Related Content
Search Google Scholar for:
More Information
Related Jobs from ScienceCareers
|
|
Science 24 September 1999: Vol. 285. no. 5436, pp. 2095 - 2104 DOI: 10.1126/science.285.5436.2095
|
|
Research Articles
X-ray Crystal Structures of 70S Ribosome Functional Complexes
Jamie H. Cate,
1*
Marat M. Yusupov,
1*
Gulnara Zh. Yusupova,
1
Thomas N. Earnest,
2
Harry F. Noller
1*
Structures of 70S ribosome complexes containing
messenger RNA and transfer RNA (tRNA), or tRNA analogs, have been
solved by x-ray crystallography at up to 7.8 angstrom resolution. Many
details of the interactions between tRNA and the ribosome, and of the packing arrangements of ribosomal RNA (rRNA) helices in and between the
ribosomal subunits, can be seen. Numerous contacts are made between the
30S subunit and the P-tRNA anticodon stem-loop; in contrast,
the anticodon region of A-tRNA is much more exposed. A complex network
of molecular interactions suggestive of a functional relay is centered
around the long penultimate stem of 16S rRNA at the subunit
interface, including interactions involving the "switch" helix and
decoding site of 16S rRNA, and RNA bridges from the
50S subunit.
1 Center for Molecular Biology of RNA, Sinsheimer
Laboratories, University of California, Santa Cruz, CA 95064, USA.
2 Macromolecular Crystallography Facility, Advanced Light
Source, Physical Biosciences Division, Lawrence Berkeley National
Laboratory, Berkeley, CA 94720, USA.
*
To whom correspondence should be addressed. E-mail: cate{at}wi.mit.edu
(J.H.C), marat{at}darwin.ucsc.edu (M.M.Y.), and
harry{at}nuvolari.ucsc.edu (H.F.N.)
Present address: Whitehead Institute for Biomedical Research
and Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
These authors contributed equally to this work.
Read the Full Text
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
- The structure of LepA, the ribosomal back translocase.
- (2008)
PNAS
105, 4673-4678
- 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 »
- 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 »
- 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 »
- The interaction networks of structured RNAs.
- A. Lescoute and E. Westhof (2006)
Nucleic Acids Res.
34, 6587-6604
| Abstract »
| Full Text »
| PDF »
- Self-splicing of a group I intron reveals partitioning of native and misfolded RNA populations in yeast.
- S. A. Jackson, S. Koduvayur, and S. A. Woodson (2006)
RNA
12, 2149-2159
| Abstract »
| Full Text »
| PDF »
- Modifications in Thermus thermophilus 23 S Ribosomal RNA Are Centered in Regions of RNA-RNA Contact.
- J. Mengel-Jorgensen, S. S. Jensen, A. Rasmussen, J. Poehlsgaard, J. J. L. Iversen, and F. Kirpekar (2006)
J. Biol. Chem.
281, 22108-22117
| Abstract »
| Full Text »
| PDF »
- Thematic review series: Lipid Posttranslational Modifications. Structural biology of protein farnesyltransferase and geranylgeranyltransferase type I.
- K. T. Lane and L. S. Beese (2006)
J. Lipid Res.
47, 681-699
| Abstract »
| Full Text »
| PDF »
- Controlling RNA self-assembly to form filaments.
- L. Nasalean, S. Baudrey, N. B. Leontis, and L. Jaeger (2006)
Nucleic Acids Res.
34, 1381-1392
| Abstract »
| Full Text »
| PDF »
- The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity.
- J. L. BRUNELLE, E. M. YOUNGMAN, D. SHARMA, and R. GREEN (2006)
RNA
12, 33-39
| Abstract »
| Full Text »
| PDF »
- Accessibility of 18S rRNA in human 40S subunits and 80S ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics.
- C. L. SHENVI, K. C. DONG, E. M. FRIEDMAN, J. A. HANSON, and J. H.D. CATE (2005)
RNA
11, 1898-1908
| Abstract »
| Full Text »
| PDF »
- Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli.
- N. M. ABDI and K. FREDRICK (2005)
RNA
11, 1624-1632
| Abstract »
| Full Text »
| PDF »
- Comparison of tRNA Motions in the Free and Ribosomal Bound Structures.
- Y. Wang and R. L. Jernigan (2005)
Biophys. J.
89, 3399-3409
| Abstract »
| Full Text »
| PDF »
- RNA Structure: Reading the Ribosome.
- H. F. Noller (2005)
Science
309, 1508-1514
| Abstract »
| Full Text »
| PDF »
- Oxazolidinones Inhibit Cellular Proliferation via Inhibition of Mitochondrial Protein Synthesis.
