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Contents |
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206 a.a.*
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204 a.a.*
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148 a.a.*
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95 a.a.*
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137 a.a.*
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127 a.a.*
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99 a.a.*
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96 a.a.*
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101 a.a.*
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97 a.a.*
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115 a.a.*
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32 a.a.*
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86 a.a.*
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78 a.a.*
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79 a.a.*
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51 a.a.*
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65 a.a.*
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83 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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Real space refined coordinates of the 30s subunit fitted into the low resolution cryo-em map of the ef-g.Gtp state of e. Coli 70s ribosome
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Structure:
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16s ribosomal RNA. Chain: a. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5. Chain: e. 30s ribosomal protein s6.
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Source:
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Escherichia coli. Organism_taxid: 562. Strain: mre 600. Strain: mre 600
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Authors:
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H.Gao,J.Sengupta,M.Valle,A Korostelev,N.Eswar,S.M.Stagg, P.Van Roey,R.K.Agrawal,S.T.Harvey,A.Sali,M.S.Chapman,J.Fran
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Key ref:
|
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H.Gao
et al.
(2003).
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
Cell,
113,
789-801.
PubMed id:
DOI:
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Date:
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29-Apr-03
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Release date:
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17-Jun-03
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P0A7V3
(RS3_ECOLI) -
30S ribosomal protein S3
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Seq:
Struc:
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233 a.a.
206 a.a.
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P0A7V8
(RS4_ECOLI) -
30S ribosomal protein S4
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Seq:
Struc:
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206 a.a.
204 a.a.
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P0A7W1
(RS5_ECOLI) -
30S ribosomal protein S5
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|
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Seq:
Struc:
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167 a.a.
148 a.a.
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|
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P02358
(RS6_ECOLI) -
30S ribosomal protein S6
|
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|
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Seq:
Struc:
|
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135 a.a.
95 a.a.
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P02359
(RS7_ECOLI) -
30S ribosomal protein S7
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Seq:
Struc:
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179 a.a.
137 a.a.
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P0A7W7
(RS8_ECOLI) -
30S ribosomal protein S8
|
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|
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Seq:
Struc:
|
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130 a.a.
127 a.a.
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P0A7X3
(RS9_ECOLI) -
30S ribosomal protein S9
|
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Seq:
Struc:
|
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|
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130 a.a.
99 a.a.
|
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|
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P0A7R5
(RS10_ECOLI) -
30S ribosomal protein S10
|
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|
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Seq:
Struc:
|
|
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103 a.a.
96 a.a.
|
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|
|
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P0A7R9
(RS11_ECOLI) -
30S ribosomal protein S11
|
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|
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Seq:
Struc:
|
|
|
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129 a.a.
101 a.a.
|
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|
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P0A7S3
(RS12_ECOLI) -
30S ribosomal protein S12
|
|
|
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Seq:
Struc:
|
|
|
|
124 a.a.
97 a.a.
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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P0A7S9
(RS13_ECOLI) -
30S ribosomal protein S13
|
|
|
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Seq:
Struc:
|
|
|
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118 a.a.
115 a.a.
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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P0AG59
(RS14_ECOLI) -
30S ribosomal protein S14
|
|
|
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Seq:
Struc:
|
|
|
|
101 a.a.
32 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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P0ADZ4
(RS15_ECOLI) -
30S ribosomal protein S15
|
|
|
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Seq:
Struc:
|
|
|
|
89 a.a.
86 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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P0A7T3
(RS16_ECOLI) -
30S ribosomal protein S16
|
|
|
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Seq:
Struc:
|
|
|
|
82 a.a.
78 a.a.
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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P0AG63
(RS17_ECOLI) -
30S ribosomal protein S17
|
|
|
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Seq:
Struc:
|
|
|
|
84 a.a.
79 a.a.
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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P0A7T7
(RS18_ECOLI) -
30S ribosomal protein S18
|
|
|
|
Seq:
Struc:
|
|
|
|
75 a.a.
