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.

Science 4 November 2005:
Vol. 310. no. 5749, pp. 827 - 834
DOI: 10.1126/science.1117230
Prev | Table of Contents | Next

Research Articles

Structures of the Bacterial Ribosome at 3.5 Å Resolution

Barbara S. Schuwirth,1,4* Maria A. Borovinskaya,3* Cathy W. Hau,2 Wen Zhang,1 Antón Vila-Sanjurjo,3 James M. Holton,3 Jamie H. Doudna Cate1,2,3{dagger}

We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.

1 Department of Chemistry, University of California, Berkeley, CA 94720, USA.
2 Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
3 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
4 Institute of Chemistry-Crystallography, Free University of Berlin, 14195 Berlin, Germany.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: jcate{at}lbl.gov

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
The Structure of the Ribosome with Elongation Factor G Trapped in the Posttranslocational State.
Y.-G. Gao, M. Selmer, C. M. Dunham, A. Weixlbaumer, A. C. Kelley, and V. Ramakrishnan (2009)
Science 326, 694-699
   Abstract »    Full Text »    PDF »
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
A. Korostelev, M. Laurberg, and H. F. Noller (2009)
PNAS 106, 18195-18200
   Abstract »    Full Text »    PDF »
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
A. Yonath (2009)
J R Soc Interface 6, S575-S585
   Abstract »    Full Text »    PDF »
Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides.
A. D. Kauffmann, R. J. Campagna, C. B. Bartels, and J. L. Childs-Disney (2009)
Nucleic Acids Res. 37, e121
   Abstract »    Full Text »    PDF »
Ion-induced folding of a kink turn that departs from the conventional sequence.
K. T. Schroeder and D. M. J. Lilley (2009)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Footprinting analysis of BWYV pseudoknot-ribosome complexes.
M.-H. Mazauric, J.-L. Leroy, K. Visscher, S. Yoshizawa, and D. Fourmy (2009)
RNA 15, 1775-1786
   Abstract »    Full Text »    PDF »
Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain.
A. C. Lamanna and K. Karbstein (2009)
PNAS 106, 14259-14264
   Abstract »    Full Text »    PDF »
Structures of the Ribosome in Intermediate States of Ratcheting.
W. Zhang, J. A. Dunkle, and J. H. D. Cate (2009)
Science 325, 1014-1017
   Abstract »    Full Text »    PDF »
The Ribosome as a Conveying Thermal Ratchet Machine.
A. S. Spirin (2009)
J. Biol. Chem. 284, 21103-21119
   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. 37, 4898-4918
   Abstract »    Full Text »    PDF »
Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing.
Y. Yu, A. Marintchev, V. G. Kolupaeva, A. Unbehaun, T. Veryasova, S.-C. Lai, P. Hong, G. Wagner, C. U. T. Hellen, and T. V. Pestova (2009)
Nucleic Acids Res. 37, 5167-5182
   Abstract »    Full Text »    PDF »
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 »
Defining the Structural Basis of Human Plasminogen Binding by Streptococcal Surface Enolase.
A. J. Cork, S. Jergic, S. Hammerschmidt, B. Kobe, V. Pancholi, J. L. P. Benesch, C. V. Robinson, N. E. Dixon, J. A. Aquilina, and M. J. Walker (2009)
J. Biol. Chem. 284, 17129-17137
   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 »
23S rRNA Nucleotides in the Peptidyl Transferase Center Are Essential for Tryptophanase Operon Induction.
R. Yang, L. R. Cruz-Vera, and C. Yanofsky (2009)
J. Bacteriol. 191, 3445-3450
   Abstract »    Full Text »    PDF »
Initiation of ribosome degradation during starvation in Escherichia coli.
M. A. Zundel, G. N. Basturea, and M. P. Deutscher (2009)
RNA 15, 977-983
   Abstract »    Full Text »    PDF »
A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly.
