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Contents |
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159 a.a.*
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145 a.a.*
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97 a.a.*
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135 a.a.*
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136 a.a.*
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88 a.a.*
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89 a.a.*
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100 a.a.*
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220 a.a.*
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164 a.a.*
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133 a.a.*
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* Residue conservation analysis
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* C-alpha coords only
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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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Fitting of components with known structure into an 11.5 a cryo-em map of the e.Coli 70s ribosome
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Structure:
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Fragment of 16s rrna helix 23. Chain: i. Fragment: residues 673-713. Other_details: modeled as analogous fragment of t. Thermophilus taken from PDB entry 1qd7. Fragment of 23s rrna. Chain: l. Fragment: residues 1051-1108. Other_details: t. Maritima RNA sequence and model taken
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Source:
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Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
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Authors:
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I.S.Gabashvili,R.K.Agrawal,C.M.T.Spahn,R.A.Grassucci, D.I.Svergun,J.Frank,P.Penczek
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Key ref:
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I.S.Gabashvili
et al.
(2000).
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
Cell,
100,
537-549.
PubMed id:
DOI:
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Date:
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11-Feb-00
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Release date:
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06-Mar-00
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P81288
(RS4_GEOSE) -
30S ribosomal protein S4
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Seq:
Struc:
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200 a.a.
159 a.a.*
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P02357
(RS5_GEOSE) -
30S ribosomal protein S5
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Seq:
Struc:
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166 a.a.
145 a.a.
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P23370
(RS6_THETH) -
30S ribosomal protein S6
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Seq:
Struc:
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101 a.a.
97 a.a.
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P17291
(RS7_THET8) -
30S ribosomal protein S7
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Seq:
Struc:
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156 a.a.
135 a.a.
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P24319
(RS8_THETH) -
30S ribosomal protein S8
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Seq:
Struc:
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138 a.a.
136 a.a.
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P80378
(RS15_THETH) -
30S ribosomal protein S15
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Seq:
Struc:
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89 a.a.
88 a.a.
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P23828
(RS17_GEOSE) -
30S ribosomal protein S17
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Seq:
Struc:
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87 a.a.
89 a.a.*
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No UniProt id for this chain
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P27150
(RL1_THETH) -
50S ribosomal protein L1
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Seq:
Struc:
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229 a.a.
220 a.a.
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Gene Ontology (GO) functional annotation
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Cellular component
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intracellular
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5 terms
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Biological process
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RNA processing
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3 terms
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Biochemical function
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structural constituent of ribosome
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4 terms
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DOI no:
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Cell
100:537-549
(2000)
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PubMed id:
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| |
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Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
|
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I.S.Gabashvili,
R.K.Agrawal,
C.M.Spahn,
R.A.Grassucci,
D.I.Svergun,
J.Frank,
P.Penczek.
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ABSTRACT
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Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl
initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map
of the complex. This map allows identification of RNA helices, peripheral
proteins, and intersubunit bridges. Comparison of double-stranded RNA regions
and positions of proteins identified in both cryo-EM and X-ray maps indicates
good overall agreement but points to rearrangements of ribosomal components
required for the subunit association. Fitting of known components of the 50S
stalk base region into the map defines the architecture of the GTPase-associated
center and reveals a major change in the orientation of the alpha-sarcin-ricin
loop. Analysis of the bridging connections between the subunits provides insight
into the dynamic signaling mechanism between the ribosomal subunits.
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Selected figure(s)
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Figure 2.
Figure 2. The 11.5 Å Resolution Cryo-EM Map of the E.
coli 70S RibosomeThe cryo-EM map is shown in (a)
subunit–subunit side view, (b) 30S subunit solvent–side
view, (c) top view, and (d) the 50S subunit solvent–side view.
