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Contents |
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174 a.a.
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30 a.a.
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29 a.a.
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29 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Structural protein
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Title:
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Ribosomal protein l10-l12(ntd) complex, space group p212121, form b
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Structure:
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50s ribosomal protein l10. Chain: a. Engineered: yes. 50s ribosomal protein l7/l12. Chain: u, v, w, x, y, z. Fragment: n-terminal domain. Engineered: yes
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Source:
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Thermotoga maritima. Organism_taxid: 2336. Gene: rplj. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rpll. Expression_system_taxid: 562
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Biol. unit:
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Heptamer (from
)
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Resolution:
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2.10Å
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R-factor:
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0.212
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R-free:
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0.286
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Authors:
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M.Diaconu,U.Kothe,F.Schluenzen,N.Fischer,J.M.Harms,A.G.Tonevitski, H.Stark,M.V.Rodnina,M.C.Wahl
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Key ref:
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M.Diaconu
et al.
(2005).
Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
Cell,
121,
991.
PubMed id:
DOI:
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Date:
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07-Apr-05
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Release date:
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12-Jul-05
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PROCHECK
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Headers
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References
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P29394
(RL10_THEMA) -
Large ribosomal subunit protein uL10 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
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Seq:
Struc:
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179 a.a.
174 a.a.
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P29396
(RL7_THEMA) -
Large ribosomal subunit protein bL12 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
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Seq:
Struc:
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128 a.a.
30 a.a.
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Enzyme class:
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Chains A, U, V, W, X, Y, Z:
E.C.?
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DOI no:
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Cell
121:991
(2005)
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PubMed id:
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Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
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M.Diaconu,
U.Kothe,
F.Schlünzen,
N.Fischer,
J.M.Harms,
A.G.Tonevitsky,
H.Stark,
M.V.Rodnina,
M.C.Wahl.
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ABSTRACT
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The L7/12 stalk of the large subunit of bacterial ribosomes encompasses protein
L10 and multiple copies of L7/12. We present crystal structures of Thermotoga
maritima L10 in complex with three L7/12 N-terminal-domain dimers, refine the
structure of an archaeal L10E N-terminal domain on the 50S subunit, and identify
these elements in cryo-electron-microscopic reconstructions of Escherichia coli
ribosomes. The mobile C-terminal helix alpha8 of L10 carries three L7/12 dimers
in T. maritima and two in E. coli, in concordance with the different length of
helix alpha8 of L10 in these organisms. The stalk is organized into three
elements (stalk base, L10 helix alpha8-L7/12 N-terminal-domain complex, and
L7/12 C-terminal domains) linked by flexible connections. Highly mobile L7/12
C-terminal domains promote recruitment of translation factors to the ribosome
and stimulate GTP hydrolysis by the ribosome bound factors through stabilization
of their active GTPase conformation.
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Selected figure(s)
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Figure 3.
Figure 3. Details of the L10-L12 Interaction
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Figure 6.
Figure 6. Functional Role of L12
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2005,
121,
991-0)
copyright 2005.
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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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|
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|
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L.Wang,
F.Yang,
D.Zhang,
Z.Chen,
R.M.Xu,
K.H.Nierhaus,
W.Gong,
and
Y.Qin
(2012).
A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.
|
| |
Nat Struct Mol Biol,
19,
403-410.
|
|
|
|
|
|
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C.Chen,
B.Stevens,
J.Kaur,
D.Cabral,
H.Liu,
Y.Wang,
H.Zhang,
G.Rosenblum,
Z.Smilansky,
Y.E.Goldman,
and
B.S.Cooperman
(2011).
Single-molecule fluorescence measurements of ribosomal translocation dynamics.
|
| |
Mol Cell,
42,
367-377.
|
|
|
|
|
|
|
C.L.Lawson,
M.L.Baker,
C.Best,
C.Bi,
M.Dougherty,
P.Feng,
G.van Ginkel,
B.Devkota,
I.Lagerstedt,
S.J.Ludtke,
R.H.Newman,
T.J.Oldfield,
I.Rees,
G.Sahni,
R.Sala,
S.Velankar,
J.Warren,
J.D.Westbrook,
K.Henrick,
G.J.Kleywegt,
H.M.Berman,
and
W.Chiu
(2011).
