Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Originally published in Science Express on 7 September 2006
Science 29 September 2006:
Vol. 313. no. 5795, pp. 1935 - 1942
DOI: 10.1126/science.1131127
Prev | Table of Contents | Next

Research Articles

Structure of the 70S Ribosome Complexed with mRNA and tRNA

Maria Selmer,* Christine M. Dunham,* Frank V. Murphy, IV, Albert Weixlbaumer, Sabine Petry, Ann C. Kelley, John R. Weir, V. Ramakrishnan{dagger}

The crystal structure of the bacterial 70S ribosome refined to 2.8 angstrom resolution reveals atomic details of its interactions with messenger RNA (mRNA) and transfer RNA (tRNA). A metal ion stabilizes a kink in the mRNA that demarcates the boundary between A and P sites, which is potentially important to prevent slippage of mRNA. Metal ions also stabilize the intersubunit interface. The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: ramak{at}mrc-lmb.cam.ac.uk

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Contribution of ribosomal residues to P-site tRNA binding.
S. Shoji, N. M. Abdi, R. Bundschuh, and K. Fredrick (2009)
Nucleic Acids Res. 37, 4033-4042
   Abstract »    Full Text »    PDF »
Structure of a mitochondrial ribosome with minimal RNA.
M. R. Sharma, T. M. Booth, L. Simpson, D. A. Maslov, and R. K. Agrawal (2009)
PNAS 106, 9637-9642
   Abstract »    Full Text »    PDF »
Classification and energetics of the base-phosphate interactions in RNA.
C. L. Zirbel, J. E. Sponer, J. Sponer, J. Stombaugh, and N. B. Leontis (2009)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.
C. Hsiao and L. D. Williams (2009)
Nucleic Acids Res. 37, 3134-3142
   Abstract »    Full Text »    PDF »
Frequency and isostericity of RNA base pairs.
J. Stombaugh, C. L. Zirbel, E. Westhof, and N. B. Leontis (2009)
Nucleic Acids Res. 37, 2294-2312
   Abstract »    Full Text »    PDF »
Inhibition of Bacterial Ribosome Assembly: a Suitable Drug Target?.
B. A. Maguire (2009)
Microbiol. Mol. Biol. Rev. 73, 22-35
   Abstract »    Full Text »    PDF »
A Gripping Tale of Ribosomal Frameshifting: Extragenic Suppressors of Frameshift Mutations Spotlight P-Site Realignment.
J. F. Atkins and G. R. Bjork (2009)
Microbiol. Mol. Biol. Rev. 73, 178-210
   Abstract »    Full Text »    PDF »
Following movement of the L1 stalk between three functional states in single ribosomes.
P. V. Cornish, D. N. Ermolenko, D. W. Staple, L. Hoang, R. P. Hickerson, H. F. Noller, and T. Ha (2009)
PNAS 106, 2571-2576
   Abstract »    Full Text »    PDF »
A single-step method for purification of active His-tagged ribosomes from a genetically engineered Escherichia coli.
J. Ederth, C. S. Mandava, S. Dasgupta, and S. Sanyal (2009)
Nucleic Acids Res. 37, e15
   Abstract »    Full Text »    PDF »
A role for the 30S subunit E site in maintenance of the translational reading frame.
A. Devaraj, S. Shoji, E. D. Holbrook, and K. Fredrick (2009)
RNA 15, 255-265
   Abstract »    Full Text »    PDF »
Kinetic and thermodynamic analysis of the role of start codon/anticodon base pairing during eukaryotic translation initiation.
S. E. Kolitz, J. E. Takacs, and J. R. Lorsch (2009)
RNA 15, 138-152
   Abstract »    Full Text »    PDF »
Structural basis for cross-resistance to ribosomal PTC antibiotics.
C. Davidovich, A. Bashan, and A. Yonath (2008)
PNAS 105, 20665-20670
   Abstract »    Full Text »    PDF »
Crystal structure of a translation termination complex formed with release factor RF2.
A. Korostelev, H. Asahara, L. Lancaster, M. Laurberg, A. Hirschi, J. Zhu, S. Trakhanov, W. G. Scott, and H. F. Noller (2008)
PNAS 105, 19684-19689
   Abstract »    Full Text »    PDF »
Mutations in Conserved Helix 69 of 23S rRNA of Thermus thermophilus That Affect Capreomycin Resistance but Not Posttranscriptional Modifications.
T. Monshupanee, S. T. Gregory, S. Douthwaite, W. Chungjatupornchai, and A. E. Dahlberg (2008)
J. Bacteriol. 190, 7754-7761
   Abstract »    Full Text »    PDF »
Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.
N. Nomura, Y. Nomura, D. Sussman, D. Klein, and B. L. Stoddard (2008)
Nucleic Acids Res. 36, 6988-6998
   Abstract »    Full Text »    PDF »
Insights into Translational Termination from the Structure of RF2 Bound to the Ribosome.