Domains and features of the 30S subunit (yellow, with helix
44 shown in red) and 50S subunit (blue) are as follows: b, body;
h, head; pt, platform; sp, spur; sh, shoulder; St, stalk base;
L1, protein L1; and CP, central protuberance. * and # mark sites
of the shoulder contacting the head in Cate et al., 1999. V
marks the v-shaped structure possibly representing helices of
the 5S rRNA. Inset (upper left) displays cryo-EM map of the
fMet-tRNA[f]^Met (green), with arrows pointing to sites
interacting with ribosomal components (left), and the expected
appearance of fMet-tRNA[f]^Met ([51]) at  vert,
similar 10 Å resolution (right).
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Figure 4.
Figure 4. Examples for Fittings of Proteins into the
Cryo-EM Density MapFittings of protein crystal structures
(carbon backbones) into the cryo-EM density (white, wire-mesh),
displayed in stereo. Top, S5 ([49]); center, S6 ( [38]); bottom,
S7 ( [31 and 59]). These protein structures are displayed on the
30S subunit map in Figure 5 in corresponding colors.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2000,
100,
537-549)
copyright 2000.
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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
|
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| |
PubMed id
|
|
Reference
|
|
|
|
|
|
C.L.Lawson
(2010).
Unified data resource for cryo-EM.
|
| |
Methods Enzymol, 483,
73-90.
|
|
|
|
|
|
|
H.Y.Liao,
and
J.Frank
(2010).
Definition and estimation of resolution in single-particle reconstructions.
|
| |
Structure, 18,
768-775.
|
|
|
|
|
|
|
J.A.Dunkle,
and
J.H.Cate
(2010).
Ribosome structure and dynamics during translocation and termination.
|
| |
Annu Rev Biophys, 39,
227-244.
|
|
|
|
|
|
|
J.Sengupta,
C.Bussiere,
J.Pallesen,
M.West,
A.W.Johnson,
and
J.Frank
(2010).
Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit.
|
| |
J Cell Biol, 189,
1079-1086.
|
|
|
|
|
|
|
M.R.Sharma,
A.Dönhöfer,
C.Barat,
V.Marquez,
P.P.Datta,
P.Fucini,
D.N.Wilson,
and
R.K.Agrawal
(2010).
PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G).
|
| |
J Biol Chem, 285,
4006-4014.
|
|
|
|
|
|
|
T.Kato,
H.Yoshida,
T.Miyata,
Y.Maki,
A.Wada,
and
K.Namba
(2010).
Structure of the 100S ribosome in the hibernation stage revealed by electron cryomicroscopy.
|
| |
Structure, 18,
719-724.
|
|
|
|
|
|
|
A.Matsumoto,
and
H.Ishida
(2009).
Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures.
|
| |
Structure, 17,
1605-1613.
|
|
|
|
|
|
|
A.S.Spirin
(2009).
The ribosome as a conveying thermal ratchet machine.
|
| |
J Biol Chem, 284,
21103-21119.
|
|
|
|
|
|
|
C.M.Clemson,
J.N.Hutchinson,
S.A.Sara,
A.W.Ensminger,
A.H.Fox,
A.Chess,
and
J.B.Lawrence
(2009).
An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles.
|
| |
Mol Cell, 33,
717-726.
|
|
|
|
|
|
|
F.Brandt,
S.A.Etchells,
J.O.Ortiz,
A.H.Elcock,
F.U.Hartl,
and
W.Baumeister
(2009).
The native 3D organization of bacterial polysomes.
|
| |
Cell, 136,
261-271.
|
|
|
|
|
|
|
H.J.Ha,
W.S.Song,
H.M.Kim,
H.S.Son,
and
K.Lee
(2009).
Functional study of the residue C899 in the 900 tetraloop of Escherichia coli small subunit ribosomal RNA.
|
| |
Biosci Biotechnol Biochem, 73,
2544-2546.
|
|
|
|
|
|
|
J.Curuksu,
J.Sponer,
and
M.Zacharias
(2009).
Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations.
|
| |
Biophys J, 97,
2004-2013.
|
|
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|
|
|
|
J.Frank
(2009).
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.
|
| |
Q Rev Biophys, 42,
139-158.
|
|
|
|
|
|
|
M.Han,
Y.Mei,
H.Khant,
and
S.J.Ludtke
(2009).
