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PDBsum entry 1lu3
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DOI no:
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EMBO J
21:3557-3567
(2002)
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PubMed id:
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Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.
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M.Valle,
J.Sengupta,
N.K.Swami,
R.A.Grassucci,
N.Burkhardt,
K.H.Nierhaus,
R.K.Agrawal,
J.Frank.
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ABSTRACT
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During the elongation cycle of protein biosynthesis, the specific amino acid
coded for by the mRNA is delivered by a complex that is comprised of the cognate
aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to
the ribosome, the anticodon end of the tRNA reaches the decoding center in the
30S subunit. Here we present the cryo- electron microscopy (EM) study of an
Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic,
kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new
conformation that appears to facilitate the initial codon-anticodon interaction.
Furthermore, the elbow region of the tRNA is seen to contact the
GTPase-associated center on the 50S subunit of the ribosome, suggesting an
active role of the tRNA in the transmission of the signal prompting the GTP
hydrolysis upon codon recognition.
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Selected figure(s)
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Figure 4.
Figure 4 Interaction of EF-Tu and aa-tRNA with the ribosome. (A
and B) Ribbons representation of the docked EF-Tu and aa-tRNA
within the ternary complex. (C and D) Focus on the interaction
between the  -sarcin−ricin
loop (SRL) and the effector loop within domain I of EF-Tu
(cyan). In (C) the coordinates of the whole ternary complex from
T.aquaticus with a GTP analog (Nissen et al., 1995) were used
for the fitting, while in (D) the crystal structure of EF-Tu
from E.coli bound to GDP (Song et al., 1999) was used.
Orientation of the ribosomes for (A) and (B) are shown as
thumbnails on the left. Labeling is the same as in Figure 5.
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Figure 5.
Figure 5 Interaction in the decoding center and accommodation of
the aa-tRNA. (A−C) Semi-transparent representation of the
ternary complex density from the cryo-EM map showing the fitted
tRNA (gold) and the A-site tRNA (red) with corresponding mRNA
codon (Yusupova et al., 2001). (C) A tRNA construct in which the
anticodon position, up to the kink, is adopted from (B) and the
rest of the tRNA from (A). (D−F) Interaction in the anticodon
loop of the tRNA in the decoding site. H69, helix 69 from 23S
rRNA; h44, helix 44 from 16S rRNA; h34, helix 34 from 16S rRNA;
cd, A-site codon in the mRNA; AC, anticodon loop; S12, protein
S12 in the 30S subunit.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
3557-3567)
copyright 2002.
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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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PDB codes:
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PDB codes:
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PDB codes:
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S.E.Kolitz,
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RNA,
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Structure,
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Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.
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PDB codes:
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H.S.Zaher,
and
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PDB codes:
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J.Frank
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T.M.Schmeing,
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326,
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PDB codes:
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W.Huggins,
S.K.Ghosh,
and
P.Wollenzien
(2009).
Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome.
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BMC Struct Biol,
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X.Agirrezabala,
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Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
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PDB codes:
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M.S.Jurica
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Searching for a wrench to throw into the splicing machine.
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Nat Chem Biol,
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Irreversible chemical steps control intersubunit dynamics during translation.
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R.A.Grassucci,
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Thiostrepton inhibition of tRNA delivery to the ribosome.
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RNA,
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Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs.
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RNA,
13,
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S.H.Scheres,
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Nat Methods,
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RNA,
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Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data.
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Structure of the E. coli signal recognition particle bound to a translating ribosome.
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| |
Nature,
444,
503-506.
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PDB code:
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|
|
|
|
|
|
|
H.Elmlund,
V.Baraznenok,
M.Lindahl,
C.O.Samuelsen,
P.J.Koeck,
S.Holmberg,
H.Hebert,
and
C.M.Gustafsson
(2006).
The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II.
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Proc Natl Acad Sci U S A,
103,
15788-15793.
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K.Mitra,
C.Schaffitzel,
F.Fabiola,
M.S.Chapman,
N.Ban,
and
J.Frank
(2006).
Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
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| |
Mol Cell,
22,
533-543.
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|
PDB codes:
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|
|
|
|
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|
L.D.Kapp,
S.E.Kolitz,
and
J.R.Lorsch
(2006).
Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation.
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| |
RNA,
12,
751-764.
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N.Hirabayashi,
N.S.Sato,
and
T.Suzuki
(2006).
Conserved loop sequence of helix 69 in Escherichia coli 23 S rRNA is involved in A-site tRNA binding and translational fidelity.
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J Biol Chem,
281,
17203-17211.
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S.Kaur,
R.Gillet,
W.Li,
R.Gursky,
and
J.Frank
(2006).
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,
16484-16489.
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W.Li,
J.Sengupta,
B.K.Rath,
and
J.Frank
(2006).
Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations.
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| |
RNA,
12,
1240-1253.
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PDB code:
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|
|
Y.Shimizu,
and
T.Ueda
(2006).
SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans-translation initiation.
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J Biol Chem,
281,
15987-15996.
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A.G.Myasnikov,
S.Marzi,
A.Simonetti,
A.M.Giuliodori,
C.O.Gualerzi,
G.Yusupova,
M.Yusupov,
and
B.P.Klaholz
(2005).
Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome.
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Nat Struct Mol Biol,
12,
1145-1149.
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D.E.Brodersen,
and
P.Nissen
(2005).
The social life of ribosomal proteins.
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FEBS J,
272,
2098-2108.
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F.Rázga,
J.Koca,
J.Sponer,
and
N.B.Leontis
(2005).
Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.
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Biophys J,
88,
3466-3485.
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G.Dinos,
D.L.Kalpaxis,
D.N.Wilson,
and
K.H.Nierhaus
(2005).
Deacylated tRNA is released from the E site upon A site occupation but before GTP is hydrolyzed by EF-Tu.
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Nucleic Acids Res,
33,
5291-5296.
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I.Agmon,
A.Bashan,
R.Zarivach,
and
A.Yonath
(2005).
Symmetry at the active site of the ribosome: structural and functional implications.
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Biol Chem,
386,
833-844.
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J.M.Ogle,
and
V.Ramakrishnan
(2005).
Structural insights into translational fidelity.
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Annu Rev Biochem,
74,
129-177.
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K.Mitra,
C.Schaffitzel,
T.Shaikh,
F.Tama,
S.Jenni,
C.L.Brooks,
N.Ban,
and
J.Frank
(2005).
Structure of the E. coli protein-conducting channel bound to a translating ribosome.
|
| |
Nature,
438,
318-324.
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PDB codes:
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|
|
K.Y.Sanbonmatsu,
S.Joseph,
and
C.S.Tung
(2005).
Simulating movement of tRNA into the ribosome during decoding.
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| |
Proc Natl Acad Sci U S A,
102,
15854-15859.
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N.Gao,
A.V.Zavialov,
W.Li,
J.Sengupta,
M.Valle,
R.P.Gursky,
M.Ehrenberg,
and
J.Frank
(2005).
Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
|
| |
Mol Cell,
18,
663-674.
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|
|
PDB codes:
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|
|
S.Petry,
D.E.Brodersen,
F.V.Murphy,
C.M.Dunham,
M.Selmer,
M.J.Tarry,
A.C.Kelley,
and
V.Ramakrishnan
(2005).
Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon.
|
| |
Cell,
123,
1255-1266.
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|
|
PDB codes:
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|
T.Daviter,
F.V.Murphy,
and
V.Ramakrishnan
(2005).
Molecular biology. A renewed focus on transfer RNA.
|
| |
Science,
308,
1123-1124.
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B.P.Klaholz,
A.G.Myasnikov,
and
M.Van Heel
(2004).
Visualization of release factor 3 on the ribosome during termination of protein synthesis.
|
| |
Nature,
427,
862-865.
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D.M.Cameron,
S.T.Gregory,
J.Thompson,
M.J.Suh,
P.A.Limbach,
and
A.E.Dahlberg
(2004).
Thermus thermophilus L11 methyltransferase, PrmA, is dispensable for growth and preferentially modifies free ribosomal protein L11 prior to ribosome assembly.
|
| |
J Bacteriol,
186,
5819-5825.
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D.Rodriguez-Correa,
and
A.E.Dahlberg
(2004).
Genetic evidence against the 16S ribosomal RNA helix 27 conformational switch model.
|
| |
RNA,
10,
28-33.
|
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|
|
|
|
|
K.B.Gromadski,
and
M.V.Rodnina
(2004).
Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome.
|
| |
Nat Struct Mol Biol,
11,
316-322.
|
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|
|
K.B.Gromadski,
and
M.V.Rodnina
(2004).
Kinetic determinants of high-fidelity tRNA discrimination on the ribosome.
|
| |
Mol Cell,
13,
191-200.
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|
|
L.D.Kapp,
and
J.R.Lorsch
(2004).
The molecular mechanics of eukaryotic translation.
|
| |
Annu Rev Biochem,
73,
657-704.
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|
|
L.D.Sherlin,
and
O.C.Uhlenbeck
(2004).
Hasty decisions on the ribosome.
|
| |
Nat Struct Mol Biol,
11,
206-208.
|
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|
|
N.Chumpolkulwong,
C.Hori-Takemoto,
T.Hosaka,
T.Inaoka,
T.Kigawa,
M.Shirouzu,
K.Ochi,
and
S.Yokoyama
(2004).
Effects of Escherichia coli ribosomal protein S12 mutations on cell-free protein synthesis.
|
| |
Eur J Biochem,
271,
1127-1134.
|
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|
|
P.F.Agris
(2004).
Decoding the genome: a modified view.
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| |
Nucleic Acids Res,
32,
223-238.
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|
P.W.Haebel,
S.Gutmann,
and
N.Ban
(2004).
Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs.
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| |
Curr Opin Struct Biol,
14,
58-65.
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|
S.C.Blanchard,
R.L.Gonzalez,
H.D.Kim,
S.Chu,
and
J.D.Puglisi
(2004).
tRNA selection and kinetic proofreading in translation.
|
| |
Nat Struct Mol Biol,
11,
1008-1014.
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|
|
T.C.Marlovits,
T.Kubori,
A.Sukhan,
D.R.Thomas,
J.E.Galán,
and
V.M.Unger
(2004).
Structural insights into the assembly of the type III secretion needle complex.
|
| |
Science,
306,
1040-1042.
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A.R.Cukras,
D.R.Southworth,
J.L.Brunelle,
G.M.Culver,
and
R.Green
(2003).
Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex.
|
| |
Mol Cell,
12,
321-328.
|
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|
|
A.Savelsbergh,
V.I.Katunin,
D.Mohr,
F.Peske,
M.V.Rodnina,
and
W.Wintermeyer
(2003).
An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation.
|
| |
Mol Cell,
11,
1517-1523.
|
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|
|
A.Vila-Sanjurjo,
W.K.Ridgeway,
V.Seymaner,
W.Zhang,
S.Santoso,
K.Yu,
and
J.H.Cate
(2003).
X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli.
|
| |
Proc Natl Acad Sci U S A,
100,
8682-8687.
|
|
|
PDB codes:
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|
|
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|
|
D.J.Scarlett,
K.K.McCaughan,
D.N.Wilson,
and
W.P.Tate
(2003).
Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2.
|
| |
J Biol Chem,
278,
15095-15104.
|
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|
G.R.Andersen,
P.Nissen,
and
J.Nyborg
(2003).
Elongation factors in protein biosynthesis.
|
| |
Trends Biochem Sci,
28,
434-441.
|
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|
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H.Gao,
J.Sengupta,
M.Valle,
A.Korostelev,
N.Eswar,
S.M.Stagg,
P.Van Roey,
R.K.Agrawal,
S.C.Harvey,
A.Sali,
M.S.Chapman,
and
J.Frank
(2003).
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
|
| |
Cell,
113,
789-801.
|
|
|
PDB codes:
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|
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|
|
J.Frank
(2003).
Toward an understanding of the structural basis of translation.
|
| |
Genome Biol,
4,
237.
|
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|
|
|
J.M.Ogle,
A.P.Carter,
and
V.Ramakrishnan
(2003).
Insights into the decoding mechanism from recent ribosome structures.
|
| |
Trends Biochem Sci,
28,
259-266.
|
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|
|
M.R.Sharma,
E.C.Koc,
P.P.Datta,
T.M.Booth,
L.L.Spremulli,
and
R.K.Agrawal
(2003).
Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins.
|
| |
Cell,
115,
97.
|
|
|
|
|
|
|
M.Valle,
A.Zavialov,
J.Sengupta,
U.Rawat,
M.Ehrenberg,
and
J.Frank
(2003).
Locking and unlocking of ribosomal motions.
|
| |
Cell,
114,
123-134.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Valle,
A.Zavialov,
W.Li,
S.M.Stagg,
J.Sengupta,
R.C.Nielsen,
P.Nissen,
S.C.Harvey,
M.Ehrenberg,
and
J.Frank
(2003).
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy.
|
| |
Nat Struct Biol,
10,
899-906.
|
|
|
PDB codes:
|
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|
|
|
|
|
M.Valle,
R.Gillet,
S.Kaur,
A.Henne,
V.Ramakrishnan,
and
J.Frank
(2003).
Visualizing tmRNA entry into a stalled ribosome.
|
| |
Science,
300,
127-130.
|
|
|
PDB code:
|
|
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|
|
|
|
|
P.Licznar,
N.Mejlhede,
M.F.Prère,
N.Wills,
R.F.Gesteland,
J.F.Atkins,
and
O.Fayet
(2003).
Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs.
|
| |
EMBO J,
22,
4770-4778.
|
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|
R.Jørgensen,
P.A.Ortiz,
A.Carr-Schmid,
P.Nissen,
T.G.Kinzy,
and
G.R.Andersen
(2003).
Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase.
|
| |
Nat Struct Biol,
10,
379-385.
|
|
|
PDB codes:
|
|
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|
|
|
|
|
S.R.Connell,
C.A.Trieber,
G.P.Dinos,
E.Einfeldt,
D.E.Taylor,
and
K.H.Nierhaus
(2003).
Mechanism of Tet(O)-mediated tetracycline resistance.
|
| |
EMBO J,
22,
945-953.
|
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|
H.Stark,
M.V.Rodnina,
H.J.Wieden,
F.Zemlin,
W.Wintermeyer,
and
M.van Heel
(2002).
Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
|
| |
Nat Struct Biol,
9,
849-854.
|
|
|
PDB code:
|
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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.
|
|
Links