51 a.a.
|
|
|
|
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|
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|
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Gene Ontology (GO) functional annotation
|
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Cellular component
|
intracellular
|
6 terms
|
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Biological process
|
response to antibiotic
|
12 terms
|
|
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Biochemical function
|
structural constituent of ribosome
|
14 terms
|
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| |
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| |
|
DOI no:
|
Cell
113:789-801
(2003)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
|
|
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,
J.Frank.
|
|
|
|
|
| |
ABSTRACT
|
|
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|
| |
|
|
Cryo-EM density maps showing the 70S ribosome of E. coli in two different
functional states related by a ratchet-like motion were analyzed using
real-space refinement. Comparison of the two resulting atomic models shows that
the ribosome changes from a compact structure to a looser one, coupled with the
rearrangement of many of the proteins. Furthermore, in contrast to the unchanged
inter-subunit bridges formed wholly by RNA, the bridges involving proteins
undergo large conformational changes following the ratchet-like motion,
suggesting an important role of ribosomal proteins in facilitating the dynamics
of translation.
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|
| |
Selected figure(s)
|
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| |
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|
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|
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Figure 6.
Figure 6. Stereo Views of the Protein Conformational
Changes between the Initiation-Like and the EF-G·GTP
Bound StatesThe proteins in the initiation-like and the
EF-G·GTP bound states are colored in red and green,
respectively.(A) mRNA entrance channel.(B) mRNA exit channel.(C)
Polypeptide exit tunnel.(D) 70S proteins.
|
|
Figure 7.
Figure 7. Diagrammatic Presentation of Interaction between
the 30S Subunit and Proteins L2, L5, and L14The interacting
regions of L2, L5, and L14 on the 30S subunit are marked with
stars. The geometrically rotational center region of the 30S
subunit is colored in cyan. Landmarks: bk, beak; sp, spur.
|
|
|
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|
| |
The above figures are
reprinted
by permission from Cell Press:
Cell
(2003,
113,
789-801)
copyright 2003.
|
|
| |
Figures were
selected
by the author.
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 |
 |
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Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
D.N.Ermolenko,
and
H.F.Noller
(2011).
mRNA translocation occurs during the second step of ribosomal intersubunit rotation.
|
| |
Nat Struct Mol Biol, 18,
457-462.
|
|
|
|
|
|
|
J.Fu,
J.B.Munro,
S.C.Blanchard,
and
J.Frank
(2011).
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
|
| |
Proc Natl Acad Sci U S A, 108,
4817-4821.
|
|
|
|
|
|
|
Q.Sun,
A.Vila-Sanjurjo,
and
M.O'Connor
(2011).
Mutations in the intersubunit bridge regions of 16S rRNA affect decoding and subunit-subunit interactions on the 70S ribosome.
|
| |
Nucleic Acids Res, 39,
3321-3330.
|
|
|
|
|
|
|
R.J.Hall,
E.Nogales,
and
R.M.Glaeser
(2011).
Accurate modeling of single-particle cryo-EM images quantitates the benefits expected from using Zernike phase contrast.
|
| |
J Struct Biol, 174,
468-475.
|
|
|
|
|
|
|
C.E.Aitken,
A.Petrov,
and
J.D.Puglisi
(2010).
Single ribosome dynamics and the mechanism of translation.
|
| |
Annu Rev Biophys, 39,
491-513.
|
|
|
|
|
|
|
I.Besseová,
K.Réblová,
N.B.Leontis,
and
J.Sponer
(2010).
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.
|
| |
Nucleic Acids Res, 38,
6247-6264.
|
|
|
|
|
|
|
J.Fu,
Y.Hashem,
I.Wower,
J.Lei,
H.Y.Liao,
C.Zwieb,
J.Wower,
and
J.Frank
(2010).
Visualizing the transfer-messenger RNA as the ribosome resumes translation.
|
| |
EMBO J, 29,
3819-3825.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Zhu,
L.Cheng,
Q.Fang,
Z.H.Zhou,
and
B.Honig
(2010).
Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.
|
| |
J Mol Biol, 397,
835-851.
|
|
|
|
|
|
|
K.Réblová,
F.Rázga,
W.Li,
H.Gao,
J.Frank,
and
J.Sponer
(2010).