Characterization of antibiotic peptide pores using cryo-EM and comparison to neutron scattering.
|
| |
Biophys J, 97,
164-172.
|
|
|
|
|
|
|
M.R.Sharma,
T.M.Booth,
L.Simpson,
D.A.Maslov,
and
R.K.Agrawal
(2009).
Structure of a mitochondrial ribosome with minimal RNA.
|
| |
Proc Natl Acad Sci U S A, 106,
9637-9642.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Shatsky,
R.J.Hall,
S.E.Brenner,
and
R.M.Glaeser
(2009).
A method for the alignment of heterogeneous macromolecules from electron microscopy.
|
| |
J Struct Biol, 166,
67-78.
|
|
|
|
|
|
|
W.Zhang,
J.A.Dunkle,
and
J.H.Cate
(2009).
Structures of the ribosome in intermediate states of ratcheting.
|
| |
Science, 325,
1014-1017.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
Z.Lu,
T.R.Shaikh,
D.Barnard,
X.Meng,
H.Mohamed,
A.Yassin,
C.A.Mannella,
R.K.Agrawal,
T.M.Lu,
and
T.Wagenknecht
(2009).
Monolithic microfluidic mixing-spraying devices for time-resolved cryo-electron microscopy.
|
| |
J Struct Biol, 168,
388-395.
|
|
|
|
|
|
|
D.Piekna-Przybylska,
P.Przybylski,
A.Baudin-Baillieu,
J.P.Rousset,
and
M.J.Fournier
(2008).
Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit.
|
| |
J Biol Chem, 283,
26026-26036.
|
|
|
|
|
|
|
J.B.Munro,
A.Vaiana,
K.Y.Sanbonmatsu,
and
S.C.Blanchard
(2008).
A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET.
|
| |
Biopolymers, 89,
565-577.
|
|
|
|
|
|
|
J.Heredia-Moya,
and
K.L.Kirk
(2008).
Synthesis of beta-(S-methyl)thioaspartic acid and derivatives.
|
| |
Bioorg Med Chem, 16,
5908-5913.
|
|
|
|
|
|
|
J.LeBarron,
R.A.Grassucci,
T.R.Shaikh,
W.T.Baxter,
J.Sengupta,
and
J.Frank
(2008).
Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.
|
| |
J Struct Biol, 164,
24-32.
|
|
|
|
|
|
|
K.Bakowska-Zywicka,
A.M.Kietrys,
and
T.Twardowski
(2008).
Antisense oligonucleotides targeting universally conserved 26S rRNA domains of plant ribosomes at different steps of polypeptide elongation.
|
| |
Oligonucleotides, 18,
175-186.
|
|
|
|
|
|
|
M.Cottevieille,
E.Larquet,
S.Jonic,
M.V.Petoukhov,
G.Caprini,
S.Paravisi,
D.I.Svergun,
M.A.Vanoni,
and
N.Boisset
(2008).
The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution: functional implications.
|
| |
J Biol Chem, 283,
8237-8249.
|
|
|
PDB code:
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|
|
|
|
|
|
M.F.Schmid,
and
C.R.Booth
(2008).
Methods for aligning and for averaging 3D volumes with missing data.
|
| |
J Struct Biol, 161,
243-248.
|
|
|
|
|
|
|
P.Julián,
A.L.Konevega,
S.H.Scheres,
M.Lázaro,
D.Gil,
W.Wintermeyer,
M.V.Rodnina,
and
M.Valle
(2008).
Structure of ratcheted ribosomes with tRNAs in hybrid states.
|
| |
Proc Natl Acad Sci U S A, 105,
16924-16927.
|
|
|
|
|
|
|
R.Ero,
L.Peil,
A.Liiv,
and
J.Remme
(2008).
Identification of pseudouridine methyltransferase in Escherichia coli.
|
| |
RNA, 14,
2223-2233.
|
|
|
|
|
|
|
S.Jonić,
C.O.Sorzano,
and
N.Boisset
(2008).