- E. E. Nagiec, L. Wu, S. M. Swaney, J. G. Chosay, D. E. Ross, J. K. Brieland, and K. L. Leach (2005)
Antimicrob. Agents Chemother.
49, 3896-3902
| Abstract »
| Full Text »
| PDF »
- Effects of nucleotide substitution and modification on the stability and structure of helix 69 from 28S rRNA.
- M. SUMITA, J.-P. DESAULNIERS, Y.-C. CHANG, H. M.-P. CHUI, L. CLOS II, and C. S. CHOW (2005)
RNA
11, 1420-1429
| Abstract »
| Full Text »
| PDF »
- Translational Operator of mRNA on the Ribosome: How Repressor Proteins Exclude Ribosome Binding.
- L. Jenner, P. Romby, B. Rees, C. Schulze-Briese, M. Springer, C. Ehresmann, B. Ehresmann, D. Moras, G. Yusupova, and M. Yusupov (2005)
Science
308, 120-123
| Abstract »
| Full Text »
| PDF »
- Interaction of Thiostrepton and Elongation Factor-G with the Ribosomal Protein L11-binding Domain.
- W. S. Bowen, N. Van Dyke, E. J. Murgola, J. S. Lodmell, and W. E. Hill (2005)
J. Biol. Chem.
280, 2934-2943
| Abstract »
| Full Text »
| PDF »
- Guanosine tetra- and pentaphosphate synthase activity in chloroplasts of a higher plant: association with 70S ribosomes and inhibition by tetracycline.
- K. Kasai, T. Kanno, Y. Endo, K. Wakasa, and Y. Tozawa (2004)
Nucleic Acids Res.
32, 5732-5741
| Abstract »
| Full Text »
| PDF »
- From the Cover: tRNA dynamics on the ribosome during translation.
- S. C. Blanchard, H. D. Kim, R. L. Gonzalez Jr., J. D. Puglisi, and S. Chu (2004)
PNAS
101, 12893-12898
| Abstract »
| Full Text »
| PDF »
- Mapping of the second tetracycline binding site on the ribosomal small subunit of E.coli.
- M. M. Anokhina, A. Barta, K. H. Nierhaus, V. A. Spiridonova, and A. M. Kopylov (2004)
Nucleic Acids Res.
32, 2594-2597
| Abstract »
| Full Text »
| PDF »
- P-site tRNA is a crucial initiator of ribosomal frameshifting.
- P. V. BARANOV, R. F. GESTELAND, and J. F. ATKINS (2004)
RNA
10, 221-230
| Abstract »
| Full Text »
| PDF »
- Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy.
- F. Tama, M. Valle, J. Frank, and C. L. Brooks III (2003)
PNAS
100, 9319-9323
| Abstract »
| Full Text »
| PDF »
- X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli.
- A. Vila-Sanjurjo, W. K. Ridgeway, V. Seymaner, W. Zhang, S. Santoso, K. Yu, and J. H. D. Cate (2003)
PNAS
100, 8682-8687
| Abstract »
| Full Text »
| PDF »
- After the ribosome structures: How are the subunits assembled?.
- J. R. WILLIAMSON (2003)
RNA
9, 165-167
| Abstract »
| Full Text »
| PDF »
- In vivo selection of spectinomycin-binding RNAs.
- J. M. Zimmerman and L. J. Maher III (2002)
Nucleic Acids Res.
30, 5425-5435
| Abstract »
| Full Text »
| PDF »
- Binding of Ribosome Recycling Factor to Ribosomes, Comparison with tRNA.
- G. Hirokawa, M. C. Kiel, A. Muto, G. Kawai, K. Igarashi, H. Kaji, and A. Kaji (2002)
J. Biol. Chem.
277, 35847-35852
| Abstract »
| Full Text »
| PDF »
- Evolutionary Conservation of Reactions in Translation.
- M. C. Ganoza, M. C. Kiel, and H. Aoki (2002)
Microbiol. Mol. Biol. Rev.
66, 460-485
| Abstract »
| Full Text »
| PDF »
- The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions.
- I. Amarantos, I. K. Zarkadis, and D. L. Kalpaxis (2002)
Nucleic Acids Res.
30, 2832-2843
| Abstract »
| Full Text »
| PDF »
- Tracing the evolution of RNA structure in ribosomes.
- G. Caetano-Anolles (2002)
Nucleic Acids Res.
