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.
Keystone Symposium

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Published Online March 29, 2001
Science DOI: 10.1126/science.1060089

Research Articles

Submitted on February 21, 2001
Accepted on March 20, 2001

Crystal Structure of the Ribosome at 5.5 Å Resolution

Marat M. Yusupov 1*, Gulnara Zh. Yusupova 1, Albion Baucom 2, Kate Lieberman 2, Thomas N. Earnest 3, J. H. D. Cate 4*, Harry F. Noller 2*

1 Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA; UPR 9004 de Biologie et de Genomiques Structurales du CNRS, IGBMC B.P. 163, 1 rue L.Fries, 67404 Illkirch Cedex - CU de Strasbourg, France.
2 Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA.
3 Berkeley Center for Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
4 Whitehead Institute, Cambridge, MA, 01242, USA.

We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound mRNA and tRNAs at 5.5 Å resolution. All of the 16S, 23S and 5S rRNA chains, the A-, P- and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 Å movements associated with tRNA translocation with intersubunit movement.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Toxic Introns and Parasitic Intein in Coxiella burnetii: Legacies of a Promiscuous Past.
R. Raghavan, L. D. Hicks, and M. F. Minnick (2008)
J. Bacteriol. 190, 5934-5943
   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 »
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 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 »
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 »
Modulating the activity of the peptidyl transferase center of the ribosome.
M. Beringer (2008)
RNA 14, 795-801
   Abstract »    Full Text »    PDF »
Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
S. Muller, F. Leclerc, I. Behm-Ansmant, J.-B. Fourmann, B. Charpentier, and C. Branlant (2008)
Nucleic Acids Res. 36, 2459-2475
   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 »
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 »
Structure/function analysis of yeast ribosomal protein L2.
A. Meskauskas, J. R. Russ, and J. D. Dinman (2008)
Nucleic Acids Res. 36, 1826-1835
   Abstract »    Full Text »    PDF »
Three PIGGYBACK genes that specifically influence leaf patterning encode ribosomal proteins.
V. Pinon, J. P. Etchells, P. Rossignol, S. A. Collier, J. M. Arroyo, R. A. Martienssen, and M. E. Byrne (2008)
Development 135, 1315-1324
   Abstract »    Full Text »    PDF »
The structure of LepA, the ribosomal back translocase.
(2008)
PNAS 105, 4673-4678
The Cech Symposium: A celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom.
Q. Vicens, M. A. Allen, S. D. Gilbert, B. Reznik, A. R. Gooding, and R. T. Batey (2008)
RNA 14, 397-403
   Abstract »    Full Text »    PDF »
rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance.
R. Rakauskaite and J. D. Dinman (2008)
Nucleic Acids Res. 36, 1497-1507
   Abstract »    Full Text »    PDF »
The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: A structural homolog of the FF domain.
B. Wu, A. Yee, Y. J. Huang, T. A. Ramelot, J. R. Cort, A. Semesi, J.-W. Jung, W. Lee, G. T. Montelione, M. A. Kennedy, et al. (2008)
Protein Sci. 17, 583-588
   Abstract »    Full Text »    PDF »
Site-specific Incorporation of Keto Amino Acids into Functional G Protein-coupled Receptors Using Unnatural Amino Acid Mutagenesis.
S. Ye, C. Kohrer, T. Huber, M. Kazmi, P. Sachdev, E. C.Y. Yan, A. Bhagat, U. L. RajBhandary, and T. P. Sakmar (2008)
J. Biol. Chem. 283, 1525-1533
   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 »
Eukaryotic ribosomal RNA determinants of aminoglycoside resistance and their role in translational fidelity.
H. Fan-Minogue and D. M. Bedwell (2008)
RNA 14, 148-157