A. Weixlbaumer, H. Jin, C. Neubauer, R. M. Voorhees, S. Petry, A. C. Kelley, and V. Ramakrishnan (2008)
Science 322, 953-956
   Abstract »    Full Text »    PDF »
Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus.
D. Rodriguez-Correa and A. E. Dahlberg (2008)
RNA 14, 2314-2318
   Abstract »    Full Text »    PDF »
Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit.
A. N. Petrov, A. Meskauskas, S. C. Roshwalb, and J. D. Dinman (2008)
Nucleic Acids Res. 36, 6187-6198
   Abstract »    Full Text »    PDF »
Ribosomal protein L3 functions as a 'rocker switch' to aid in coordinating of large subunit-associated functions in eukaryotes and Archaea.
A. Meskauskas and J. D. Dinman (2008)
Nucleic Acids Res. 36, 6175-6186
   Abstract »    Full Text »    PDF »
Irreversible chemical steps control intersubunit dynamics during translation.
R. A. Marshall, M. Dorywalska, and J. D. Puglisi (2008)
PNAS 105, 15364-15369
   Abstract »    Full Text »    PDF »
R{chi}-01, a New Family of Oxazolidinones That Overcome Ribosome-Based Linezolid Resistance.
E. Skripkin, T. S. McConnell, J. DeVito, L. Lawrence, J. A. Ippolito, E. M. Duffy, J. Sutcliffe, and F. Franceschi (2008)
Antimicrob. Agents Chemother. 52, 3550-3557
   Abstract »    Full Text »    PDF »
Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG.
J. E. Brock, S. Pourshahian, J. Giliberti, P. A. Limbach, and G. R. Janssen (2008)
RNA 14, 2159-2169
   Abstract »    Full Text »    PDF »
Pyrrolo-C as a molecular probe for monitoring conformations of the tRNA 3' end.
C.-M. Zhang, C. Liu, T. Christian, H. Gamper, J. Rozenski, D. Pan, J. B. Randolph, E. Wickstrom, B. S. Cooperman, and Y.-M. Hou (2008)
RNA 14, 2245-2253
   Abstract »    Full Text »    PDF »
YbeA is the m3{Psi} methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.
E. Purta, K. H. Kaminska, J. M. Kasprzak, J. M. Bujnicki, and S. Douthwaite (2008)
RNA 14, 2234-2244
   Abstract »    Full Text »    PDF »
The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit.
L. Lancaster, N. J. Lambert, E. J. Maklan, L. H. Horan, and H. F. Noller (2008)
RNA 14, 1999-2012
   Abstract »    Full Text »    PDF »
Molecular signatures of ribosomal evolution.
E. Roberts, A. Sethi, J. Montoya, C. R. Woese, and Z. Luthey-Schulten (2008)
PNAS 105, 13953-13958
   Abstract »    Full Text »    PDF »
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning.
D. N. Wilson, F. Schluenzen, J. M. Harms, A. L. Starosta, S. R. Connell, and P. Fucini (2008)
PNAS 105, 13339-13344
   Abstract »    Full Text »    PDF »
Anticodon loop mutations perturb reading frame maintenance by the E site tRNA.
C. L. Sanders, K. J. Lohr, H. L. Gambill, R. B. Curran, and J. F. Curran (2008)
RNA 14, 1874-1881
   Abstract »    Full Text »    PDF »
A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis.
P. Barraud, E. Schmitt, Y. Mechulam, F. Dardel, and C. Tisne (2008)
Nucleic Acids Res. 36, 4894-4901
   Abstract »    Full Text »    PDF »
Genetic identification of yeast 18S rRNA residues required for efficient recruitment of initiator tRNAMet and AUG selection.
J. Dong, J. S. Nanda, H. Rahman, M. R. Pruitt, B.-S. Shin, C.-M. Wong, J. R. Lorsch, and A. G. Hinnebusch (2008)
Genes & Dev. 22, 2242-2255
   Abstract »    Full Text »    PDF »
Structural basis for hygromycin B inhibition of protein biosynthesis.
M. A. Borovinskaya, S. Shoji, K. Fredrick, and J. H.D. Cate (2008)
RNA 14, 1590-1599
   Abstract »    Full Text »    PDF »
Revealing unique properties of the ribosome using a network based analysis.
H. David-Eden and Y. Mandel-Gutfreund (2008)
Nucleic Acids Res. 36, 4641-4652
   Abstract »    Full Text »    PDF »
Role of hybrid tRNA-binding states in ribosomal translocation.
S. E. Walker, S. Shoji, D. Pan, B. S. Cooperman, and K. Fredrick (2008)
PNAS 105, 9192-9197
   Abstract »    Full Text »    PDF »
RNA structure-based ribosome recruitment: Lessons from the Dicistroviridae intergenic region IRESes.