30, 2575-2587
| Abstract »
| Full Text »
| PDF »
- Single Ribosomal Protein Mutations in Antibiotic-Resistant Bacteria Analyzed by Mass Spectrometry.
- S. K. Wilcox, G. S. Cavey, and J. D. Pearson (2001)
Antimicrob. Agents Chemother.
45, 3046-3055
| Abstract »
| Full Text »
| PDF »
- Introduction.
- W. G. Bergen (2001)
J. Nutr.
131, 2976S-2977
| Full Text »
| PDF »
- A Ribosomal ATPase Is a Target for Hygromycin B Inhibition on Escherichia coli Ribosomes.
- M. C. Ganoza and M. C. Kiel (2001)
Antimicrob. Agents Chemother.
45, 2813-2819
| Abstract »
| Full Text »
- Electrostatics of nanosystems: Application to microtubules and the ribosome.
- N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon (2001)
PNAS
| Abstract »
| Full Text »
| PDF »
- Effects of base change mutations within an Escherichia coli ribosomal RNA leader region on rRNA maturation and ribosome formation.
- J. Schaferkordt and R. Wagner (2001)
Nucleic Acids Res.
29, 3394-3403
| Abstract »
| Full Text »
| PDF »
- Spontaneous Erythromycin Resistance Mutation in a 23S rRNA Gene, rrlA, of the Extreme Thermophile Thermus thermophilus IB-21.
- S. T. Gregory, J. H. D. Cate, and A. E. Dahlberg (2001)
J. Bacteriol.
183, 4382-4385
| Abstract »
| Full Text »
| PDF »
- Nucleolar protein Nop12p participates in synthesis of 25S rRNA in Saccharomyces cerevisiae.
- K. Wu, P. Wu, and J. P. Aris (2001)
Nucleic Acids Res.
29, 2938-2949
| Abstract »
| Full Text »
| PDF »
- Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit.
- J. M. Ogle, D. E. Brodersen, W. M. Clemons Jr., M. J. Tarry, A. P. Carter, and V. Ramakrishnan (2001)
Science
292, 897-902
| Abstract »
| Full Text »
| PDF »
- The thermodynamic origin of the stability of a thermophilic ribozyme.
- X.-W. Fang, B. L. Golden, K. Littrell, V. Shelton, P. Thiyagarajan, T. Pan, and T. R. Sosnick (2001)
PNAS
98, 4355-4360
| Abstract »
| Full Text »
| PDF »
- RNA tertiary interactions in the large ribosomal subunit: The A-minor motif.
- P. Nissen, J. A. Ippolito, N. Ban, P. B. Moore, and T. A. Steitz (2001)
PNAS
| Abstract »
| Full Text »
- Hepatitis C Virus IRES RNA-Induced Changes in the Conformation of the 40S Ribosomal Subunit.
- C. M. T. Spahn, J. S. Kieft, R. A. Grassucci, P. A. Penczek, K. Zhou, J. A. Doudna, and J. Frank (2001)
Science
291, 1959-1962
| Abstract »
| Full Text »
- An important 2'-OH group for an RNA-protein interaction.
- Y.-M. Hou, X. Zhang, J. A. Holland, and D. R. Davis (2001)
Nucleic Acids Res.
29, 976-985
| Abstract »
| Full Text »
| PDF »
- Crystal Structure of an Initiation Factor Bound to the 30S Ribosomal Subunit.
- A. P. Carter, W. M. Clemons Jr., D. E. Brodersen, R. J. Morgan-Warren, T. Hartsch, B. T. Wimberly, and V. Ramakrishnan (2001)
Science
291, 498-501
| Abstract »
| Full Text »
- Macrolide Resistance Conferred by Base Substitutions in 23S rRNA.
- B. Vester and S. Douthwaite (2001)
Antimicrob. Agents Chemother.
45, 1-12
| Full Text »
- Improved statistical methods reveal direct interactions between 16S and 23S rRNA.
- S. T. Kelley, V. R. Akmaev, and G. D. Stormo (2000)
Nucleic Acids Res.
28, 4938-4943
| Abstract »
| Full Text »
| PDF »
- Aminoglycosides: Perspectives on Mechanisms of Action and Resistance and Strategies to Counter Resistance.
- L. P. Kotra, J. Haddad, and S. Mobashery (2000)
Antimicrob. Agents Chemother.
44, 3249-3256
| Full Text »
- Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.
- J. Wuyts, P. De Rijk, Y. Van de Peer, G. Pison, P. Rousseeuw, and R. De Wachter (2000)
Nucleic Acids Res.
