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234 a.a.
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206 a.a.
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208 a.a.
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150 a.a.
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101 a.a.
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155 a.a.
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138 a.a.
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127 a.a.
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98 a.a.
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119 a.a.
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124 a.a.
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125 a.a.
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60 a.a.
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88 a.a.
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83 a.a.
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104 a.a.
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73 a.a.
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80 a.a.
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99 a.a.
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90 a.a.
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* Residue conservation analysis
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PDB id:
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Ribosome
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Title:
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Crystal structure of five 70s ribosomes from escherichia coli in complex with protein y. This file contains the 30s subunit of one 70s ribosome. The entire crystal structure contains five 70s ribosomes and is described in remark 400.
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Structure:
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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.
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Source:
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Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
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Biol. unit:
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21mer (from
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Resolution:
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11.50Å
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R-factor:
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0.395
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R-free:
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0.401
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Authors:
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A.Vila-Sanjurjo,B.S.Schuwirth,C.W.Hau,J.H.Cate
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Key ref:
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A.Vila-Sanjurjo
et al.
(2004).
Structural basis for the control of translation initiation during stress.
Nat Struct Mol Biol,
11,
1054-1059.
PubMed id:
DOI:
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Date:
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06-Oct-04
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Release date:
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16-Nov-04
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PROCHECK
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Headers
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References
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No UniProt id for this chain
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No UniProt id for this chain
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DOI no:
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Nat Struct Mol Biol
11:1054-1059
(2004)
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PubMed id:
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Structural basis for the control of translation initiation during stress.
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A.Vila-Sanjurjo,
B.S.Schuwirth,
C.W.Hau,
J.H.Cate.
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ABSTRACT
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During environmental stress, organisms limit protein synthesis by storing
inactive ribosomes that are rapidly reactivated when conditions improve. Here we
present structural and biochemical data showing that protein Y, an Escherichia
coli stress protein, fills the tRNA- and mRNA-binding channel of the small
ribosomal subunit to stabilize intact ribosomes. Protein Y inhibits translation
initiation during cold shock but not at normal temperatures. Furthermore,
protein Y competes with conserved translation initiation factors that, in
bacteria, are required for ribosomal subunit dissociation. The mechanism used by
protein Y to reduce translation initiation during stress and quickly release
ribosomes for renewed translation initiation may therefore occur widely in
nature.
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Selected figure(s)
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Figure 1.
Figure 1. Structural model of protein Y binding to the ribosome
as determined by X-ray crystallography. (a) Location of PY
density in the 70S ribosome. The 30S subunit is gold, the 50S
subunit is light blue, positive difference electron density is
blue, negative density is red, and PY is cyan. Helix 69 of 23S
rRNA is marked with an asterisk. (b) PY density in the 30S
subunit as seen from the perspective of the subunit interface,
indicated by the arrow in a. The density occurs between the
platform (P) and the head (H) of the 30S subunit. The A, P and E
sites, and the body (B) of the small subunit are marked. (c)
Details of the docking of the N-terminal core of PY (PDB entry
1L4S 3) into the difference electron density. The position of
the disordered C-terminal tail is indicated. The view is from
the perspective of the arrow in b.
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Figure 2.
Figure 2. Details of the PY-binding site within the ribosome.
(a) Stereo view of the location of critical 16S rRNA residues
G926, C1400, C1402 and A1493 (green) relative to PY. Helix 69
(H69) of 23S rRNA is blue. Conserved residues within PY are
magenta^3. (b) Overlap of PY with A- and P-site tRNAs. A-, P-
and E-site tRNAs are cyan, green and gray, respectively. The
positions of the 30S and 50S subunits, the path of mRNA, and the
location of the C-terminal tail of PY are indicated. (c) Overlap
of the difference electron density corresponding to PY with mRNA
(red). The positive density, E-, A- and P-site tRNAs are
color-coded as above. The negative density is not shown for
clarity. The 5' and 3' ends of the mRNA are marked.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2004,
11,
1054-1059)
copyright 2004.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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E.Hamon,
P.Horvatovich,
E.Izquierdo,
F.Bringel,
E.Marchioni,
D.Aoudé-Werner,
and
S.Ennahar
(2011).
Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance.
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BMC Microbiol,
11,
63.
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E.Palonen,
M.Lindström,
and
H.Korkeala
(2010).
Adaptation of enteropathogenic Yersinia to low growth temperature.
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Crit Rev Microbiol,
36,
54-67.
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H.Tse,
J.J.Cai,
H.W.Tsoi,
E.P.Lam,
and
K.Y.Yuen
(2010).
Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes.
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BMC Genomics,
11,
491.
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J.Dworkin,
and
I.M.Shah
(2010).
Exit from dormancy in microbial organisms.
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Nat Rev Microbiol,
8,
890-896.