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
|
| |
Nucleic Acids Res, 38,
1325-1340.
|
|
|
|
|
|
|
M.Rusu,
and
S.Birmanns
(2010).
Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.
|
| |
J Struct Biol, 170,
164-171.
|
|
|
|
|
|
|
M.Shatsky,
R.J.Hall,
E.Nogales,
J.Malik,
and
S.E.Brenner
(2010).
Automated multi-model reconstruction from single-particle electron microscopy data.
|
| |
J Struct Biol, 170,
98.
|
|
|
|
|
|
|
P.Khade,
and
S.Joseph
(2010).
Functional interactions by transfer RNAs in the ribosome.
|
| |
FEBS Lett, 584,
420-426.
|
|
|
|
|
|
|
X.Xu,
and
D.Cao
(2010).
Thermodynamic stability of polypeptides folding within modeled ribosomal exit tunnel: a density functional study.
|
| |
Eur Phys J E Soft Matter, 32,
307-318.
|
|
|
|
|
|
|
A.Korostelev,
M.Laurberg,
and
H.F.Noller
(2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
|
| |
Proc Natl Acad Sci U S A, 106,
18195-18200.
|
|
|
|
|
|
|
A.M.Karmali,
T.L.Blundell,
and
N.Furnham
(2009).
Model-building strategies for low-resolution X-ray crystallographic data.
|
| |
Acta Crystallogr D Biol Crystallogr, 65,
121-127.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
D.P.Giedroc,
and
P.V.Cornish
(2009).
Frameshifting RNA pseudoknots: structure and mechanism.
|
| |
Virus Res, 139,
193-208.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
I.Tinoco,
and
J.D.Wen
(2009).
Simulation and analysis of single-ribosome translation.
|
| |
Phys Biol, 6,
25006.
|
|
|
|
|
|
|
J.Frank
(2009).
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.
|
| |
Q Rev Biophys, 42,
139-158.
|
|
|
|
|
|
|
M.Beck,
J.A.Malmström,
V.Lange,
A.Schmidt,
E.W.Deutsch,
and
R.Aebersold
(2009).
Visual proteomics of the human pathogen Leptospira interrogans.
|
| |
Nat Methods, 6,
817-823.
|
|
|
|
|
|
|
M.O'Connor
(2009).
Helix 69 in 23S rRNA modulates decoding by wild type and suppressor tRNAs.
|
| |
Mol Genet Genomics, 282,
371-380.
|
|
|
|
|
|
|
N.Volkmann
(2009).
Confidence intervals for fitting of atomic models into low-resolution densities.
|
| |
Acta Crystallogr D Biol Crystallogr, 65,
679-689.
|
|
|
|
|
|
|
P.V.Cornish,
D.N.Ermolenko,
D.W.Staple,
L.Hoang,
R.P.Hickerson,
H.F.Noller,
and
T.Ha
(2009).
Following movement of the L1 stalk between three functional states in single ribosomes.
|
| |
Proc Natl Acad Sci U S A, 106,
2571-2576.
|
|
|
|
|
|
|
S.Shoji,
S.E.Walker,
and
K.Fredrick
(2009).
Ribosomal translocation: one step closer to the molecular mechanism.
|
| |
ACS Chem Biol, 4,
93.
|
|
|
|
|
|
|
T.M.Schmeing,
and
V.Ramakrishnan
(2009).
What recent ribosome structures have revealed about the mechanism of translation.
|
| |
Nature, 461,
1234-1242.
|
|
|
|
|
|
|
T.Tenson,
and
V.Hauryliuk
(2009).
Does the ribosome have initiation and elongation modes of translation?
|
| |
Mol Microbiol, 72,
1310-1315.
|
|
|
|
|
|
|
X.Agirrezabala,
and
J.Frank
(2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
|
| |
Q Rev Biophys, 42,
159-200.
|
|
|
|
|
|
|
X.Shi,
K.Chiu,
S.Ghosh,
and
S.Joseph
(2009).
