F.Noller
(2005).
RNA structure: reading the ribosome.
|
| |
Science,
309,
1508-1514.
|
|
|
|
|
|
|
H.Gao,
and
J.Frank
(2005).
Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement.
|
| |
Structure,
13,
401-406.
|
|
|
|
|
|
|
I.Agmon,
A.Bashan,
R.Zarivach,
and
A.Yonath
(2005).
Symmetry at the active site of the ribosome: structural and functional implications.
|
| |
Biol Chem,
386,
833-844.
|
|
|
|
|
|
|
J.A.Sutcliffe
(2005).
Improving on nature: antibiotics that target the ribosome.
|
| |
Curr Opin Microbiol,
8,
534-542.
|
|
|
|
|
|
|
J.J.Gillespie,
C.H.McKenna,
M.J.Yoder,
R.R.Gutell,
J.S.Johnston,
J.Kathirithamby,
and
A.I.Cognato
(2005).
Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera).
|
| |
Insect Mol Biol,
14,
625-643.
|
|
|
|
|
|
|
J.M.Ogle,
and
V.Ramakrishnan
(2005).
Structural insights into translational fidelity.
|
| |
Annu Rev Biochem,
74,
129-177.
|
|
|
|
|
|
|
J.Poehlsgaard,
and
S.Douthwaite
(2005).
The bacterial ribosome as a target for antibiotics.
|
| |
Nat Rev Microbiol,
3,
870-881.
|
|
|
|
|
|
|
L.L.Ilag,
H.Videler,
A.R.McKay,
F.Sobott,
P.Fucini,
K.H.Nierhaus,
and
C.V.Robinson
(2005).
Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria.
|
| |
Proc Natl Acad Sci U S A,
102,
8192-8197.
|
|
|
|
|
|
|
M.Dorywalska,
S.C.Blanchard,
R.L.Gonzalez,
H.D.Kim,
S.Chu,
and
J.D.Puglisi
(2005).
Site-specific labeling of the ribosome for single-molecule spectroscopy.
|
| |
Nucleic Acids Res,
33,
182-189.
|
|
|
|
|
|
|
M.Guillier,
F.Allemand,
M.Graffe,
S.Raibaud,
F.Dardel,
M.Springer,
and
C.Chiaruttini
(2005).
The N-terminal extension of Escherichia coli ribosomal protein L20 is important for ribosome assembly, but dispensable for translational feedback control.
|
| |
RNA,
11,
728-738.
|
|
|
|
|
|
|
M.J.Suh,
D.M.Hamburg,
S.T.Gregory,
A.E.Dahlberg,
and
P.A.Limbach
(2005).
Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry.
|
| |
Proteomics,
5,
4818-4831.
|
|
|
|
|
|
|
M.N.Lambert,
J.A.Hoerter,
M.J.Pereira,
and
N.G.Walter
(2005).
Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA.
|
| |
RNA,
11,
1688-1700.
|
|
|
|
|
|
|
M.W.Talkington,
G.Siuzdak,
and
J.R.Williamson
(2005).
An assembly landscape for the 30S ribosomal subunit.
|
| |
Nature,
438,
628-632.
|
|
|
|
|
|
|
N.M.Parakhnevitch,
A.A.Malygin,
and
G.G.Karpova
(2005).
Recombinant human ribosomal protein S16: expression, purification, refolding, and structural stability.
|
| |
Biochemistry (Mosc),
70,
777-781.
|
|
|
|
|
|
|
P.B.Moore
(2005).
Structural biology. A ribosomal coup: E. coli at last!
|
| |
Science,
310,
793-795.
|
|
|
|
|
|
|
P.B.Moore,
and
T.A.Steitz
(2005).
The ribosome revealed.
|
| |
Trends Biochem Sci,
30,
281-283.
|
|
|
|
|
|
|
P.Giavalisco,
D.Wilson,
T.Kreitler,
H.Lehrach,
J.Klose,
J.Gobom,
and
P.Fucini
(2005).
High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome.
|
| |
Plant Mol Biol,
57,
577-591.
|
|
|
|
|
|
|
S.Dutta,
and
H.M.Berman
(2005).
Large macromolecular complexes in the Protein Data Bank: a status report.
|
| |
Structure,
13,
381-388.
|
|
|
|
|
|
|
S.Ferreira-Cerca,
G.Pöll,
P.E.Gleizes,
H.Tschochner,
and
P.Milkereit
(2005).
Roles of eukaryotic ribosomal proteins in maturation and transport of pre-18S rRNA and ribosome function.
|
| |
Mol Cell,
20,
263-275.
|
|
|
|
|
|
|
S.Ghosh,
and
S.Joseph
(2005).
Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit.
|
| |
RNA,
11,
657-667.
|
|
|
|
|
|
|
S.T.Gregory,
J.F.Carr,
D.Rodriguez-Correa,
and
A.E.Dahlberg
(2005).