EMDataBank.org: unified data resource for CryoEM.
|
| |
Nucleic Acids Res,
39,
D456-D464.
|
|
|
|
|
|
|
C.R.Smulski,
S.A.Longhi,
M.J.Ayub,
M.M.Edreira,
L.Simonetti,
K.A.Gómez,
J.N.Basile,
O.Chaloin,
J.Hoebeke,
and
M.J.Levin
(2011).
Interaction map of the Trypanosoma cruzi ribosomal P protein complex (stalk) and the elongation factor 2.
|
| |
J Mol Recognit,
24,
359-370.
|
|
|
|
|
|
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H.Camargo,
G.Nusspaumer,
D.Abia,
V.Briceño,
M.Remacha,
and
J.P.Ballesta
(2011).
The amino terminal end determines the stability and assembling capacity of eukaryotic ribosomal stalk proteins P1 and P2.
|
| |
Nucleic Acids Res,
39,
3735-3743.
|
|
|
|
|
|
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M.V.Rodnina,
and
W.Wintermeyer
(2011).
The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation.
|
| |
Biochem Soc Trans,
39,
658-662.
|
|
|
|
|
|
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P.Smits,
H.Antonicka,
P.M.van Hasselt,
W.Weraarpachai,
W.Haller,
M.Schreurs,
H.Venselaar,
R.J.Rodenburg,
J.A.Smeitink,
and
L.P.van den Heuvel
(2011).
Mutation in subdomain G' of mitochondrial elongation factor G1 is associated with combined OXPHOS deficiency in fibroblasts but not in muscle.
|
| |
Eur J Hum Genet,
19,
275-279.
|
|
|
|
|
|
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B.Sander,
M.M.Golas,
R.Lührmann,
and
H.Stark
(2010).
An approach for de novo structure determination of dynamic molecular assemblies by electron cryomicroscopy.
|
| |
Structure,
18,
667-676.
|
|
|
|
|
|
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C.E.Aitken,
and
J.D.Puglisi
(2010).
Following the intersubunit conformation of the ribosome during translation in real time.
|
| |
Nat Struct Mol Biol,
17,
793-800.
|
|
|
|
|
|
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C.J.Jang,
and
E.Jan
(2010).
Modular domains of the Dicistroviridae intergenic internal ribosome entry site.
|
| |
RNA,
16,
1182-1195.
|
|
|
|
|
|
|
C.L.Lawson
(2010).
Unified data resource for cryo-EM.
|
| |
Methods Enzymol,
483,
73-90.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
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I.Wohlgemuth,
C.Pohl,
and
M.V.Rodnina
(2010).
Optimization of speed and accuracy of decoding in translation.
|
| |
EMBO J,
29,
3701-3709.
|
|
|
|
|
|
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J.A.Dunkle,
and
J.H.Cate
(2010).
Ribosome structure and dynamics during translocation and termination.
|
| |
Annu Rev Biophys,
39,
227-244.
|
|
|
|
|
|
|
K.M.Lee,
C.W.Yu,
D.S.Chan,
T.Y.Chiu,
G.Zhu,
K.H.Sze,
P.C.Shaw,
and
K.B.Wong
(2010).
Solution structure of the dimerization domain of ribosomal protein P2 provides insights for the structural organization of eukaryotic stalk.
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| |
Nucleic Acids Res,
38,
5206-5216.
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PDB code:
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N.Clementi,
A.Chirkova,
B.Puffer,
R.Micura,
and
N.Polacek
(2010).
Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation.
|
| |
Nat Chem Biol,
6,
344-351.
|
|
|
|
|
|
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R.Francisco-Velilla,
and
M.Remacha
(2010).
In vivo formation of a stable pentameric (P2alpha/P1beta)-P0-(P1alpha/P2beta) ribosomal stalk complex in Saccharomyces cerevisiae.
|
| |
Yeast,
27,
693-704.
|
|
|
|
|
|
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R.M.Voorhees,
T.M.Schmeing,
A.C.Kelley,
and
V.Ramakrishnan
(2010).
The mechanism for activation of GTP hydrolysis on the ribosome.
|
| |
Science,
330,
835-838.
|
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PDB codes:
|
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|
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W.E.Running,
and
J.P.Reilly
(2010).
