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Structure of the 30S ribosomal subunit


Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 Å resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein–RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.

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Figure 1: Electron density maps of the 30S.
Figure 2: Overview of the 30S structure.
Figure 3: Different modes of interhelical packing in 16S RNA.
Figure 4: Structure of the 5′ domain of 16S RNA.
Figure 5: Structure of the central domain of 16S RNA.
Figure 6: Structure of the 3′ major and 3′ minor domains of 16S RNA.
Figure 7: Proteins from the central and 5′ domains.
Figure 9: Proteins from the head.
Figure 8: Proteins near the functional centre of the 30S.


  1. 1

    Garrett, R. A. et al. (eds) The Ribosome. Structure, Function, Antibiotics and Cellular Interactions (ASM, Washington DC, 2000).

    Google Scholar 

  2. 2

    von Böhlen, K. et al. Characterization and preliminary attempts for derivatization of crystals of large ribosomal subunits from Haloarcula marismortui diffracting to 3 Å resolution. J. Mol. Biol. 222, 11–15 (1991).

    Article  Google Scholar 

  3. 3

    Clemons, W. M. et al. Structure of a bacterial 30S ribosomal subunit at 5.5 Å resolution. Nature 400, 833– 840 (1999).

    ADS  CAS  Article  Google Scholar 

  4. 4

    Trakhanov, S. D. Crystallization of 70S ribosomes and 30S ribosomal subunits from Thermus thermophilus. FEBS Lett. 220, 319– 322 (1987).

    Article  Google Scholar 

  5. 5

    Glotz, C. et al. Three-dimensional crystals of ribosomes and their subunits from eu- and archaebacteria. Biochem. Int. 15, 953–960 (1987).

    CAS  PubMed  Google Scholar 

  6. 6

    Yonath, A. et al. Characterization of crystals of small ribosomal subunits. J. Mol. Biol. 203, 831–834 (1988).

    CAS  Article  Google Scholar 

  7. 7

    Yusupov, M. M., Tischenko, S. V., Trakhanov, S. D., Ryazantsev, S. N. & Garber, M. B. A new crystalline form of 30S ribosomal subunits from Thermus thermophilus. FEBS Lett. 238, 113–115 (1988).

    Article  Google Scholar 

  8. 8

    Yonath, A. Crystallographic studies on the ribosome, a large macromolecular assembly exhibiting severe nonisomorphism, extreme beam sensitivity and no internal symmetry. Acta Crystallogr. A 54, 945– 955 (1998).

    CAS  Article  Google Scholar 

  9. 9

    Tocilj, A. et al. The small ribosomal subunit from Thermus thermophilus at 4.5 Å resolution: pattern fittings and the identification of a functional site. Proc. Natl Acad. Sci. USA 96, 14252– 14257 (1999).

    ADS  CAS  Article  Google Scholar 

  10. 10

    Carter, A. P. et al. Functional insights from the structure of the 30S ribosomal subunit and its interaction with antibiotics. Nature 407, 340–348 (2000).

    ADS  CAS  Article  Google Scholar 

  11. 11

    Hartmann, R. K. & Erdmann, V. A. Thermus thermophilus 16S rRNA is transcribed from an isolated transcription unit. J. Bacteriol. 171, 2933– 2941 (1989).

    CAS  Article  Google Scholar 

  12. 12

    Choli, T., Franceschi, F., Yonath, A. & Wittmann-Liebold, B. Isolation and characterization of a new ribosomal protein from the thermophilic eubacteria, Thermus thermophilus, T. aquaticus and T. flavus . Biol. Chem. Hoppe Seyler 374, 377– 383 (1993).

    CAS  Article  Google Scholar 

  13. 13

    Mueller, F. & Brimacombe, R. A new model for the three-dimensional folding of Escherichia coli 16S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 Å. J. Mol. Biol. 271, 524–544 (1997).

    CAS  Article  Google Scholar 

  14. 14

    Gabashvili, I. S., Agrawal, R. K., Grassucci, R. & Frank, J. Structure and structural variations of the Escherichia coli 30S ribosomal subunit as revealed by three-dimensional cryo-electron microscopy. J. Mol. Biol. 286, 1285–1291 (1999).

    CAS  Article  Google Scholar 

  15. 15

    Gabashvili, I. S. et al. Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell 100, 537– 549 (2000).