Mutational analysis of 16S and 23S rRNA genes of Thermus thermophilus.
|
| |
J Bacteriol,
187,
4804-4812.
|
|
|
|
|
|
|
T.Auerbach-Nevo,
R.Zarivach,
M.Peretz,
and
A.Yonath
(2005).
Reproducible growth of well diffracting ribosomal crystals.
|
| |
Acta Crystallogr D Biol Crystallogr,
61,
713-719.
|
|
|
|
|
|
|
A.Chworos,
I.Severcan,
A.Y.Koyfman,
P.Weinkam,
E.Oroudjev,
H.G.Hansma,
and
L.Jaeger
(2004).
Building programmable jigsaw puzzles with RNA.
|
| |
Science,
306,
2068-2072.
|
|
|
|
|
|
|
A.K.Henras,
C.Dez,
and
Y.Henry
(2004).
RNA structure and function in C/D and H/ACA s(no)RNPs.
|
| |
Curr Opin Struct Biol,
14,
335-343.
|
|
|
|
|
|
|
A.Yonath,
and
A.Bashan
(2004).
Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
|
| |
Annu Rev Microbiol,
58,
233-251.
|
|
|
|
|
|
|
C.Abad-Zapatero
(2004).
Notes of a protein crystallographer; our unsung heroes.
|
| |
Structure,
12,
523-527.
|
|
|
|
|
|
|
C.Herve du Penhoat,
H.S.Atreya,
Y.Shen,
G.Liu,
T.B.Acton,
R.Xiao,
Z.Li,
D.Murray,
G.T.Montelione,
and
T.Szyperski
(2004).
The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold.
|
| |
Protein Sci,
13,
1407-1416.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.M.Spahn,
E.Jan,
A.Mulder,
R.A.Grassucci,
P.Sarnow,
and
J.Frank
(2004).
Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
|
| |
Cell,
118,
465-475.
|
|
|
|
|
|
|
C.M.Spahn,
M.G.Gomez-Lorenzo,
R.A.Grassucci,
R.Jørgensen,
G.R.Andersen,
R.Beckmann,
P.A.Penczek,
J.P.Ballesta,
and
J.Frank
(2004).
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
|
| |
EMBO J,
23,
1008-1019.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.S.Tung,
and
K.Y.Sanbonmatsu
(2004).
Atomic model of the Thermus thermophilus 70S ribosome developed in silico.
|
| |
Biophys J,
87,
2714-2722.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.H.Mathews
(2004).
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.
|
| |
RNA,
10,
1178-1190.
|
|
|
|
|
|
|
D.Rodriguez-Correa,
and
A.E.Dahlberg
(2004).
Genetic evidence against the 16S ribosomal RNA helix 27 conformational switch model.
|
| |
RNA,
10,
28-33.
|
|
|
|
|
|
|
I.Moll,
G.Hirokawa,
M.C.Kiel,
A.Kaji,
and
U.Bläsi
(2004).
Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs.
|
| |
Nucleic Acids Res,
32,
3354-3363.
|
|
|
|
|
|
|
J.Hsieh,
A.J.Andrews,
and
C.A.Fierke
(2004).
Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P.
|
| |
Biopolymers,
73,
79-89.
|
|
|
|
|
|
|
K.L.Holmes,
and
G.M.Culver
(2004).
Mapping structural differences between 30S ribosomal subunit assembly intermediates.
|
| |
Nat Struct Mol Biol,
11,
179-186.
|
|
|
|
|
|
|
L.Cochella,
and
R.Green
(2004).
Isolation of antibiotic resistance mutations in the rRNA by using an in vitro selection system.
|
| |
Proc Natl Acad Sci U S A,
101,
3786-3791.
|
|
|
|
|
|
|
M.Léger,
S.Sidani,
and
L.Brakier-Gingras
(2004).
A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1.
|
| |
RNA,
10,
1225-1235.
|
|
|
|
|
|
|
R.B.Russell,
F.Alber,
P.Aloy,
F.P.Davis,
D.Korkin,
M.Pichaud,
M.Topf,
and
A.Sali
(2004).
A structural perspective on protein-protein interactions.
|
| |
Curr Opin Struct Biol,
14,
313-324.
|
|
|
|
|
|
|
S.C.Blanchard,
H.D.Kim,
R.L.Gonzalez,
J.D.Puglisi,
and
S.Chu
(2004).
tRNA dynamics on the ribosome during translation.
|
| |
Proc Natl Acad Sci U S A,
101,
12893-12898.
|
|
|
|
|
|
|
T.A.Goody,
S.E.Melcher,
D.G.Norman,
and
D.M.Lilley
(2004).
The kink-turn motif in RNA is dimorphic, and metal ion-dependent.
|
| |
RNA,
10,
254-264.
|
|
|
|
|
|
|
T.Auerbach,
A.Bashan,
and
A.Yonath
(2004).