Variation of the chemical reactivity of Thermus thermophilus HB8 ribosomal proteins as a function of pH.
|
| |
Proteomics,
10,
3669-3687.
|
|
|
|
|
|
|
X.Agirrezabala,
and
J.Frank
(2010).
From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery.
|
| |
Hum Genomics,
4,
226-237.
|
|
|
|
|
|
|
Y.Yang,
H.Cimen,
M.J.Han,
T.Shi,
J.H.Deng,
H.Koc,
O.M.Palacios,
L.Montier,
Y.Bai,
Q.Tong,
and
E.C.Koc
(2010).
NAD+-dependent deacetylase SIRT3 regulates mitochondrial protein synthesis by deacetylation of the ribosomal protein MRPL10.
|
| |
J Biol Chem,
285,
7417-7429.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
B.S.Shin,
J.R.Kim,
M.G.Acker,
K.N.Maher,
J.R.Lorsch,
and
T.E.Dever
(2009).
rRNA suppressor of a eukaryotic translation initiation factor 5B/initiation factor 2 mutant reveals a binding site for translational GTPases on the small ribosomal subunit.
|
| |
Mol Cell Biol,
29,
808-821.
|
|
|
|
|
|
|
D.J.Taylor,
B.Devkota,
A.D.Huang,
M.Topf,
E.Narayanan,
A.Sali,
S.C.Harvey,
and
J.Frank
(2009).
Comprehensive molecular structure of the eukaryotic ribosome.
|
| |
Structure,
17,
1591-1604.
|
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|
PDB codes:
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E.L.Cooper,
J.García-Lara,
and
S.J.Foster
(2009).
YsxC, an essential protein in Staphylococcus aureus crucial for ribosome assembly/stability.
|
| |
BMC Microbiol,
9,
266.
|
|
|
|
|
|
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H.Qin,
C.Grigoriadou,
and
B.S.Cooperman
(2009).
Interaction of IF2 with the ribosomal GTPase-associated center during 70S initiation complex formation.
|
| |
Biochemistry,
48,
4699-4706.
|
|
|
|
|
|
|
H.S.Zaher,
and
R.Green
(2009).
Fidelity at the molecular level: lessons from protein synthesis.
|
| |
Cell,
136,
746-762.
|
|
|
|
|
|
|
J.Ederth,
C.S.Mandava,
S.Dasgupta,
and
S.Sanyal
(2009).
A single-step method for purification of active His-tagged ribosomes from a genetically engineered Escherichia coli.
|
| |
Nucleic Acids Res,
37,
e15.
|
|
|
|
|
|
|
J.P.Mower,
and
L.Bonen
(2009).
Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae.
|
| |
BMC Evol Biol,
9,
265.
|
|
|
|
|
|
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K.Y.Lo,
Z.Li,
F.Wang,
E.M.Marcotte,
and
A.W.Johnson
(2009).
Ribosome stalk assembly requires the dual-specificity phosphatase Yvh1 for the exchange of Mrt4 with P0.
|
| |
J Cell Biol,
186,
849-862.
|
|
|
|
|
|
|
M.Rodríguez-Mateos,
D.Abia,
J.J.García-Gómez,
A.Morreale,
J.de la Cruz,
C.Santos,
M.Remacha,
and
J.P.Ballesta
(2009).
The amino terminal domain from Mrt4 protein can functionally replace the RNA binding domain of the ribosomal P0 protein.
|
| |
Nucleic Acids Res,
37,
3514-3521.
|
|
|
|
|
|
|
M.V.Rodnina
(2009).
Visualizing the protein synthesis machinery: new focus on the translational GTPase elongation factor Tu.
|
| |
Proc Natl Acad Sci U S A,
106,
969-970.
|
|
|
|
|
|
|
P.B.Moore
(2009).
The ribosome returned.
|
| |
J Biol,
8,
8.
|
|
|
|
|
|
|
S.B.Qian,
L.Waldron,
N.Choudhary,
R.E.Klevit,
W.J.Chazin,
and
C.Patterson
(2009).
Engineering a ubiquitin ligase reveals conformational flexibility required for ubiquitin transfer.
|
| |
J Biol Chem,
284,
26797-26802.
|
|
|
|
|
|
|
S.Kemmler,
L.Occhipinti,
M.Veisu,
and
V.G.Panse
(2009).