    CAS  Article  Google Scholar 

  16. 16

    Stern, S., Weiser, B. & Noller, H. F. Model for the three-dimensional folding of 16S ribosomal RNA. J. Mol. Biol. 204, 447– 481 (1988).

    CAS  Article  Google Scholar 

  17. 17

    Malhotra, A. & Harvey, S. C. A quantitative model of the Escherichia coli 16S RNA in the 30S ribosomal subunit. J. Mol. Biol. 240, 308–340 ( 1994).

    CAS  Article  Google Scholar 

  18. 18

    Ramakrishnan, V. Distribution of protein and RNA in the 30S ribosomal subunit. Science 231, 1562–1564 ( 1986).

    ADS  CAS  Article  Google Scholar 

  19. 19

    Wimberly, B., Varani, G. & Tinoco, I. The conformation of loop E of eukaryotic 5S ribosomal RNA. Biochemistry 32, 1078– 1087 (1993).

    CAS  Article  Google Scholar 

  20. 20

    Lodmell, J. S. & Dahlberg, A. E. A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA. Science 277, 1262– 1267 (1997).

    CAS  Article  Google Scholar 

  21. 21

    Gutell, R. R. in Ribosomal RNA Structure, Evolution, Processing and Function in Protein Biosynthesis (eds Dahlberg, A. E. &&amp&amp&amp& Zimmermann, R. A.) 111–128 (CRC, Boca Raton, 1996).

    Google Scholar 

  22. 22

    Nikulin, A. et al. Crystal structure of the S15-rRNA complex. Nature Struct. Biol. 7, 273–277 (2000).

    CAS  Article  Google Scholar 

  23. 23

    Agalarov, S. C., Sridhar Prasad, G., Funke, P. M., Stout, C. D. & Williamson, J. R. Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. Science 288, 107–113 (2000).

    ADS  CAS  Article  Google Scholar 

  24. 24

    Powers, T. & Noller, H. F. Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA. RNA 1, 194–209 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. 25

    Mueller, F. & Brimacombe, R. A new model for the three-dimensional folding of Escherichia coli 16S ribosomal RNA. II. The RNA-protein interaction data. J. Mol. Biol. 271, 545 –565 (1997).

    CAS  Article  Google Scholar 

  26. 26

    Capel, M. S. et al. A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. Science 238, 1403–1406 (1987).

    ADS  CAS  Article  Google Scholar 

  27. 27

    Nowotny, V. & Nierhaus, K. H. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry 27, 7051–7055 (1988).

    CAS  Article  Google Scholar 

  28. 28

    Stern, S., Powers, T., Changchien, L. -M. & Noller, H. F. RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA. Science 244, 783– 790 (1989).

    ADS  CAS  Article  Google Scholar 

  29. 29

    Held, W. A., Ballou, B., Mizushima, S. & Nomura, M. Assembly mapping of 30S ribosomal proteins from Escherichia coli. Further studies. J. Biol. Chem. 249, 3103– 3111 (1974).

    CAS  PubMed  Google Scholar 

  30. 30

    Otwinowski, Z. & Minor, W. in Methods in Enzymology (eds Carter, C. W. & Sweet, R. M.) 307–325 (Academic, New York, 1997).

    Google Scholar 

  31. 31

    Terwilliger, T. & Berendzen, J. Automated MAD and MIR structure determination. Acta Crystallogr. D 55, 849–861 (1999).

    CAS  Article  Google Scholar 

  32. 32

    Abrahams, J. P. Bias reduction in phase refinement by modified interference functions: introducing the gamma correction. Acta Crystallogr. D 53, 371–376 (1997).

    CAS  Article  Google Scholar 

  33. 33

    de la Fortelle, E. & Bricogne, G. in Methods in Enzymology (eds Carter, C. W. & Sweet, R. M.) 472– 493 (Academic, New York, 1997).

    Google Scholar 

  34. 34

    Cowtan, K. & Main, P. Miscellaneous algorithms for density modification. Acta Crystallogr. D 54, 487 –493 (1998).

    CAS  Article  Google Scholar 

  35. 35

    Jones, T. A. & Kjeldgaard, M. Electron-density map interpretation. Methods Enzymol. 277B, 173– 207 (1997).