Comparison of single-particle analysis and electron tomography approaches: an overview.
|
| |
J Microsc, 232,
562-579.
|
|
|
|
|
|
|
S.M.Stagg,
G.C.Lander,
J.Quispe,
N.R.Voss,
A.Cheng,
H.Bradlow,
S.Bradlow,
B.Carragher,
and
C.S.Potter
(2008).
A test-bed for optimizing high-resolution single particle reconstructions.
|
| |
J Struct Biol, 163,
29-39.
|
|
|
|
|
|
|
T.Monshupanee,
S.T.Gregory,
S.Douthwaite,
W.Chungjatupornchai,
and
A.E.Dahlberg
(2008).
Mutations in conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications.
|
| |
J Bacteriol, 190,
7754-7761.
|
|
|
|
|
|
|
T.R.Shaikh,
H.Gao,
W.T.Baxter,
F.J.Asturias,
N.Boisset,
A.Leith,
and
J.Frank
(2008).
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.
|
| |
Nat Protoc, 3,
1941-1974.
|
|
|
|
|
|
|
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J.Lei,
J.L.Brunelle,
R.F.Ortiz-Meoz,
R.Green,
and
J.Frank
(2008).
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome.
|
| |
Mol Cell, 32,
190-197.
|
|
|
|
|
|
|
A.L.Konevega,
N.Fischer,
Y.P.Semenkov,
H.Stark,
W.Wintermeyer,
and
M.V.Rodnina
(2007).
Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.
|
| |
Nat Struct Mol Biol, 14,
318-324.
|
|
|
|
|
|
|
A.L.Manuell,
J.Quispe,
and
S.P.Mayfield
(2007).
Structure of the chloroplast ribosome: novel domains for translation regulation.
|
| |
PLoS Biol, 5,
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|
|
|
|
|
|
|
C.Barat,
P.P.Datta,
V.S.Raj,
M.R.Sharma,
H.Kaji,
A.Kaji,
and
R.K.Agrawal
(2007).
Progression of the ribosome recycling factor through the ribosome dissociates the two ribosomal subunits.
|
| |
Mol Cell, 27,
250-261.
|
|
|
|
|
|
|
C.O.Sorzano,
S.Jonic,
M.Cottevieille,
E.Larquet,
N.Boisset,
and
S.Marco
(2007).
3D electron microscopy of biological nanomachines: principles and applications.
|
| |
Eur Biophys J, 36,
995.
|
|
|
|
|
|
|
C.V.Robinson,
A.Sali,
and
W.Baumeister
(2007).
The molecular sociology of the cell.
|
| |
Nature, 450,
973-982.
|
|
|
|
|
|
|
D.J.Taylor,
J.Nilsson,
A.R.Merrill,
G.R.Andersen,
P.Nissen,
and
J.Frank
(2007).
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
|
| |
EMBO J, 26,
2421-2431.
|
|
|
PDB codes:
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|
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|
|
F.Rázga,
J.Koca,
A.Mokdad,
and
J.Sponer
(2007).
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.
|
| |
Nucleic Acids Res, 35,
4007-4017.
|
|
|
|
|
|
|
G.Hirokawa,
H.Kaji,
and
A.Kaji
(2007).
Inhibition of antiassociation activity of translation initiation factor 3 by paromomycin.
|
| |
Antimicrob Agents Chemother, 51,
175-180.
|
|
|
|
|
|
|
H.Gao,
Z.Zhou,
U.Rawat,
C.Huang,
L.Bouakaz,
C.Wang,
Z.Cheng,
Y.Liu,
A.Zavialov,
R.Gursky,
S.Sanyal,
M.Ehrenberg,
J.Frank,
and
H.Song
(2007).
RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors.
|
| |
Cell, 129,
929-941.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Lacadena,
E.Alvarez-García,
N.Carreras-Sangrà,
E.Herrero-Galán,
J.Alegre-Cebollada,
L.García-Ortega,
M.Oñaderra,
J.G.Gavilanes,
and
A.Martínez del Pozo
(2007).