J. S. Pfingsten and J. S. Kieft (2008)
RNA 14, 1255-1263
   Abstract »    Full Text »    PDF »
Perturbation of the tRNA Tertiary Core Differentially Affects Specific Steps of the Elongation Cycle.
D. Pan, C.-M. Zhang, S. Kirillov, Y.-M. Hou, and B. S. Cooperman (2008)
J. Biol. Chem. 283, 18431-18440
   Abstract »    Full Text »    PDF »
Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon-codon hydrogen bonds as a major determinant of tRNA compositional variations.
I. Targanski and V. Cherkasova (2008)
RNA 14, 1095-1109
   Abstract »    Full Text »    PDF »
Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments.
T. Yokoyama and T. Suzuki (2008)
Nucleic Acids Res. 36, 3539-3551
   Abstract »    Full Text »    PDF »
A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting.
P.-Y. Liao, P. Gupta, A. N. Petrov, J. D. Dinman, and K. H. Lee (2008)
Nucleic Acids Res. 36, 2619-2629
   Abstract »    Full Text »    PDF »
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.
J. Kondo and E. Westhof (2008)
Nucleic Acids Res. 36, 2654-2666
   Abstract »    Full Text »    PDF »
Functional importance of individual rRNA 2'-O-ribose methylations revealed by high-resolution phenotyping.
J. Esguerra, J. Warringer, and A. Blomberg (2008)
RNA 14, 649-656
   Abstract »    Full Text »    PDF »
pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA.
S. C. Abeysirigunawardena and C. S. Chow (2008)
RNA 14, 782-792
   Abstract »    Full Text »    PDF »
Ribosomal proteins promote leaf adaxial identity.
Y. Yao, Q. Ling, H. Wang, and H. Huang (2008)
Development 135, 1325-1334
   Abstract »    Full Text »    PDF »
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
A. B. Taylor, B. Meyer, B. Z. Leal, P. Kotter, V. Schirf, B. Demeler, P. J. Hart, K.-D. Entian, and J. Wohnert (2008)
Nucleic Acids Res. 36, 1542-1554
   Abstract »    Full Text »    PDF »
Interactions of an Essential Bacillus subtilis GTPase, YsxC, with Ribosomes.
C. Wicker-Planquart, A.-E. Foucher, M. Louwagie, R. A. Britton, and J.-M. Jault (2008)
J. Bacteriol. 190, 681-690
   Abstract »    Full Text »    PDF »
Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit.
M. Simonovic and T. A. Steitz (2008)
PNAS 105, 500-505
   Abstract »    Full Text »    PDF »
The 3D rRNA modification maps database: with interactive tools for ribosome analysis.
D. Piekna-Przybylska, W. A. Decatur, and M. J. Fournier (2008)
Nucleic Acids Res. 36, D178-D183
   Abstract »    Full Text »    PDF »
STITCH: interaction networks of chemicals and proteins.
M. Kuhn, C. von Mering, M. Campillos, L. J. Jensen, and P. Bork (2008)
Nucleic Acids Res. 36, D684-D688
   Abstract »    Full Text »    PDF »
The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA.
S.-M. Toh, L. Xiong, T. Bae, and A. S. Mankin (2008)
RNA 14, 98-106
   Abstract »    Full Text »    PDF »
A novel chromatography system to isolate active ribosomes from pathogenic bacteria.
B. A. Maguire, L. M. Wondrack, L. G. Contillo, and Z. Xu (2008)
RNA 14, 188-195
   Abstract »    Full Text »    PDF »
Inaugural Article: The process of mRNA-tRNA translocation.
J. Frank, H. Gao, J. Sengupta, N. Gao, and D. J. Taylor (2007)
PNAS 104, 19671-19678
   Abstract »    Full Text »    PDF »
Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
M. R. Sharma, D. N. Wilson, P. P. Datta, C. Barat, F. Schluenzen, P. Fucini, and R. K. Agrawal (2007)
PNAS 104, 19315-19320
   Abstract »    Full Text »    PDF »
Characterization of 16S rRNA mutations that decrease the fidelity of translation initiation.
D. Qin, N. M. Abdi, and K. Fredrick (2007)
RNA 13, 2348-2355
   Abstract »    Full Text »    PDF »
Three Binding Sites for Stalk Protein Dimers Are Generally Present in Ribosomes from Archaeal Organism.
Y. Maki, T. Hashimoto, M. Zhou, T. Naganuma, J. Ohta, T. Nomura, C. V. Robinson, and T. Uchiumi (2007)
J. Biol. Chem. 282, 32827-32833
   Abstract »    Full Text »    PDF »
Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA.