Ribosomal antibiotics: structural basis for resistance, synergism and selectivity.
|
| |
Trends Biotechnol,
22,
570-576.
|
|
|
|
|
|
|
W.Huggins,
and
P.Wollenzien
(2004).
A 16S rRNA-tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome.
|
| |
Nucleic Acids Res,
32,
6548-6556.
|
|
|
|
|
|
|
W.P.Tate,
and
E.S.Poole
(2004).
The ribosome: lifting the veil from a fascinating organelle.
|
| |
Bioessays,
26,
582-588.
|
|
|
|
|
|
|
A.A.Leonov,
P.V.Sergiev,
A.A.Bogdanov,
R.Brimacombe,
and
O.A.Dontsova
(2003).
Affinity purification of ribosomes with a lethal G2655C mutation in 23 S rRNA that affects the translocation.
|
| |
J Biol Chem,
278,
25664-25670.
|
|
|
|
|
|
|
A.Bashan,
R.Zarivach,
F.Schluenzen,
I.Agmon,
J.Harms,
T.Auerbach,
D.Baram,
R.Berisio,
H.Bartels,
H.A.Hansen,
P.Fucini,
D.Wilson,
M.Peretz,
M.Kessler,
and
A.Yonath
(2003).
Ribosomal crystallography: peptide bond formation and its inhibition.
|
| |
Biopolymers,
70,
19-41.
|
|
|
|
|
|
|
A.Serganov,
A.Polonskaia,
B.Ehresmann,
C.Ehresmann,
and
D.J.Patel
(2003).
Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA.
|
| |
EMBO J,
22,
1898-1908.
|
|
|
|
|
|
|
A.Vila-Sanjurjo,
W.K.Ridgeway,
V.Seymaner,
W.Zhang,
S.Santoso,
K.Yu,
and
J.H.Cate
(2003).
X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli.
|
| |
Proc Natl Acad Sci U S A,
100,
8682-8687.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Yonath
(2003).
Ribosomal tolerance and peptide bond formation.
|
| |
Biol Chem,
384,
1411-1419.
|
|
|
|
|
|
|
D.E.Brodersen,
W.M.Clemons,
A.P.Carter,
B.T.Wimberly,
and
V.Ramakrishnan
(2003).
Phasing the 30S ribosomal subunit structure.
|
| |
Acta Crystallogr D Biol Crystallogr,
59,
2044-2050.
|
|
|
|
|
|
|
E.P.Plant,
K.L.Jacobs,
J.W.Harger,
A.Meskauskas,
J.L.Jacobs,
J.L.Baxter,
A.N.Petrov,
and
J.D.Dinman
(2003).
The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting.
|
| |
RNA,
9,
168-174.
|
|
|
|
|
|
|
F.Robert,
and
L.Brakier-Gingras
(2003).
A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome.
|
| |
J Biol Chem,
278,
44913-44920.
|
|
|
|
|
|
|
G.M.Culver
(2003).
Assembly of the 30S ribosomal subunit.
|
| |
Biopolymers,
68,
234-249.
|
|
|
|
|
|
|
G.Villescas-Diaz,
and
M.Zacharias
(2003).
Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis.
|
| |
Biophys J,
85,
416-425.
|
|
|
|
|
|
|
H.Gao,
J.Sengupta,
M.Valle,
A.Korostelev,
N.Eswar,
S.M.Stagg,
P.Van Roey,
R.K.Agrawal,
S.C.Harvey,
A.Sali,
M.S.Chapman,
and
J.Frank
(2003).
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
|
| |
Cell,
113,
789-801.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
I.Kanevsky,
N.Vasilenko,
H.Dumay-Odelot,
and
P.Fossé
(2003).
In vitro characterization of a base pairing interaction between the primer binding site and the minimal packaging signal of avian leukosis virus genomic RNA.
|
| |
Nucleic Acids Res,
31,
7070-7082.
|
|
|
|
|
|
|
I.S.Gabashvili,
M.Whirl-Carrillo,
M.Bada,
D.R.Banatao,
and
R.B.Altman
(2003).
Ribosomal dynamics inferred from variations in experimental measurements.
|
| |
RNA,
9,
1301-1307.
|
|
|
|
|
|
|
J.Dresios,
P.Panopoulos,
K.Suzuki,
and
D.Synetos
(2003).
A dispensable yeast ribosomal protein optimizes peptidyltransferase activity and affects translocation.
|
| |
J Biol Chem,
278,
3314-3322.
|
|
|
|
|
|
|
J.Frank
(2003).
Toward an understanding of the structural basis of translation.
|
| |
Genome Biol,
4,
237.
|
|
|
|
|
|
|
J.Frank
(2003).
Electron microscopy of functional ribosome complexes.
|
| |
Biopolymers,
68,
223-233.
|
|
|
|
|
|
|
J.R.Williamson
(2003).