   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 »
Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination.
M. Ejby, M. A. Sorensen, and S. Pedersen (2007)
PNAS 104, 19410-19415
   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 »
Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5.
O. Galkin, A. A. Bentley, S. Gupta, B.-A. Compton, B. Mazumder, T. G. Kinzy, W. C. Merrick, M. Hatzoglou, T. V. Pestova, C. U.T. Hellen, et al. (2007)
RNA 13, 2116-2128
   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 »
Fluctuations of Transfer RNAs between Classical and Hybrid States.
H. D. Kim, J. D. Puglisi, and S. Chu (2007)
Biophys. J. 93, 3575-3582
   Abstract »    Full Text »    PDF »
Mutational Analysis of the Ribosomal Protein Rpl10 from Yeast.
A. Hofer, C. Bussiere, and A. W. Johnson (2007)
J. Biol. Chem. 282, 32630-32639
   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 »
A practical guide to the art of RNA gene prediction.
I. M. Meyer (2007)
Brief Bioinform 8, 396-414
   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 »
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 »
The Unusual 23S rRNA Gene of Coxiella burnetii: Two Self-Splicing Group I Introns Flank a 34-Base-Pair Exon, and One Element Lacks the Canonical {Omega}G.
R. Raghavan, S. R. Miller, L. D. Hicks, and M. F. Minnick (2007)
J. Bacteriol. 189, 6572-6579
   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 »
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 »
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 »
From the Cover: The role of fluctuations in tRNA selection by the ribosome.
T.-H. Lee, S. C. Blanchard, H. D. Kim, J. D. Puglisi, and S. Chu (2007)
PNAS 104, 13661-13665
   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 »
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 »
Novel activity of eukaryotic translocase, eEF2: dissociation of the 80S ribosome into subunits with ATP but not with GTP.
N. Demeshkina, G. Hirokawa, A. Kaji, and H. Kaji (2007)
Nucleic Acids Res. 35, 4597-4607
   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 »
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
Y. Bessho, R. Shibata, S.-i. Sekine, K. Murayama, K. Higashijima, C. Hori-Takemoto, M. Shirouzu, S. Kuramitsu, and S. Yokoyama (2007)
PNAS 104, 8293-8298
   Abstract »    Full Text »    PDF »
RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
K. Lagesen, P. Hallin, E. A. Rodland, H.-H. Staerfeldt, T. Rognes, and D. W. Ussery (2007)
Nucleic Acids Res. 35, 3100-3108
   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 »
Post-transcriptional modification mapping in the Clostridium acetobutylicum 16S rRNA by mass spectrometry and reverse transcriptase assays.
G. Emmerechts, S. Barbe, P. Herdewijn, J. Anne, and J. Rozenski (2007)
Nucleic Acids Res. 35, 3494-3503
   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 »
New photoreactive tRNA derivatives for probing the peptidyl transferase center of the ribosome.
A. V. Manuilov, S. S. Hixson, and R. A. Zimmermann (2007)
RNA 13, 793-800
   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 »
Intersubunit movement is required for ribosomal translocation.
L. H. Horan and H. F. Noller (2007)
PNAS 104, 4881-4885
   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 »
Proteomics Analysis of Thermoplasma acidophilum with a Focus on Protein Complexes.
N. Sun, F. Beck, R. W. Knispel, F. Siedler, B. Scheffer, S. Nickell, W. Baumeister, and I. Nagy (2007)
Mol. Cell. Proteomics 6, 492-502
   Abstract »    Full Text »    PDF »
Methyltransferase That Modifies Guanine 966 of the 16 S rRNA: FUNCTIONAL IDENTIFICATION AND TERTIARY STRUCTURE.
D. V. Lesnyak, J. Osipiuk, T. Skarina, P. V. Sergiev, A. A. Bogdanov, A. Edwards, A. Savchenko, A. Joachimiak, and O. A. Dontsova (2007)