B.-W. Ying, D. Fourmy, and S. Yoshizawa (2007)
RNA 13, 2042-2050
   Abstract »    Full Text »    PDF »
RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA.
P. P. Vaidyanathan, M. P. Deutscher, and A. Malhotra (2007)
RNA 13, 1868-1876
   Abstract »    Full Text »    PDF »
Saturation mutagenesis of a +1 programmed frameshift-inducing mRNA sequence derived from a yeast retrotransposon.
C. Guarraia, L. Norris, A. Raman, and P. J. Farabaugh (2007)
RNA 13, 1940-1947
   Abstract »    Full Text »    PDF »
Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
A. Korostelev, S. Trakhanov, H. Asahara, M. Laurberg, L. Lancaster, and H. F. Noller (2007)
PNAS 104, 16840-16843
   Abstract »    Full Text »    PDF »
Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data.
W. Li and J. Frank (2007)
PNAS 104, 16540-16545
   Abstract »    Full Text »    PDF »
Mutations in Residues Involved in Zinc Binding in the Catalytic Site of Escherichia coli Threonyl-tRNA Synthetase Confer a Dominant Lethal Phenotype.
J. Caillet, M. Graffe, F. Eyermann, P. Romby, and M. Springer (2007)
J. Bacteriol. 189, 6839-6848
   Abstract »    Full Text »    PDF »
Ribosome Biogenesis and the Translation Process in Escherichia coli.
M. Kaczanowska and M. Ryden-Aulin (2007)
Microbiol. Mol. Biol. Rev. 71, 477-494
   Abstract »    Full Text »    PDF »
Fluorescent labeling of tRNAs for dynamics experiments.
T. Betteridge, H. Liu, H. Gamper, S. Kirillov, B. S. Cooperman, and Y.-M. Hou (2007)
RNA 13, 1594-1601
   Abstract »    Full Text »    PDF »
Genetic analysis of the E site during RF2 programmed frameshifting.
C. L. Sanders and J. F. Curran (2007)
RNA 13, 1483-1491
   Abstract »    Full Text »    PDF »
The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift.
M. Leger, D. Dulude, S. V. Steinberg, and L. Brakier-Gingras (2007)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Use of a Dominant rpsL Allele Conferring Streptomycin Dependence for Positive and Negative Selection in Thermus thermophilus.
E. Blas-Galindo, F. Cava, E. Lopez-Vinas, J. Mendieta, and J. Berenguer (2007)
Appl. Envir. Microbiol. 73, 5138-5145
   Abstract »    Full Text »    PDF »
G-ribo motif favors the formation of pseudoknots in ribosomal RNA.
S. V. Steinberg and Y. I. Boutorine (2007)
RNA 13, 1036-1042
   Abstract »    Full Text »    PDF »
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.
F. Razga, J. Koca, A. Mokdad, and J. Sponer (2007)
Nucleic Acids Res. 35, 4007-4017
   Abstract »    Full Text »    PDF »
Functional genetic selection of Helix 66 in Escherichia coli 23S rRNA identified the eukaryotic-binding sequence for ribosomal protein L2.
K. Kitahara, A. Kajiura, N. S. Sato, and T. Suzuki (2007)
Nucleic Acids Res. 35, 4018-4029
   Abstract »    Full Text »    PDF »
Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.
C. M. Dunham, M. Selmer, S. S. Phelps, A. C. Kelley, T. Suzuki, S. Joseph, and V. Ramakrishnan (2007)
RNA 13, 817-823
   Abstract »    Full Text »    PDF »
Escherichia coli ribosomal protein L20 binds as a single monomer to its own mRNA bearing two potential binding sites.
F. Allemand, J. Haentjens, C. Chiaruttini, C. Royer, and M. Springer (2007)
Nucleic Acids Res. 35, 3016-3031
   Abstract »    Full Text »    PDF »
Anticodon-dependent conservation of bacterial tRNA gene sequences.
M. E. Saks and J. S. Conery (2007)
RNA 13, 651-660
   Abstract »    Full Text »    PDF »
G-ribo: A new structural motif in ribosomal RNA.
S. V. Steinberg and Y. I. Boutorine (2007)
RNA 13, 549-554
   Abstract »    Full Text »    PDF »
Ribosomal RNA guanine-(N2)-methyltransferases and their targets.
P. V. Sergiev, A. A. Bogdanov, and O. A. Dontsova (2007)
Nucleic Acids Res. 35, 2295-2301
   Abstract »    Full Text »    PDF »
Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.
C. Davidovich, A. Bashan, T. Auerbach-Nevo, R. D. Yaggie, R. R. Gontarek, and A. Yonath (2007)
PNAS 104, 4291-4296
   Abstract »    Full Text »    PDF »
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA.
D. Piekna-Przybylska, W. A. Decatur, and M. J. Fournier (2007)
RNA 13, 305-312
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)