After the ribosome structures: how are the subunits assembled?
|
| |
RNA,
9,
165-167.
|
|
|
|
|
|
|
J.W.Noah,
T.G.Shapkina,
K.Nanda,
W.Huggins,
and
P.Wollenzien
(2003).
Conformational change in the 16S rRNA in the Escherichia coli 70S ribosome induced by P/P- and P/E-site tRNAPhe binding.
|
| |
Biochemistry,
42,
14386-14396.
|
|
|
|
|
|
|
K.Inoue,
J.Alsina,
J.Chen,
and
M.Inouye
(2003).
Suppression of defective ribosome assembly in a rbfA deletion mutant by overexpression of Era, an essential GTPase in Escherichia coli.
|
| |
Mol Microbiol,
48,
1005-1016.
|
|
|
|
|
|
|
K.Réblová,
N.Spacková,
R.Stefl,
K.Csaszar,
J.Koca,
N.B.Leontis,
and
J.Sponer
(2003).
Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.
|
| |
Biophys J,
84,
3564-3582.
|
|
|
|
|
|
|
L.J.Murray,
W.B.Arendall,
D.C.Richardson,
and
J.S.Richardson
(2003).
RNA backbone is rotameric.
|
| |
Proc Natl Acad Sci U S A,
100,
13904-13909.
|
|
|
|
|
|
|
M.Machius
(2003).
Structural biology: a high-tech tool for biomedical research.
|
| |
Curr Opin Nephrol Hypertens,
12,
431-438.
|
|
|
|
|
|
|
P.B.Moore,
and
T.A.Steitz
(2003).
The structural basis of large ribosomal subunit function.
|
| |
Annu Rev Biochem,
72,
813-850.
|
|
|
|
|
|
|
P.G.Foster,
C.R.Nunes,
P.Greene,
D.Moustakas,
and
R.M.Stroud
(2003).
The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate.
|
| |
Structure,
11,
1609-1620.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.B.Vakulenko,
and
S.Mobashery
(2003).
Versatility of aminoglycosides and prospects for their future.
|
| |
Clin Microbiol Rev,
16,
430-450.
|
|
|
|
|
|
|
S.Behrens,
C.Rühland,
J.Inácio,
H.Huber,
A.Fonseca,
I.Spencer-Martins,
B.M.Fuchs,
and
R.Amann
(2003).
In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes.
|
| |
Appl Environ Microbiol,
69,
1748-1758.
|
|
|
|
|
|
|
S.C.Harvey,
C.Wang,
S.Teletchea,
and
R.Lavery
(2003).
Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking.
|
| |
J Comput Chem,
24,
1-9.
|
|
|
|
|
|
|
S.Joseph
(2003).
After the ribosome structure: how does translocation work?
|
| |
RNA,
9,
160-164.
|
|
|
|
|
|
|
S.Marzi,
W.Knight,
L.Brandi,
E.Caserta,
N.Soboleva,
W.E.Hill,
C.O.Gualerzi,
and
J.S.Lodmell
(2003).
Ribosomal localization of translation initiation factor IF2.
|
| |
RNA,
9,
958-969.
|
|
|
|
|
|
|
S.Matsumura,
Y.Ikawa,
and
T.Inoue
(2003).
Biochemical characterization of the kink-turn RNA motif.
|
| |
Nucleic Acids Res,
31,
5544-5551.
|
|
|
|
|
|
|
S.R.Connell,
D.M.Tracz,
K.H.Nierhaus,
and
D.E.Taylor
(2003).
Ribosomal protection proteins and their mechanism of tetracycline resistance.
|
| |
Antimicrob Agents Chemother,
47,
3675-3681.
|
|
|
|
|
|
|
S.Szép,
J.Wang,
and
P.B.Moore
(2003).
The crystal structure of a 26-nucleotide RNA containing a hook-turn.
|
| |
RNA,
9,
44-51.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
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.
|
| |
EMBO Rep,
4,
499-504.
|
|
|
|
|
|
|
Y.Nakamura,
and
K.Ito
(2003).
Making sense of mimic in translation termination.
|
| |
Trends Biochem Sci,
28,
99.
|
|
|
|
|
|
|
A.B.Simonson,
and
J.A.Lake
(2002).
The transorientation hypothesis for codon recognition during protein synthesis.
|
| |
Nature,
416,
281-285.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Balandina,
D.Kamashev,
and
J.Rouviere-Yaniv
(2002).
The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids.
|
| |
J Biol Chem,
277,
27622-27628.
|
|
|
|
|
|
|
A.Minsky,
E.Shimoni,
and
D.Frenkiel-Krispin
(2002).
Stress, order and survival.
|
| |
Nat Rev Mol Cell Biol,
3,
50-60.
|
|
|
|
|
|
|
A.Yonath
(2002).