Bases in 16S rRNA important for subunit association, tRNA binding, and translocation.
|
| |
Biochemistry, 48,
6772-6782.
|
|
|
|
|
|
|
A.Korostelev,
D.N.Ermolenko,
and
H.F.Noller
(2008).
Structural dynamics of the ribosome.
|
| |
Curr Opin Chem Biol, 12,
674-683.
|
|
|
|
|
|
|
A.N.Petrov,
A.Meskauskas,
S.C.Roshwalb,
and
J.D.Dinman
(2008).
Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit.
|
| |
Nucleic Acids Res, 36,
6187-6198.
|
|
|
|
|
|
|
C.C.Jolley,
S.A.Wells,
P.Fromme,
and
M.F.Thorpe
(2008).
Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations.
|
| |
Biophys J, 94,
1613-1621.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
L.G.Trabuco,
E.Villa,
K.Mitra,
J.Frank,
and
K.Schulten
(2008).
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
|
| |
Structure, 16,
673-683.
|
|
|
|
|
|
|
M.Orzechowski,
and
F.Tama
(2008).
Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations.
|
| |
Biophys J, 95,
5692-5705.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
P.V.Cornish,
D.N.Ermolenko,
H.F.Noller,
and
T.Ha
(2008).
Spontaneous intersubunit rotation in single ribosomes.
|
| |
Mol Cell, 30,
578-588.
|
|
|
|
|
|
|
R.K.Tan,
B.Devkota,
and
S.C.Harvey
(2008).
YUP.SCX: coaxing atomic models into medium resolution electron density maps.
|
| |
J Struct Biol, 163,
163-174.
|
|
|
|
|
|
|
T.Miyoshi,
and
T.Uchiumi
(2008).
Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes.
|
| |
Nucleic Acids Res, 36,
1783-1791.
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D.J.Taylor,
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H.Gao,
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H.R.Jonker,
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R.A.Grassucci,
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A.Liiv,
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RNA, 12,
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Mol Cell, 22,
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PDB codes:
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K.Mitra,
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RNA, 12,
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Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density.
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PDB code:
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F.Alber,
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RNA, 11,
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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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K.Y.Sanbonmatsu,
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Simulating movement of tRNA into the ribosome during decoding.
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Proc Natl Acad Sci U S A, 102,
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RNA, 11,
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RNA, 11,
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Mol Cell, 18,
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PDB codes:
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P.P.Datta,
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Mol Cell, 20,
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PDB code:
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P.V.Sergiev,
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RNA, 11,
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S.R.Miller,
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Three-dimensional structures of translating ribosomes by Cryo-EM.
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| |
Mol Cell, 14,
57-66.
|
|
|
|
|
|
|
S.H.White,
and
G.von Heijne
(2004).
The machinery of membrane protein assembly.
|
| |
Curr Opin Struct Biol, 14,
397-404.
|
|
|
|
|
|
|
U.Maiväli,
and
J.Remme
(2004).
Definition of bases in 23S rRNA essential for ribosomal subunit association.
|
| |
RNA, 10,
600-604.
|
|
|
|
|
|
|
Z.Druzina,
and
B.S.Cooperman
(2004).
Photolabile anticodon stem-loop analogs of tRNAPhe as probes of ribosomal structure and structural fluctuation at the decoding center.
|
| |
RNA, 10,
1550-1562.
|
|
|
|
|
|
|
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.Frank
(2003).
Toward an understanding of the structural basis of translation.
|
| |
Genome Biol, 4,
237.
|
|
|
|
|
|
|
J.M.Zengel,
A.Jerauld,
A.Walker,
M.C.Wahl,
and
L.Lindahl
(2003).
The extended loops of ribosomal proteins L4 and L22 are not required for ribosome assembly or L4-mediated autogenous control.
|
| |
RNA, 9,
1188-1197.
|
|
|
|
|
|
|
M.Valle,
A.Zavialov,
J.Sengupta,
U.Rawat,
M.Ehrenberg,
and
J.Frank
(2003).
Locking and unlocking of ribosomal motions.
|
| |
Cell, 114,
123-134.
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PDB codes:
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Links