Fungal ribotoxins: molecular dissection of a family of natural killers.
|
| |
FEMS Microbiol Rev, 31,
212-237.
|
|
|
|
|
|
|
M.R.Sharma,
D.N.Wilson,
P.P.Datta,
C.Barat,
F.Schluenzen,
P.Fucini,
and
R.K.Agrawal
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Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
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Proc Natl Acad Sci U S A, 104,
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PDB codes:
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N.Gao,
A.V.Zavialov,
M.Ehrenberg,
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Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
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J Mol Biol, 374,
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PDB code:
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P.P.Datta,
D.N.Wilson,
M.Kawazoe,
N.K.Swami,
T.Kaminishi,
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T.M.Booth,
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Structural aspects of RbfA action during small ribosomal subunit assembly.
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Mol Cell, 28,
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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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Nucleic Acids Res, 35,
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R.Gillet,
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Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
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J Biol Chem, 282,
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PDB code:
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A.Pulk,
U.Maiväli,
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Identification of nucleotides in E. coli 16S rRNA essential for ribosome subunit association.
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RNA, 12,
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Mechanism of recycling of post-termination ribosomal complexes in eubacteria: a new role of initiation factor 3.
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I.K.Ali,
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Deletion of a conserved, central ribosomal intersubunit RNA bridge.
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Mol Cell, 23,
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K.Mitra,
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F.Fabiola,
M.S.Chapman,
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Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
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Mol Cell, 22,
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PDB codes:
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K.Mitra,
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Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.
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N.Spacková,
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Molecular dynamics simulations of sarcin-ricin rRNA motif.
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O.Rackham,
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Functional epitopes at the ribosome subunit interface.
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Nat Chem Biol, 2,
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Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.
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Proc Natl Acad Sci U S A, 103,
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D.N.Wilson,
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J.M.Harms,
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X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
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EMBO J, 24,
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PDB code:
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F.Rázga,
J.Koca,
J.Sponer,
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Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement.
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Structure, 13,
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H.Gao,
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The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components.
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Proc Natl Acad Sci U S A, 102,
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5S rRNA: Structure and Function from Head to Toe.
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Int J Biomed Sci, 1,
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K.Lipkow,
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Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli.
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J Bacteriol, 187,
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K.Mitra,
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Structure of the E. coli protein-conducting channel bound to a translating ribosome.
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Nature, 438,
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PDB codes:
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L.Cochella,
and
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An active role for tRNA in decoding beyond codon:anticodon pairing.
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Science, 308,
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M.Sumita,
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L.Clos,
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Effects of nucleotide substitution and modification on the stability and structure of helix 69 from 28S rRNA.
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RNA, 11,
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N.Gao,
A.V.Zavialov,
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J.Sengupta,
M.Valle,
R.P.Gursky,
M.Ehrenberg,
and
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Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
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Mol Cell, 18,
663-674.
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PDB codes:
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N.V.Hud,
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Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size.
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Annu Rev Biophys Biomol Struct, 34,
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P.P.Datta,
M.R.Sharma,
L.Qi,
J.Frank,
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Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM.
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Mol Cell, 20,
723-731.
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PDB code:
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R.J.Gilbert,
L.Beales,
D.Blond,
M.N.Simon,
B.Y.Lin,
F.V.Chisari,
D.I.Stuart,
and
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Hepatitis B small surface antigen particles are octahedral.
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Proc Natl Acad Sci U S A, 102,
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C.A.Angell
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Amorphous water.
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Annu Rev Phys Chem, 55,
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C.M.Spahn,
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A.Mulder,
R.A.Grassucci,
P.Sarnow,
and
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Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
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Cell, 118,
465-475.
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C.M.Spahn,
M.G.Gomez-Lorenzo,
R.A.Grassucci,
R.Jørgensen,
G.R.Andersen,
R.Beckmann,
P.A.Penczek,
J.P.Ballesta,
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Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
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EMBO J, 23,
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PDB codes:
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I.I.Serysheva
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Structural insights into excitation-contraction coupling by electron cryomicroscopy.
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Biochemistry (Mosc), 69,
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J.Sengupta,
J.Nilsson,
R.Gursky,
C.M.Spahn,
P.Nissen,
and
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Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-EM.