The search and its outcome: high-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states.
|
| |
Annu Rev Biophys Biomol Struct,
31,
257-273.
|
|
|
|
|
|
|
C.Gueydan,
C.Wauquier,
C.De Mees,
G.Huez,
and
V.Kruys
(2002).
Identification of ribosomal proteins specific to higher eukaryotic organisms.
|
| |
J Biol Chem,
277,
45034-45040.
|
|
|
|
|
|
|
C.S.Tung,
S.Joseph,
and
K.Y.Sanbonmatsu
(2002).
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
|
| |
Nat Struct Biol,
9,
750-755.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
F.Fraternali,
and
L.Cavallo
(2002).
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome.
|
| |
Nucleic Acids Res,
30,
2950-2960.
|
|
|
|
|
|
|
G.A.Otto,
P.J.Lukavsky,
A.M.Lancaster,
P.Sarnow,
and
J.D.Puglisi
(2002).
Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction.
|
| |
RNA,
8,
913-923.
|
|
|
|
|
|
|
G.Caetano-Anollés
(2002).
Tracing the evolution of RNA structure in ribosomes.
|
| |
Nucleic Acids Res,
30,
2575-2587.
|
|
|
|
|
|
|
G.Stahl,
G.P.McCarty,
and
P.J.Farabaugh
(2002).
Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding.
|
| |
Trends Biochem Sci,
27,
178-183.
|
|
|
|
|
|
|
H.D.Kim,
G.U.Nienhaus,
T.Ha,
J.W.Orr,
J.R.Williamson,
and
S.Chu
(2002).
Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules.
|
| |
Proc Natl Acad Sci U S A,
99,
4284-4289.
|
|
|
|
|
|
|
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.
|
| |
Nucleic Acids Res,
30,
2832-2843.
|
|
|
|
|
|
|
J.Frank
(2002).
Single-particle imaging of macromolecules by cryo-electron microscopy.
|
| |
Annu Rev Biophys Biomol Struct,
31,
303-319.
|
|
|
|
|
|
|
J.Ma,
A.Campbell,
and
S.Karlin
(2002).
Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures.
|
| |
J Bacteriol,
184,
5733-5745.
|
|
|
|
|
|
|
J.Rinke-Appel,
M.Osswald,
K.von Knoblauch,
F.Mueller,
R.Brimacombe,
P.Sergiev,
O.Avdeeva,
A.Bogdanov,
and
O.Dontsova
(2002).
Crosslinking of 4.5S RNA to the Escherichia coli ribosome in the presence or absence of the protein Ffh.
|
| |
RNA,
8,
612-625.
|
|
|
|
|
|
|
M.A.Schäfer,
A.O.Tastan,
S.Patzke,
G.Blaha,
C.M.Spahn,
D.N.Wilson,
and
K.H.Nierhaus
(2002).
Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit.
|
| |
J Biol Chem,
277,
19095-19105.
|
|
|
|
|
|
|
M.Ehrenberg,
and
T.Tenson
(2002).
A new beginning of the end of translation.
|
| |
Nat Struct Biol,
9,
85-87.
|
|
|
|
|
|
|
M.G.Gagnon,
and
S.V.Steinberg
(2002).
GU receptors of double helices mediate tRNA movement in the ribosome.
|
| |
RNA,
8,
873-877.
|
|
|
|
|
|
|
M.Liu,
and
S.Douthwaite
(2002).
Methylation at nucleotide G745 or G748 in 23S rRNA distinguishes Gram-negative from Gram-positive bacteria.
|
| |
Mol Microbiol,
44,
195-204.
|
|
|
|
|
|
|
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.
|
| |
Proc Natl Acad Sci U S A,
99,
1819-1824.
|
|
|
|
|
|
|
M.Whirl-Carrillo,
I.S.Gabashvili,
M.Bada,
D.R.Banatao,
and
R.B.Altman
(2002).
Mining biochemical information: lessons taught by the ribosome.
|
| |
RNA,
8,
279-289.
|
|
|
|
|
|
|
M.Yoshihama,
T.Uechi,
S.Asakawa,
K.Kawasaki,
S.Kato,
S.Higa,
N.Maeda,
S.Minoshima,
T.Tanaka,
N.Shimizu,
and
N.Kenmochi
(2002).
The human ribosomal protein genes: sequencing and comparative analysis of 73 genes.
|
| |
Genome Res,
12,
379-390.
|
|
|
|
|
|
|
O.Lecompte,
R.Ripp,
J.C.Thierry,
D.Moras,
and
O.Poch
(2002).
Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale.
|
| |
Nucleic Acids Res,
30,
5382-5390.
|
|
|
|
|
|
|
P.S.Klosterman,
M.Tamura,
S.R.Holbrook,
and
S.E.Brenner
(2002).