28, 4698-4708
| Abstract »
| Full Text »
| PDF »
- Covariance of Complementary rRNA Loop Nucleotides Does Not Necessarily Represent Functional Pseudoknot Formation In Vivo.
- N. S. Chernyaeva and E. J. Murgola (2000)
J. Bacteriol.
182, 5671-5675
| Abstract »
| Full Text »
- UV-induced crosslinks in the 16S rRNAs of Escherichia coli, Bacillus subtilis and Thermus aquaticus and their implications for ribosome structure and photochemistry.
- J. W. Noah, T. Shapkina, and P. Wollenzien (2000)
Nucleic Acids Res.
28, 3785-3792
| Abstract »
| Full Text »
| PDF »
- Termination and Peptide Release at the Upstream Open Reading Frame Are Required for Downstream Translation on Synthetic Shunt-Competent mRNA Leaders.
- M. Hemmings-Mieszczak, T. Hohn, and T. Preiss (2000)
Mol. Cell. Biol.
20, 6212-6223
| Abstract »
| Full Text »
- The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 A Resolution.
- N. Ban, P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz (2000)
Science
289, 905-920
| Abstract »
| Full Text »
- The Structural Basis of Ribosome Activity in Peptide Bond Synthesis.
- P. Nissen, J. Hansen, N. Ban, P. B. Moore, and T. A. Steitz (2000)
Science
289, 920-930
| Abstract »
| Full Text »
- Visualization of tRNA Movements on the Escherichia coli 70S Ribosome During the Elongation Cycle.
- R. K. Agrawal, C. M.T. Spahn, P. Penczek, R. A. Grassucci, K. H. Nierhaus, and J. Frank (2000)
J. Cell Biol.
150, 447-460
| Abstract »
| Full Text »
| PDF »
- New chromatographic and biochemical strategies for quick preparative isolation of tRNA.
- E. Cayama, A. Yepez, F. Rotondo, E. Bandeira, A. C. Ferreras, and F. J. Triana-Alonso (2000)
Nucleic Acids Res.
28, e64
| Abstract »
| Full Text »
| PDF »
- Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA.
- M. Meroueh, P. J. Grohar, J. Qiu, J. SantaLucia Jr, S. A. Scaringe, and C. S. Chow (2000)
Nucleic Acids Res.
28, 2075-2083
| Abstract »
| Full Text »
| PDF »
- A Map of Protein-rRNA Distribution in the 70 S Escherichia coli Ribosome.
- D. I. Svergun and K. H. Nierhaus (2000)
J. Biol. Chem.
275, 14432-14439
| Abstract »
| Full Text »
| PDF »
- Structure of the S15,S6,S18-rRNA Complex: Assembly of the 30S Ribosome Central Domain.
- S. C. Agalarov, G. S. Prasad, P. M. Funke, C. D. Stout, and J. R. Williamson (2000)
Science
288, 107-112
| Abstract »
| Full Text »
- Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
- M. Lu and T. A. Steitz (2000)
PNAS
97, 2023-2028
| Abstract »
| Full Text »
| PDF »
- Crystal Structure of Thermotoga maritima Ribosome Recycling Factor: A tRNA Mimic.
- M. Selmer, S. Al-Karadaghi, G. Hirokawa, A. Kaji, and A. Liljas (1999)
Science
286, 2349-2352
| Abstract »
| Full Text »
- Quality Control Mechanisms During Translation.
- M. Ibba and a. D. Söll (1999)
Science
286, 1893-1897
| Abstract »
| Full Text »
- A First Glimpse at the Structure of the TOM Translocase from the Mitochondrial Outer Membrane.
- A. Verschoor and T. Lithgow (1999)
J. Cell Biol.
147, 905-908
| Abstract »
| Full Text »
| PDF »
- Identification of an RNA-Protein Bridge Spanning the Ribosomal Subunit Interface.
- G. M. Culver, J. H. Cate, G. Z. Yusupova, M. M. Yusupov, and H. F. Noller (1999)
Science
285, 2133-2135
| Abstract »
| Full Text »
- Crystal Structure of the Ribosome at 5.5 A Resolution.
- M. M. Yusupov, G. Zh. Yusupova, A. Baucom, K. Lieberman, T. N. Earnest, J. H. D. Cate, and H. F. Noller (2001)
Science
292, 883-896
| Abstract »
| Full Text »
| PDF »
- Transit of tRNA through the Escherichia coli Ribosome. CROSS-LINKING OF THE 3' END OF tRNA TO SPECIFIC NUCLEOTIDES OF THE 23 S RIBOSOMAL RNA AT THE A, P, AND E SITES.