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Nat Struct Mol Biol, 11,
957-962.
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PDB code:
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Q.X.Jiang,
D.N.Wang,
and
R.MacKinnon
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Electron microscopic analysis of KvAP voltage-dependent K+ channels in an open conformation.
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Nature, 430,
806-810.
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R.K.Agrawal,
M.R.Sharma,
M.C.Kiel,
G.Hirokawa,
T.M.Booth,
C.M.Spahn,
R.A.Grassucci,
A.Kaji,
and
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Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications.
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Proc Natl Acad Sci U S A, 101,
8900-8905.
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PDB codes:
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S.Subramaniam,
and
J.L.Milne
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Three-dimensional electron microscopy at molecular resolution.
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Annu Rev Biophys Biomol Struct, 33,
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U.Maiväli,
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Definition of bases in 23S rRNA essential for ribosomal subunit association.
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RNA, 10,
600-604.
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W.V.Nicholson
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Object detection by correlation coefficients using azimuthally averaged reference projections.
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IEEE Trans Biomed Eng, 51,
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W.V.Nicholson,
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Correlation-based methods of automatic particle detection in electron microscopy images with smoothing by anisotropic diffusion.
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J Microsc, 213,
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A.Nikulin,
I.Eliseikina,
S.Tishchenko,
N.Nevskaya,
N.Davydova,
O.Platonova,
W.Piendl,
M.Selmer,
A.Liljas,
D.Drygin,
R.Zimmermann,
M.Garber,
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Structure of the L1 protuberance in the ribosome.
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Nat Struct Biol, 10,
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PDB code:
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A.V.Zavialov,
and
M.Ehrenberg
(2003).
Peptidyl-tRNA regulates the GTPase activity of translation factors.
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Cell, 114,
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F.Tama,
M.Valle,
J.Frank,
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Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy.
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Proc Natl Acad Sci U S A, 100,
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H.Gao,
J.Sengupta,
M.Valle,
A.Korostelev,
N.Eswar,
S.M.Stagg,
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R.K.Agrawal,
S.C.Harvey,
A.Sali,
M.S.Chapman,
and
J.Frank
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Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
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Cell, 113,
789-801.
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PDB codes:
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I.S.Gabashvili,
M.Whirl-Carrillo,
M.Bada,
D.R.Banatao,
and
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Ribosomal dynamics inferred from variations in experimental measurements.
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RNA, 9,
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J.Frank
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Toward an understanding of the structural basis of translation.
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Genome Biol, 4,
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J.Frank
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Electron microscopy of functional ribosome complexes.
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Biopolymers, 68,
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M.R.Sharma,
E.C.Koc,
P.P.Datta,
T.M.Booth,
L.L.Spremulli,
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Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins.
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Cell, 115,
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M.Valle,
A.Zavialov,
J.Sengupta,
U.Rawat,
M.Ehrenberg,
and
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Locking and unlocking of ribosomal motions.
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Cell, 114,
123-134.
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PDB codes:
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S.R.Connell,
C.A.Trieber,
G.P.Dinos,
E.Einfeldt,
D.E.Taylor,
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Mechanism of Tet(O)-mediated tetracycline resistance.
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EMBO J, 22,
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U.B.Rawat,
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R.A.Grassucci,
J.Linde,
B.Vestergaard,
M.Ehrenberg,
and
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A cryo-electron microscopic study of ribosome-bound termination factor RF2.
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Nature, 421,
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PDB codes:
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C.S.Tung,
S.Joseph,
and
K.Y.Sanbonmatsu
(2002).
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
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Nat Struct Biol, 9,
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PDB code:
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D.Mandelman,
P.Gonzalo,
J.P.Lavergne,
C.Corbier,
J.P.Reboud,
and
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Crystallization and preliminary X-ray study of an N-terminal fragment of rat liver ribosomal P2 protein.
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Acta Crystallogr D Biol Crystallogr, 58,
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G.Caetano-Anollés
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Tracing the evolution of RNA structure in ribosomes.
