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.
Structures of the Bacterial Ribosome at 3.5 Å Resolution
Barbara S. Schuwirth,1,4*Maria A. Borovinskaya,3*Cathy W. Hau,2Wen Zhang,1Antón Vila-Sanjurjo,3James M. Holton,3Jamie H. Doudna Cate1,2,3
We describe two structures of the intact bacterial ribosomefrom Escherichia coli determined to a resolution of 3.5 angstromsby x-ray crystallography. These structures provide a detailedview of the interface between the small and large ribosomalsubunits and the conformation of the peptidyl transferase centerin the context of the intact ribosome. Differences between thetwo ribosomes reveal a high degree of flexibility between thehead and the rest of the small subunit. Swiveling of the headof the small subunit observed in the present structures, coupledto 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.
To whom correspondence should be addressed. E-mail: jcate{at}lbl.gov
The editors suggest the following Related Resources on Science sites:
In Science Magazine
PERSPECTIVES
Peter B. Moore (4 November 2005) Science310 (5749), 793.
[DOI: 10.1126/science.1120539] |Summary »|Full Text »|PDF »
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
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.
|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 »
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.
|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 »
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 »
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.
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.
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.
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.
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.
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.
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.
Conformational energy and structure in canonical and noncanonical forms of tRNA determined by temperature analysis of the rate of s4U8 C13 photocrosslinking.
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.
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 »
Evolutionary rates vary among rRNA structural elements.
S. Smit, J. Widmann, and R. Knight (2007)
Nucleic Acids Res.
35, 3339-3354
|Abstract »|Full Text »|PDF »
Ribosomal Features Essential for tna Operon Induction: Tryptophan Binding at the Peptidyl Transferase Center.
L. R. Cruz-Vera, A. New, C. Squires, and C. Yanofsky (2007)
J. Bacteriol.
189, 3140-3146
|Abstract »|Full Text »|PDF »
Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
R. J. C. Gilbert, Y. Gordiyenko, T. von der Haar, A. F.-P. Sonnen, G. Hofmann, M. Nardelli, D. I. Stuart, and J. E. G. McCarthy (2007)
PNAS
104, 5788-5793
|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 »
Targeted Protein Degradation by Salmonella under Phagosome-mimicking Culture Conditions Investigated Using Comparative Peptidomics.
N. P. Manes, J. K. Gustin, J. Rue, H. M. Mottaz, S. O. Purvine, A. D. Norbeck, M. E. Monroe, J. S. D. Zimmer, T. O. Metz, J. N. Adkins, et al. (2007)
Mol. Cell. Proteomics
6, 717-727
|Abstract »|Full Text »|PDF »
Intersubunit movement is required for ribosomal translocation.