SCOR: a Structural Classification of RNA database.
|
| |
Nucleic Acids Res,
30,
392-394.
|
|
|
|
|
|
|
T.Steiner,
J.T.Kaiser,
S.Marinkoviç,
R.Huber,
and
M.C.Wahl
(2002).
Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities.
|
| |
EMBO J,
21,
4641-4653.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
V.Ramakrishnan
(2002).
Ribosome structure and the mechanism of translation.
|
| |
Cell,
108,
557-572.
|
|
|
|
|
|
|
W.A.Decatur,
and
M.J.Fournier
(2002).
rRNA modifications and ribosome function.
|
| |
Trends Biochem Sci,
27,
344-351.
|
|
|
|
|
|
|
Z.Zhang,
P.Harrison,
and
M.Gerstein
(2002).
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.
|
| |
Genome Res,
12,
1466-1482.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
A.E.Dahlberg
(2001).
Ribosome structure. The ribosome in action.
|
| |
Science,
292,
868-869.
|
|
|
|
|
|
|
A.Roll-Mecak,
B.S.Shin,
T.E.Dever,
and
S.K.Burley
(2001).
Engaging the ribosome: universal IFs of translation.
|
| |
Trends Biochem Sci,
26,
705-709.
|
|
|
|
|
|
|
B.A.Maguire,
and
R.A.Zimmermann
(2001).
The ribosome in focus.
|
| |
Cell,
104,
813-816.
|
|
|
|
|
|
|
B.F.McEwen,
and
J.Frank
(2001).
Electron tomographic and other approaches for imaging molecular machines.
|
| |
Curr Opin Neurobiol,
11,
594-600.
|
|
|
|
|
|
|
B.Gopal,
K.G.Papavinasasundaram,
G.Dodson,
M.J.Colston,
S.A.Major,
and
A.N.Lane
(2001).
Spectroscopic and thermodynamic characterization of the transcription antitermination factor NusE and its interaction with NusB from Mycobacterium tuberculosis.
|
| |
Biochemistry,
40,
920-928.
|
|
|
|
|
|
|
B.Springer,
Y.G.Kidan,
T.Prammananan,
K.Ellrott,
E.C.Böttger,
and
P.Sander
(2001).
Mechanisms of streptomycin resistance: selection of mutations in the 16S rRNA gene conferring resistance.
|
| |
Antimicrob Agents Chemother,
45,
2877-2884.
|
|
|
|
|
|
|
C.A.Côté,
and
B.A.Peculis
(2001).
Role of the ITS2-proximal stem and evidence for indirect recognition of processing sites in pre-rRNA processing in yeast.
|
| |
Nucleic Acids Res,
29,
2106-2116.
|
|
|
|
|
|
|
C.M.Spahn,
G.Blaha,
R.K.Agrawal,
P.Penczek,
R.A.Grassucci,
C.A.Trieber,
S.R.Connell,
D.E.Taylor,
K.H.Nierhaus,
and
J.Frank
(2001).
Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance.
|
| |
Mol Cell,
7,
1037-1045.
|
|
|
|
|
|
|
C.M.Spahn,
J.S.Kieft,
R.A.Grassucci,
P.A.Penczek,
K.Zhou,
J.A.Doudna,
and
J.Frank
(2001).
Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit.
|
| |
Science,
291,
1959-1962.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
C.O.Gualerzi,
L.Brandi,
E.Caserta,
C.Garofalo,
M.Lammi,
A.La Teana,
D.Petrelli,
R.Spurio,
J.Tomsic,
and
C.L.Pon
(2001).
Initiation factors in the early events of mRNA translation in bacteria.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
363-376.
|
|
|
|
|
|
|
C.R.Woese
(2001).
Translation: in retrospect and prospect.
|
| |
RNA,
7,
1055-1067.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
D.H.Bamford,
R.J.Gilbert,
J.M.Grimes,
and
D.I.Stuart
(2001).
Macromolecular assemblies: greater than their parts.
|
| |
Curr Opin Struct Biol,
11,
107-113.
|
|
|
|
|
|
|
D.J.Klein,
T.M.Schmeing,
P.B.Moore,
and
T.A.Steitz
(2001).
The kink-turn: a new RNA secondary structure motif.
|
| |
EMBO J,
20,
4214-4221.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.K.Treiber,
and
J.R.Williamson
(2001).
Beyond kinetic traps in RNA folding.
|
| |
Curr Opin Struct Biol,
11,
309-314.
|
|
|
|
|
|
|
D.Petrelli,
A.LaTeana,
C.Garofalo,
R.Spurio,
C.L.Pon,
and
C.O.Gualerzi
(2001).
Translation initiation factor IF3: two domains, five functions, one mechanism?
|
| |
EMBO J,
20,
4560-4569.
|
|
|
|
|
|
|
E.C.Koc,
W.Burkhart,
K.Blackburn,
H.Koc,
A.Moseley,
and
L.L.Spremulli
(2001).
Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approach.
|
| |
Protein Sci,
10,
471-481.
|
|
|
|
|
|
|
F.Leontiadou,
D.Triantafillidou,
and
T.Choli-Papadopoulou
(2001).
On the characterization of the putative S20-thx operon of Thermus thermophilus.
|
| |
Biol Chem,
382,
1001-1006.
|
|
|
|
|
|
|
F.Robert,
and
L.Brakier-Gingras
(2001).
Ribosomal protein S7 from Escherichia coli uses the same determinants to bind 16S ribosomal RNA and its messenger RNA.
|
| |
Nucleic Acids Res,
29,
677-682.
|
|
|
|
|
|
|
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.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.
|
|
|
|
|
|
|
I.Moll,
M.Huber,
S.Grill,
P.Sairafi,
F.Mueller,
R.Brimacombe,
P.Londei,
and
U.Bläsi
(2001).
Evidence against an Interaction between the mRNA downstream box and 16S rRNA in translation initiation.
|
| |
J Bacteriol,
183,
3499-3505.
|
|
|
|
|
|
|
J.Frank
(2001).
Cryo-electron microscopy as an investigative tool: the ribosome as an example.
|
| |
Bioessays,
23,
725-732.
|
|
|
|
|
|
|
J.Frank,
and
R.K.Agrawal
(2001).
Ratchet-like movements between the two ribosomal subunits: their implications in elongation factor recognition and tRNA translocation.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
67-75.
|
|
|
|
|
|
|
J.L.Hansen,
T.M.Schmeing,
D.J.Klein,
J.A.Ippolito,
N.Ban,
P.Nissen,
B.Freeborn,
P.B.Moore,
and
T.A.Steitz
(2001).
Progress toward an understanding of the structure and enzymatic mechanism of the large ribosomal subunit.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
33-42.
|
|
|
|
|
|
|
J.Moser,
W.D.Schubert,
V.Beier,
I.Bringemeier,
D.Jahn,
and
D.W.Heinz
(2001).
V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis.
|
| |
EMBO J,
20,
6583-6590.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Sengupta,
R.K.Agrawal,
and
J.Frank
(2001).
Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA.
|
| |
Proc Natl Acad Sci U S A,
98,
11991-11996.
|
|
|
|
|
|
|
L.Jaeger,
E.Westhof,
and
N.B.Leontis
(2001).
TectoRNA: modular assembly units for the construction of RNA nano-objects.
|
| |
Nucleic Acids Res,
29,
455-463.
|
|
|
|
|
|
|
L.P.Beales,
D.J.Rowlands,
and
A.Holzenburg
(2001).
The internal ribosome entry site (IRES) of hepatitis C virus visualized by electron microscopy.
|
| |
RNA,
7,
661-670.
|
|
|
|
|
|
|
M.I.Recht,
and
J.R.Williamson
(2001).
Thermodynamics and kinetics of central domain assembly.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
591-598.
|
|
|
|
|
|
|
M.I.Zvereva,
P.V.Ivanov,
Y.Teraoka,
N.I.Topilina,
O.A.Dontsova,
A.A.Bogdanov,
M.Kalkum,
K.H.Nierhaus,
and
O.V.Shpanchenko
(2001).
Complex of transfer-messenger RNA and elongation factor Tu. Unexpected modes of interaction.
|
| |
J Biol Chem,
276,
47702-47708.
|
|
|
|
|
|
|
M.Nomura
(2001).
Ribosomal RNA genes, RNA polymerases, nucleolar structures, and synthesis of rRNA in the yeast Saccharomyces cerevisiae.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
555-565.
|
|
|
|
|
|
|
M.Pioletti,
F.Schlünzen,
J.Harms,
R.Zarivach,
M.Glühmann,
H.Avila,
A.Bashan,
H.Bartels,
T.Auerbach,
C.Jacobi,
T.Hartsch,
A.Yonath,
and
F.Franceschi
(2001).
Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3.
|
| |
EMBO J,
20,
1829-1839.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.V.Rodnina,
and
W.Wintermeyer
(2001).
Ribosome fidelity: tRNA discrimination, proofreading and induced fit.
|
| |
Trends Biochem Sci,
26,
124-130.
|
|
|
|
|
|
|
M.W.Smith,
A.Meskauskas,
P.Wang,
P.V.Sergiev,
and
J.D.Dinman
(2001).
Saturation mutagenesis of 5S rRNA in Saccharomyces cerevisiae.
|
| |
Mol Cell Biol,
21,
8264-8275.
|
|
|
|
|
|
|
M.van Heel
(2001).
Do single (ribosome) molecules phase themselves?
|
| |
Cold Spring Harb Symp Quant Biol,
66,
77-86.
|
|
|
|
|
|
|
N.A.Baker,
D.Sept,
S.Joseph,
M.J.Holst,
and
J.A.McCammon
(2001).