D. L. Bellur and S. A. Woodson (2009)
Nucleic Acids Res. 37, 1886-1896
   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 »
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 »
Engineering and Characterization of the Ribosomal L10{middle dot}L12 Stalk Complex: A STRUCTURAL ELEMENT RESPONSIBLE FOR HIGH TURNOVER OF THE ELONGATION FACTOR G-DEPENDENT GTPase.
T. Miyoshi, T. Nomura, and T. Uchiumi (2009)
J. Biol. Chem. 284, 85-92
   Abstract »    Full Text »    PDF »
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea.
Z. M.-P. Lee, C. Bussema III, and T. M. Schmidt (2009)
Nucleic Acids Res. 37, D489-D493
   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 »
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 »
In Vitro Activity of TR-700, the Antibacterial Moiety of the Prodrug TR-701, against Linezolid-Resistant Strains.
K. J. Shaw, S. Poppe, R. Schaadt, V. Brown-Driver, J. Finn, C. M. Pillar, D. Shinabarger, and G. Zurenko (2008)
Antimicrob. Agents Chemother. 52, 4442-4447
   Abstract »    Full Text »    PDF »
Revisiting the mechanism of macrolide-antibiotic resistance mediated by ribosomal protein L22.
S. D. Moore and R. T. Sauer (2008)
PNAS 105, 18261-18266
   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 »
Biochemical Evidence for the Heptameric Complex L10(L12)6 in the Thermus thermophilus Ribosome: In Vitro Analysis of its Molecular Assembly and Functional Properties.
T. Nomura, M. Nakatsuchi, D. Sugita, M. Nomura, T. Kaminishi, C. Takemoto, M. Shirouzu, T. Miyoshi, S. Yokoyama, A. Hachimori, et al. (2008)
J. Biochem. 144, 665-673
   Abstract »    Full Text »    PDF »
Side-chain recognition and gating in the ribosome exit tunnel.
P. M. Petrone, C. D. Snow, D. Lucent, and V. S. Pande (2008)
PNAS 105, 16549-16554
   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 »
Core flexibility of a truncated metazoan mitochondrial tRNA.
A. A. Frazer-Abel and P. J. Hagerman (2008)
Nucleic Acids Res. 36, 5472-5481
   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 »
Effects of N2,N2 -dimethylguanosine on RNA structure and stability: Crystal structure of an RNA duplex with tandem m2 2G:A pairs.
P. S. Pallan, C. Kreutz, S. Bosio, R. Micura, and M. Egli (2008)
RNA 14, 2125-2135
   Abstract »    Full Text »    PDF »
Ribosome Performance Is Enhanced by a Rich Cluster of Pseudouridines in the A-site Finger Region of the Large Subunit.
D. Piekna-Przybylska, P. Przybylski, A. Baudin-Baillieu, J.-P. Rousset, and M. J. Fournier (2008)
J. Biol. Chem. 283, 26026-26036
   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 »
Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.
W. Rypniewski, D. A. Adamiak, J. Milecki, and R. W. Adamiak (2008)
RNA 14, 1845-1851
   Abstract »    Full Text »    PDF »
Effects on Translation Pausing of Alterations in Protein and RNA Components of the Ribosome Exit Tunnel.
M. G. Lawrence, L. Lindahl, and J. M. Zengel (2008)
J. Bacteriol. 190, 5862-5869
   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 »
RNA secondary structure of the feline immunodeficiency virus 5'UTR and Gag coding region.
L. James and B. Sargueil (2008)
Nucleic Acids Res. 36, 4653-4666
   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 »
S1 Ribosomal Protein Functions in Translation Initiation and Ribonuclease RegB Activation Are Mediated by Similar RNA-Protein Interactions: AN NMR AND SAXS ANALYSIS.
P. Aliprandi, C. Sizun, J. Perez, F. Mareuil, S. Caputo, J.-L. Leroy, B. Odaert, S. Laalami, M. Uzan, and F. Bontems (2008)
J. Biol. Chem. 283, 13289-13301
   Abstract »    Full Text »    PDF »
Arabidopsis Ribosomal Proteins RPL23aA and RPL23aB Are Differentially Targeted to the Nucleolus and Are Disparately Required for Normal Development.