Yvh1 is required for a late maturation step in the 60S biogenesis pathway.
|
| |
J Cell Biol,
186,
863-880.
|
|
|
|
|
|
|
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,
R.M.Voorhees,
A.C.Kelley,
Y.G.Gao,
F.V.Murphy,
J.R.Weir,
and
V.Ramakrishnan
(2009).
The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.
|
| |
Science,
326,
688-694.
|
|
|
PDB codes:
|
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|
|
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|
|
|
T.M.Schmeing,
and
V.Ramakrishnan
(2009).
What recent ribosome structures have revealed about the mechanism of translation.
|
| |
Nature,
461,
1234-1242.
|
|
|
|
|
|
|
V.Briceño,
H.Camargo,
M.Remacha,
C.Santos,
and
J.P.Ballesta
(2009).
Structural and functional characterization of the amino terminal domain of the yeast ribosomal stalk P1 and P2 proteins.
|
| |
Int J Biochem Cell Biol,
41,
1315-1322.
|
|
|
|
|
|
|
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.P.Li,
J.C.Chiou,
M.Remacha,
J.P.Ballesta,
and
N.E.Tumer
(2009).
A two-step binding model proposed for the electrostatic interactions of ricin a chain with ribosomes.
|
| |
Biochemistry,
48,
3853-3863.
|
|
|
|
|
|
|
Y.G.Gao,
M.Selmer,
C.M.Dunham,
A.Weixlbaumer,
A.C.Kelley,
and
V.Ramakrishnan
(2009).
The structure of the ribosome with elongation factor G trapped in the posttranslocational state.
|
| |
Science,
326,
694-699.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.García-Marcos,
S.A.Sánchez,
P.Parada,
J.Eid,
D.M.Jameson,
M.Remacha,
E.Gratton,
and
J.P.Ballesta
(2008).
Yeast ribosomal stalk heterogeneity in vivo shown by two-photon FCS and molecular brightness analysis.
|
| |
Biophys J,
94,
2884-2890.
|
|
|
|
|
|
|
A.Korostelev,
D.N.Ermolenko,
and
H.F.Noller
(2008).
Structural dynamics of the ribosome.
|
| |
Curr Opin Chem Biol,
12,
674-683.
|
|
|
|
|
|
|
C.Wicker-Planquart,
A.E.Foucher,
M.Louwagie,
R.A.Britton,
and
J.M.Jault
(2008).
Interactions of an essential Bacillus subtilis GTPase, YsxC, with ribosomes.
|
| |
J Bacteriol,
190,
681-690.
|
|
|
|
|
|
|
D.N.Wilson,
F.Schluenzen,
J.M.Harms,
A.L.Starosta,
S.R.Connell,
and
P.Fucini
(2008).
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning.
|
| |
Proc Natl Acad Sci U S A,
105,
13339-13344.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.C.Chiou,
X.P.Li,
M.Remacha,
J.P.Ballesta,
and
N.E.Tumer
(2008).
The ribosomal stalk is required for ribosome binding, depurination of the rRNA and cytotoxicity of ricin A chain in Saccharomyces cerevisiae.
|
| |
Mol Microbiol,
70,
1441-1452.
|
|
|
|
|
|
|
J.M.Harms,
D.N.Wilson,
F.Schluenzen,
S.R.Connell,
T.Stachelhaus,
Z.Zaborowska,
C.M.Spahn,
and
P.Fucini
(2008).
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
|
| |
Mol Cell,
30,
26-38.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
O.Kurkcuoglu,
P.Doruker,
T.Z.Sen,
A.Kloczkowski,
and
R.L.Jernigan
(2008).
The ribosome structure controls and directs mRNA entry, translocation and exit dynamics.
|
| |
Phys Biol,
5,
046005.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
S.Ledoux,
and
O.C.Uhlenbeck
(2008).
Different aa-tRNAs are selected uniformly on the ribosome.
|
| |
Mol Cell,
31,
114-123.
|
|
|
|
|
|
|
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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A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.
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Structure,
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PDB code:
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The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation.
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Nat Struct Mol Biol,
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PDB code:
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PDB codes:
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X.Zhang,
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PDB code:
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P.Dube,
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PDB code:
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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
code is
shown on the right.
|
| |
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