J. Biol. Chem. 282, 5880-5887
   Abstract »    Full Text »    PDF »
Internal strain regulates the nucleotide binding site of the kinesin leading head.
C. Hyeon and J. N. Onuchic (2007)
PNAS 104, 2175-2180
   Abstract »    Full Text »    PDF »
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
H. R. A. Jonker, S. Ilin, S. K. Grimm, J. Wohnert, and H. Schwalbe (2007)
Nucleic Acids Res. 35, 441-454
   Abstract »    Full Text »    PDF »
The CRM domain: An RNA binding module derived from an ancient ribosome-associated protein.
A. Barkan, L. Klipcan, O. Ostersetzer, T. Kawamura, Y. Asakura, and K. P. Watkins (2007)
RNA 13, 55-64
   Abstract »    Full Text »    PDF »
Inhibition of Antiassociation Activity of Translation Initiation Factor 3 by Paromomycin.
G. Hirokawa, H. Kaji, and A. Kaji (2007)
Antimicrob. Agents Chemother. 51, 175-180
   Abstract »    Full Text »    PDF »
Close Packing of Helices 3 and 12 of 16 S rRNA Is Required for the Normal Ribosome Function.
M. G. Gagnon, A. Mukhopadhyay, and S. V. Steinberg (2006)
J. Biol. Chem. 281, 39349-39357
   Abstract »    Full Text »    PDF »
The interaction networks of structured RNAs.
A. Lescoute and E. Westhof (2006)
Nucleic Acids Res. 34, 6587-6604
   Abstract »    Full Text »    PDF »
An Arc of Unpaired "Hinge Bases" Facilitates Information Exchange among Functional Centers of the Ribosome.
R. Rakauskaite and J. D. Dinman (2006)
Mol. Cell. Biol. 26, 8992-9002
   Abstract »    Full Text »    PDF »
A novel single amino acid change in small subunit ribosomal protein S5 has profound effects on translational fidelity.
N. Kirthi, B. Roy-Chaudhuri, T. Kelley, and G. M. Culver (2006)
RNA 12, 2080-2091
   Abstract »    Full Text »    PDF »
Structural Basis for Ribosome Recruitment and Manipulation by a Viral IRES RNA.
J. S. Pfingsten, D. A. Costantino, and J. S. Kieft (2006)
Science 314, 1450-1454
   Abstract »    Full Text »    PDF »
Involvement of Helix 34 of 16 S rRNA in Decoding and Translocation on the Ribosome.
A. Kubarenko, P. Sergiev, W. Wintermeyer, O. Dontsova, and M. V. Rodnina (2006)
J. Biol. Chem. 281, 35235-35244
   Abstract »    Full Text »    PDF »
Stability of the 'L12 stalk' in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria.
D. Shcherbakov, M. Dontsova, M. Tribus, M. Garber, and W. Piendl (2006)
Nucleic Acids Res. 34, 5800-5814
   Abstract »    Full Text »    PDF »
The A-site Finger in 23 S rRNA Acts as a Functional Attenuator for Translocation.
T. Komoda, N. S. Sato, S. S. Phelps, N. Namba, S. Joseph, and T. Suzuki (2006)
J. Biol. Chem. 281, 32303-32309
   Abstract »    Full Text »    PDF »
Structural basis for mRNA and tRNA positioning on the ribosome.
V. Berk, W. Zhang, R. D. Pai, and J. H. D. Cate (2006)
PNAS 103, 15830-15834
   Abstract »    Full Text »    PDF »
Unusual mechanical stability of a minimal RNA kissing complex.
P. T. X. Li, C. Bustamante, and I. Tinoco Jr. (2006)
PNAS 103, 15847-15852
   Abstract »    Full Text »    PDF »
Comprehensive genetic selection revealed essential bases in the peptidyl-transferase center.
N. S. Sato, N. Hirabayashi, I. Agmon, A. Yonath, and T. Suzuki (2006)
PNAS 103, 15386-15391
   Abstract »    Full Text »    PDF »
Mutations in the Intersubunit Bridge Regions of 23 S rRNA.
A. Liiv and M. O'Connor (2006)
J. Biol. Chem. 281, 29850-29862
   Abstract »    Full Text »    PDF »
Structure of the 70S Ribosome Complexed with mRNA and tRNA.
M. Selmer, C. M. Dunham, F. V. Murphy IV, A. Weixlbaumer, S. Petry, A. C. Kelley, J. R. Weir, and V. Ramakrishnan (2006)
Science 313, 1935-1942
   Abstract »    Full Text »    PDF »


ADVERTISEMENT
Click Me!

ADVERTISEMENT
Click Me!

To Advertise     Find Products

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