R. F. Degenhardt and P. C. Bonham-Smith (2008)
Plant Physiology 147, 128-142
   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 »
Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes.
T. Miyoshi and T. Uchiumi (2008)
Nucleic Acids Res. 36, 1783-1791
   Abstract »    Full Text »    PDF »
From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal.
S. Smit, K. Rother, J. Heringa, and R. Knight (2008)
RNA 14, 410-416
   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 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 »
In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton.
A. Garcia-Marcos, A. Morreale, E. Guarinos, E. Briones, M. Remacha, A. R. Ortiz, and J. P. G. Ballesta (2007)
Nucleic Acids Res. 35, 7109-7117
   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 »
Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit.
S. J. Schroeder, G. Blaha, and P. B. Moore (2007)
Antimicrob. Agents Chemother. 51, 4462-4465
   Abstract »    Full Text »    PDF »
Novel Plasmid-Mediated 16S rRNA m1A1408 Methyltransferase, NpmA, Found in a Clinically Isolated Escherichia coli Strain Resistant to Structurally Diverse Aminoglycosides.
J.-i. Wachino, K. Shibayama, H. Kurokawa, K. Kimura, K. Yamane, S. Suzuki, N. Shibata, Y. Ike, and Y. Arakawa (2007)
Antimicrob. Agents Chemother. 51, 4401-4409
   Abstract »    Full Text »    PDF »
Thiostrepton inhibition of tRNA delivery to the ribosome.
R. L. Gonzalez Jr, S. Chu, and J. D. Puglisi (2007)
RNA 13, 2091-2097
   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 »
Conformational energy and structure in canonical and noncanonical forms of tRNA determined by temperature analysis of the rate of s4U8 C13 photocrosslinking.
W. Huggins, T. Shapkina, and P. Wollenzien (2007)
RNA 13, 2000-2011
   Abstract »    Full Text »    PDF »
Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE.
G. N. Basturea and M. P. Deutscher (2007)
RNA 13, 1969-1976
   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 »
Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure.
H. Li, R. Liang, D. H. Turner, L. J. Rothberg, and S. Duan (2007)
RNA 13, 2034-2041
   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 »
Alterations in the Two Globular Domains or in the Connecting {alpha}-Helix of Bacterial Ribosomal Protein L9 Induces +1 Frameshifts.
R. Leipuviene and G. R. Bjork (2007)
J. Bacteriol. 189, 7024-7031
   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 »
Detecting the Coevolution of Biosequences An Example of RNA Interaction Prediction.
C.-H. Yeang, J. F. J. Darot, H. F. Noller, and D. Haussler (2007)
Mol. Biol. Evol. 24, 2119-2131
   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 »
Potential New Antibiotic Sites in the Ribosome Revealed by Deleterious Mutations in RNA of the Large Ribosomal Subunit.
A. Yassin and A. S. Mankin (2007)
J. Biol. Chem. 282, 24329-24342
   Abstract »    Full Text »    PDF »
RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria.
C. Yanofsky (2007)
RNA 13, 1141-1154
   Abstract »    Full Text »    PDF »
Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine.
E. C. Kouvela, G. V. Gerbanas, M. A. Xaplanteri, A. D. Petropoulos, G. P. Dinos, and D. L. Kalpaxis (2007)
Nucleic Acids Res. 35, 5108-5119
   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 »
RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition.
S. L. Ameres, D. Shcherbakov, E. Nikonova, W. Piendl, R. Schroeder, and K. Semrad (2007)
Nucleic Acids Res. 35, 3752-3763
   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 »


To Advertise     Find Products

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