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J.O.Ortiz,
F.Brandt,
V.R.Matias,
L.Sennels,
J.Rappsilber,
S.H.Scheres,
M.Eibauer,
F.U.Hartl,
and
W.Baumeister
(2010).
Structure of hibernating ribosomes studied by cryoelectron tomography in vitro and in situ.
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J Cell Biol,
190,
613-621.
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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).
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J Biol Chem,
285,
4006-4014.
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M.Ueta,
C.Wada,
and
A.Wada
(2010).
Formation of 100S ribosomes in Staphylococcus aureus by the hibernation promoting factor homolog SaHPF.
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Genes Cells,
15,
43-58.
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T.Yamamoto,
Y.Shimizu,
T.Ueda,
and
Y.Shiro
(2010).
Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry.
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J Biol Chem,
285,
5646-5652.
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G.Y.Soung,
J.L.Miller,
H.Koc,
and
E.C.Koc
(2009).
Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes.
|
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J Proteome Res,
8,
3390-3402.
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J.Kalisiak,
S.A.Trauger,
E.Kalisiak,
H.Morita,
V.V.Fokin,
M.W.Adams,
K.B.Sharpless,
and
G.Siuzdak
(2009).
Identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach.
|
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J Am Chem Soc,
131,
378-386.
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Y.Zhang,
and
M.Inouye
(2009).
The Inhibitory Mechanism of Protein Synthesis by YoeB, an Escherichia coli Toxin.
|
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J Biol Chem,
284,
6627-6638.
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M.Y.Pavlov,
A.Antoun,
M.Lovmar,
and
M.Ehrenberg
(2008).
Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting.
|
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EMBO J,
27,
1706-1717.
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R.Bingel-Erlenmeyer,
R.Kohler,
G.Kramer,
A.Sandikci,
S.Antolić,
T.Maier,
C.Schaffitzel,
B.Wiedmann,
B.Bukau,
and
N.Ban
(2008).
A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing.
|
| |
Nature,
452,
108-111.
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PDB codes:
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R.Rieder,
and
B.Zavizion
(2008).
Monitoring the physiologic stress response: a novel biophysical approach for the rapid detection of bacteria in platelet concentrate.
|
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Transfusion,
48,
2596-2605.
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A.M.Giuliodori,
A.Brandi,
M.Giangrossi,
C.O.Gualerzi,
and
C.L.Pon
(2007).
Cold-stress-induced de novo expression of infC and role of IF3 in cold-shock translational bias.
|
| |
RNA,
13,
1355-1365.
|
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A.M.Giuliodori,
C.O.Gualerzi,
S.Soto,
J.Vila,
and
M.M.Tavío
(2007).
Review on bacterial stress topics.
|
| |
Ann N Y Acad Sci,
1113,
95.
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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.
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PDB codes:
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M.R.Sharma,
D.N.Wilson,
P.P.Datta,
C.Barat,
F.Schluenzen,
P.Fucini,
and
R.K.Agrawal
(2007).
Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
|
| |
Proc Natl Acad Sci U S A,
104,
19315-19320.
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PDB codes:
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P.P.Datta,
D.N.Wilson,
M.Kawazoe,
N.K.Swami,
T.Kaminishi,
M.R.Sharma,
T.M.Booth,
C.Takemoto,
P.Fucini,
S.Yokoyama,
and
R.K.Agrawal
(2007).
Structural aspects of RbfA action during small ribosomal subunit assembly.
|
| |
Mol Cell,
28,
434-445.
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PDB codes:
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P.Palecková,
J.Felsberg,
J.Bobek,
and
K.Mikulík
(2007).
tmRNA abundance in Streptomyces aureofaciens, S. griseus and S. collinus under stress-inducing conditions.
|
| |
Folia Microbiol (Praha),
52,
463-470.
|
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D.G.Shpakovskii,
E.K.Shematorova,
and
G.V.Shpakovskii
(2006).
Human PMS2 gene family: origin, molecular evolution, and biological implications.
|
| |
Dokl Biochem Biophys,
408,
175-179.
|
|
|
|
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|
G.Hirokawa,
R.M.Nijman,
V.S.Raj,
H.Kaji,
K.Igarashi,
and
A.Kaji
(2005).
The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits.
|
| |
RNA,
11,
1317-1328.
|
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M.Ueta,
H.Yoshida,
C.Wada,
T.Baba,
H.Mori,
and
A.Wada
(2005).
Ribosome binding proteins YhbH and YfiA have opposite functions during 100S formation in the stationary phase of Escherichia coli.
|
| |
Genes Cells,
10,
1103-1112.
|
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|
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|
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D.N.Wilson,
and
K.H.Nierhaus
(2004).
The how and Y of cold shock.
|
| |
Nat Struct Mol Biol,
11,
1026-1028.
|
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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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Links