- J. Wower, S. V. Kirillov, I. K. Wower, S. Guven, S. S. Hixson, and R. A. Zimmermann (2000)
J. Biol. Chem.
275, 37887-37894
| Abstract »
| Full Text »
| PDF »
- Regulation of Ribosome Detachment from the Mammalian Endoplasmic Reticulum Membrane.
- M. D. Potter and C. V. Nicchitta (2000)
J. Biol. Chem.
275, 33828-33835
| Abstract »
| Full Text »
| PDF »
- Physiochemical Properties of Rat Liver Mitochondrial Ribosomes.
- V. B. Patel, C. C. Cunningham, and R. R. Hantgan (2001)
J. Biol. Chem.
276, 6739-6746
| Abstract »
| Full Text »
| PDF »
- Cryo-electron Microscopic Localization of Protein L7/L12 within the Escherichia coli 70 S Ribosome by Difference Mapping and Nanogold Labeling.
- L. Montesano-Roditis, D. G. Glitz, R. R. Traut, and P. L. Stewart (2001)
J. Biol. Chem.
276, 14117-14123
| Abstract »
| Full Text »
| PDF »
- A Newly Synthesized, Ribosome-bound Polypeptide Chain Adopts Conformations Dissimilar from Early in Vitro Refolding Intermediates.
- P. L. Clark and J. King (2001)
J. Biol. Chem.
276, 25411-25420
| Abstract »
| Full Text »
| PDF »
- Structural Compensation for the Deficit of rRNA with Proteins in the Mammalian Mitochondrial Ribosome. SYSTEMATIC ANALYSIS OF PROTEIN COMPONENTS OF THE LARGE RIBOSOMAL SUBUNIT FROM MAMMALIAN MITOCHONDRIA.
- T. Suzuki, M. Terasaki, C. Takemoto-Hori, T. Hanada, T. Ueda, A. Wada, and K. Watanabe (2001)
J. Biol. Chem.
276, 21724-21736
| Abstract »
| Full Text »
| PDF »
- Oxazolidinones Mechanism of Action: Inhibition of the First Peptide Bond Formation.
- U. Patel, Y. P. Yan, F. W. Hobbs Jr., J. Kaczmarczyk, A. M. Slee, D. L. Pompliano, M. G. Kurilla, and E. V. Bobkova (2001)
J. Biol. Chem.
276, 37199-37205
| Abstract »
| Full Text »
| PDF »
- Proteomic Analysis of the Mammalian Mitochondrial Ribosome. IDENTIFICATION OF PROTEIN COMPONENTS IN THE 28 S SMALL SUBUNIT.
- T. Suzuki, M. Terasaki, C. Takemoto-Hori, T. Hanada, T. Ueda, A. Wada, and K. Watanabe (2001)
J. Biol. Chem.
276, 33181-33195
| Abstract »
| Full Text »
| PDF »
- Nonsense Mutations in cspA Cause Ribosome Trapping Leading to Complete Growth Inhibition and Cell Death at Low Temperature in Escherichia coli.
- B. Xia, J.-P. Etchegaray, and M. Inouye (2001)
J. Biol. Chem.
276, 35581-35588
| Abstract »
| Full Text »
| PDF »
- Functional Characterization of Yeast Mitochondrial Release Factor 1.
- M. E. Askarian-Amiri, H. J. Pel, D. Guevremont, K. K. McCaughan, E. S. Poole, V. G. Sumpter, and W. P. Tate (2000)
J. Biol. Chem.
275, 17241-17248
| Abstract »
| Full Text »
| PDF »
- Operational RNA Code for Amino Acids in Relation to Genetic Code in Evolution.
- L. Ribas de Pouplana and P. Schimmel (2001)
J. Biol. Chem.
276, 6881-6884
| Full Text »
| PDF »
- RNA tertiary interactions in the large ribosomal subunit: The A-minor motif.
- P. Nissen, J. A. Ippolito, N. Ban, P. B. Moore, and T. A. Steitz (2001)
PNAS
98, 4899-4903
| Abstract »
| Full Text »
| PDF »
- Selecting rRNA binding sites for the ribosomal proteins L4 and L6 from randomly fragmented rRNA: Application of a method called SERF.
- U. Stelzl, C. M. T. Spahn, and K. H. Nierhaus (2000)
PNAS
97, 4597-4602
| Abstract »
| Full Text »
| PDF »
- Electrostatics of nanosystems: Application to microtubules and the ribosome.
- N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon (2001)
PNAS
98, 10037-10041
| Abstract »
| Full Text »
| PDF »
|
|