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Nucleic Acids Res, 30,
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Binding of ribosome recycling factor to ribosomes, comparison with tRNA.
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J Biol Chem, 277,
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H.Stark,
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Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
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Nat Struct Biol, 9,
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PDB code:
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J.A.Doudna,
and
V.L.Rath
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Structure and function of the eukaryotic ribosome: the next frontier.
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Cell, 109,
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J.Brink,
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Quaternary structure of human fatty acid synthase by electron cryomicroscopy.
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Proc Natl Acad Sci U S A, 99,
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Single-particle imaging of macromolecules by cryo-electron microscopy.
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Annu Rev Biophys Biomol Struct, 31,
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J.L.Craighead,
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Structure of yeast RNA polymerase II in solution: implications for enzyme regulation and interaction with promoter DNA.
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Structure, 10,
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M.A.Schäfer,
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Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit.
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J Biol Chem, 277,
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M.Valle,
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K.H.Nierhaus,
R.K.Agrawal,
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Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.
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EMBO J, 21,
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PDB codes:
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T.Uchiumi,
S.Honma,
Y.Endo,
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Ribosomal proteins at the stalk region modulate functional rRNA structures in the GTPase center.
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J Biol Chem, 277,
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Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches.
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Curr Opin Struct Biol, 12,
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A.Roll-Mecak,
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Engaging the ribosome: universal IFs of translation.
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Trends Biochem Sci, 26,
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B.F.McEwen,
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Electron tomographic and other approaches for imaging molecular machines.
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Curr Opin Neurobiol, 11,
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C.M.Spahn,
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R.K.Agrawal,
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R.A.Grassucci,
C.A.Trieber,
S.R.Connell,
D.E.Taylor,
K.H.Nierhaus,
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Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance.
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Mol Cell, 7,
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C.M.Spahn,
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Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit.
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Science, 291,
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C.M.Spahn,
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Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
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Cell, 107,
373-386.
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PDB codes:
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E.Nogales,
and
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Molecular Machines: putting the pieces together.
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J Cell Biol, 152,
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G.R.Andersen,
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Structural studies of eukaryotic elongation factors.
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Cold Spring Harb Symp Quant Biol, 66,
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H.F.Noller,
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Structure of the ribosome at 5.5 A resolution and its interactions with functional ligands.
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Cold Spring Harb Symp Quant Biol, 66,
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I.S.Gabashvili,
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The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22.
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Mol Cell, 8,
181-188.
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Cold Spring Harb Symp Quant Biol, 66,
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Staphylococcus aureus domain V functions in Escherichia coli ribosomes provided a conserved interaction with domain IV is restored.
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RNA, 7,
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M.V.Rodnina,
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Cryoelectron microscopy of lambda phage DNA condensates in vitreous ice: the fine structure of DNA toroids.
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Proc Natl Acad Sci U S A, 98,
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Correlating the X-ray structures for halo- and thermophilic ribosomal subunits with biochemical data for the Escherichia coli ribosome.
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Cold Spring Harb Symp Quant Biol, 66,
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R.Beckmann,
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Cold Spring Harb Symp Quant Biol, 66,
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Architecture of the protein-conducting channel associated with the translating 80S ribosome.
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Cell, 107,
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A mechanism for stop codon recognition by the ribosome: a bioinformatic approach.
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A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome.
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Structure, 8,
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Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 A resolution.
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The bacterial ribosome at atomic resolution.
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Structure, 8,
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R.K.Agrawal,
C.M.Spahn,
P.Penczek,
R.A.Grassucci,
K.H.Nierhaus,
and
J.Frank
(2000).
Visualization of tRNA movements on the Escherichia coli 70S ribosome during the elongation cycle.
|
| |
J Cell Biol, 150,
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PDB code:
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|
|
W.Wriggers,
R.K.Agrawal,
D.L.Drew,
A.McCammon,
and
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(2000).
Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures.
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Biophys J, 79,
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Y.Tao,
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(2000).
Recent developments in cryo-electron microscopy reconstruction of single particles.
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Curr Opin Struct Biol, 10,
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|
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|
|
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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