    Article  Google Scholar 

  36. 36

    Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  Google Scholar 

  37. 37

    Carson, M. Ribbons 2.0. J. Appl. Cryst. 24, 958– 961 (1991).

    Article  Google Scholar 

  38. 38

    Davies, C., Gerstner, R. B., Draper, D. E., Ramakrishnan, V. & White, S. W. The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif. EMBO J. 17, 4545–4558 (1998).

    CAS  Article  Google Scholar 

  39. 39

    Markus, M. A., Gerstner, R. B., Draper, D. E. & Torchia, D. A. The solution structure of ribosomal protein S4 delta41 reveals two subdomains and a positively charged surface that may interact with RNA. EMBO J. 17, 4559–4571 ( 1998).

    CAS  Article  Google Scholar 

  40. 40

    Ramakrishnan, V. & White, S. W. Structure of ribosomal protein S5 reveals sites of interaction with 16S RNA. Nature 358, 768–771 ( 1992).

    ADS  CAS  Article  Google Scholar 

  41. 41

    Lindahl, M. et al. Crystal structure of the ribosomal protein S6 from Thermus thermophilus. EMBO J. 13, 1249– 1254 (1994).

    CAS  Article  Google Scholar 

  42. 42

    Wimberly, B. T., White, S. W. & Ramakrishnan, V. The structure of ribosomal protein S7 at 1.9 Å resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids. Structure 5, 1187– 1198 (1997).

    CAS  Article  Google Scholar 

  43. 43

    Hosaka, H. et al. Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor. Structure 5, 1199–1208 (1997).

    CAS  Article  Google Scholar 

  44. 44

    Davies, C., Ramakrishnan, V. & White, S. W. Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 Å resolution. Structure 4, 1093–1104 ( 1996).

    CAS  Article  Google Scholar 

  45. 45

    Nevskaya, N. et al. Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site. J. Mol. Biol. 279, 233 –244 (1998).

    CAS  Article  Google Scholar 

  46. 46

    Berglund, H., Rak, A., Serganov, A., Garber, M. & Härd, T. Solution structure of the ribosomal RNA binding protein S15 from Thermus thermophilus. Nature Struct. Biol. 4, 20–23 (1997).

    CAS  Article  Google Scholar 

  47. 47

    Clemons, W. M., Davies, C., White, S. W. & Ramakrishnan, V. Conformational variability of the N-terminal helix in the structure of ribosomal protein S15. Structure 6, 429–438 (1998).

    CAS  Article  Google Scholar 

  48. 48

    Allard, P. Another piece of the ribosome: Solution structure of S16 and its location in the 30S subunit. Structure 8, 875– 882 (2000).

    CAS  Article  Google Scholar 

  49. 49

    Golden, B. L., Hoffman, D. W., Ramakrishnan, V. & White, S. W. Ribosomal protein S17: characterization of the three-dimensional structure by 1H- and 15N-NMR. Biochemistry 32, 12812–12820 ( 1993).

    CAS  Article  Google Scholar 

  50. 50

    Helgstrand, M. et al. Solution structure of the ribosomal protein S19 from Thermus thermophilus. J. Mol. Biol. 292, 1071 –1081 (2000).

    Article  Google Scholar 

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This work was supported by the Medical Research Council (UK) and a US National Institutes of Health grant to V.R. and S. W. White. Beamlines at Argonne and Brookhaven were supported by the US Department of Energy. D.E.B. was supported by an EMBO long-term postdoctoral fellowship,and W.M.C. by an NIH predoctoral fellowship. We thank B. S. Brunschwig and M. H. Chou for gifts of osmium hexammine and osmium bipyridine; T. Terwilliger for help with phasing using SOLVE; T. A. Leaf-Jones for providing us a version of O with RNA tools; and our colleagues at the LMB for their advice and encouragement. We are indebted to A. Joachimiak, S. L. Ginell, R. Ravelli, S. McSweeney, G. Leonard, A. Thompson, H. Lewis, L. Berman, M. Papiz, S. Girdwood and M. MacDonald for help and advice on synchrotron beamlines.

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Correspondence to V. Ramakrishnan.

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Wimberly, B., Brodersen, D., Clemons, W. et al. Structure of the 30S ribosomal subunit. Nature 407, 327–339 (2000).

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