Electrostatics of nanosystems: application to microtubules and the ribosome.
|
| |
Proc Natl Acad Sci U S A,
98,
10037-10041.
|
|
|
|
|
|
|
N.B.Leontis,
and
E.Westhof
(2001).
Geometric nomenclature and classification of RNA base pairs.
|
| |
RNA,
7,
499-512.
|
|
|
|
|
|
|
P.B.Moore
(2001).
The ribosome at atomic resolution.
|
| |
Biochemistry,
40,
3243-3250.
|
|
|
|
|
|
|
P.Nissen,
J.A.Ippolito,
N.Ban,
P.B.Moore,
and
T.A.Steitz
(2001).
RNA tertiary interactions in the large ribosomal subunit: the A-minor motif.
|
| |
Proc Natl Acad Sci U S A,
98,
4899-4903.
|
|
|
|
|
|
|
P.Sergiev,
A.Leonov,
S.Dokudovskaya,
O.Shpanchenko,
O.Dontsova,
A.Bogdanov,
J.Rinke-Appel,
F.Mueller,
M.Osswald,
K.von Knoblauch,
and
R.Brimacombe
(2001).
Correlating the X-ray structures for halo- and thermophilic ribosomal subunits with biochemical data for the Escherichia coli ribosome.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
87.
|
|
|
|
|
|
|
R.Willumeit,
G.Diedrich,
S.Forthmann,
J.Beckmann,
R.P.May,
H.B.Stuhrmann,
and
K.H.Nierhaus
(2001).
Mapping proteins of the 50S subunit from Escherichia coli ribosomes.
|
| |
Biochim Biophys Acta,
1520,
7.
|
|
|
|
|
|
|
S.Jones,
D.T.Daley,
N.M.Luscombe,
H.M.Berman,
and
J.M.Thornton
(2001).
Protein-RNA interactions: a structural analysis.
|
| |
Nucleic Acids Res,
29,
943-954.
|
|
|
|
|
|
|
S.Soelaiman,
K.Jakes,
N.Wu,
C.Li,
and
M.Shoham
(2001).
Crystal structure of colicin E3: implications for cell entry and ribosome inactivation.
|
| |
Mol Cell,
8,
1053-1062.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.T.Gregory,
J.H.Cate,
and
A.E.Dahlberg
(2001).
Spontaneous erythromycin resistance mutation in a 23S rRNA gene, rrlA, of the extreme thermophile Thermus thermophilus IB-21.
|
| |
J Bacteriol,
183,
4382-4385.
|
|
|
|
|
|
|
T.Yoshida,
S.Uchiyama,
H.Nakano,
H.Kashimori,
H.Kijima,
T.Ohshima,
Y.Saihara,
T.Ishino,
H.Shimahara,
T.Yoshida,
K.Yokose,
T.Ohkubo,
A.Kaji,
and
Y.Kobayashi
(2001).
Solution structure of the ribosome recycling factor from Aquifex aeolicus.
|
| |
Biochemistry,
40,
2387-2396.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
U.Nagaswamy,
X.Gao,
S.A.Martinis,
and
G.E.Fox
(2001).
NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop.
|
| |
Nucleic Acids Res,
29,
5129-5139.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
V.Ramakrishnan,
and
P.B.Moore
(2001).
Atomic structures at last: the ribosome in 2000.
|
| |
Curr Opin Struct Biol,
11,
144-154.
|
|
|
|
|
|
|
Y.G.Kim,
S.Maas,
and
A.Rich
(2001).
Comparative mutational analysis of cis-acting RNA signals for translational frameshifting in HIV-1 and HTLV-2.
|
| |
Nucleic Acids Res,
29,
1125-1131.
|
|
|
|
|
|
|
Z.Li,
G.Stahl,
and
P.J.Farabaugh
(2001).
Programmed +1 frameshifting stimulated by complementarity between a downstream mRNA sequence and an error-correcting region of rRNA.
|
| |
RNA,
7,
275-284.
|
|
|
|
|
|
|
M.W.Hentze,
E.Izaurralde,
and
B.Séraphin
(2000).
A new era for the RNA world. Conference: RNA 2000.
|
| |
EMBO Rep,
1,
394-398.
|
|
|
|
|
|
|
R.Brimacombe
(2000).
The bacterial ribosome at atomic resolution.
|
| |
Structure,
8,
R195-R200.
|
|
|
|
|
|
|
S.Chandra Sanyal,
and
A.Liljas
(2000).
The end of the beginning: structural studies of ribosomal proteins.
|
| |
Curr Opin Struct Biol,
10,
633-636.
|
|
|
|
|
|
|
S.Connell,
and
K.Nierhaus
(2000).
Translational termination not yet at its end.
|
| |
Chembiochem,
1,
250-253.
|
|
|
|
|
|
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
code is
shown on the right.
|
| |
Links
