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All-atom homology model of the Escherichia coli 30S ribosomal subunit

Nature Structural Biology volume 9, pages 750–755 (2002)Cite this article

Abstract

Understanding the structural basis of ribosomal function requires close comparison between biochemical and structural data. Although a large amount of biochemical data are available for the Escherichia coli ribosome, the structure has not been solved to atomic resolution. Using a new RNA homology procedure, we have modeled the all-atom structure of the E. coli 30S ribosomal subunit. We find that the tertiary structure of the ribosome core, including the A-, P- and E-sites, is highly conserved. The hypervariable regions in our structure, which differ from the structure of the 30S ribosomal subunit from Thermus thermophilus, are consistent with the cryo-EM map of the E. coli ribosome.

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Figure 1: Secondary and tertiary structures of the 16S rRNA.
Figure 2: Homology model of a base pair in a helix.
Figure 3: Modeling the E. coli spur structure (residues 67–102) using a motif modeling approach.
Figure 4: Comparing model with experimental structures of 16S rRNA.

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Protein Data Bank

References

  1. Wimberly, B.T. et al. Nature 407, 327–339 (2000).

    Article  CAS  Google Scholar 

  2. Schluenzen, F. et al. Cell 102, 615–623 (2000).

    Article  CAS  Google Scholar 

  3. Green, R. & Noller, H.F. Annu. Rev Biochem 66, 679–716 (1997).

    Article  CAS  Google Scholar 

  4. O'Connor, M. in The Ribosome: Structure, Function, Antibiotics, & Cellular Interactions (eds Garrett, R.A. et al.) 217–227 (ASM Press, Washington, D.C.; 2000).

    Book  Google Scholar 

  5. Sanchez, R. & Sali, A. Curr. Opin. Struct. Biol. 7, 206–214 (1997).

    Article  CAS  Google Scholar 

  6. Westhof, E. Theochem 105, 203–210 (1993).

    Article  CAS  Google Scholar 

  7. Westhof, E. & Altman, S. Proc. Natl. Acad. Sci. USA 9, 5133–5137 (1994).

    Article  Google Scholar 

  8. Stern, S., Weiser, B. & Noller, H.F. J. Mol. Biol. 204, 447–481 (1988).

    Article  CAS  Google Scholar 

  9. Malhotra, A. & Harvey, S.C. J. Mol. Biol. 240, 308–340 (1994).

    Article  CAS  Google Scholar 

  10. Mueller, F. & Brimacombe, R. J. Mol. Biol. 271, 524–544 (1997).

    Article  CAS  Google Scholar 

  11. Carter, A.P. et al. Nature 407, 340–348 (2000).

    Article  CAS  Google Scholar 

  12. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. Science 289, 905–920 (2000).

    Article  CAS  Google Scholar 

  13. Harms, J. et al. Cell 107, 679–688 (2001).

    Article  CAS  Google Scholar 

  14. Neefs, J., Van de Peer, Y., De Rijk, P., Chapelle, S & De Wachter, R. Nucleic Acids Res. 21, 3025–3049 (1993).

    Article  CAS  Google Scholar 

  15. Guetell, R.R. Nucleic Acids Res. 22, 3502–3507 (1994).

    Article  Google Scholar 

  16. Guetell, R.R. in Ribosomal RNA. Structure, Evolution, Processing, and Function in Protein Biosynthesis (eds Dahlberg, A. & Zimmerman, B.) 111–128 (CRC Press, Boca Raton; 1996).

    Google Scholar 

  17. Watson, J.D. & Crick, F.H.C. Nature 171, 737–738 (1953).

    Article  CAS  Google Scholar 

  18. Tung, C.S. in Computation of Biomolecular Structures (eds Soumpasis, D.M. & Jobin, T.M.) 87–97 (Springer-Verlag, New York; 1993).

    Book  Google Scholar 

  19. Tung, C.S. J. Biomol. Struct. Dyn. 17, 347–354 (1999).

    Article  CAS  Google Scholar 

  20. Weiner, S.J., Kollman, P.A., Nguyen, D.T. & Case, D.A. J. Comput. Chem. 7, 230–252 (1986).

    Article  CAS  Google Scholar 

  21. Pieper, U., Eswar, N., Stuart, A.C., Llyin, V.A. & Sali, A. Nucleic Acids Res. 30, 255–259 (2002).

    Article  CAS  Google Scholar 

  22. Yusupov, M.M. et al. Science 292, 883–896 (2001).

    Article  CAS  Google Scholar 

  23. Kozin, M.B. & Svergun, D.I. J. Appl. Crystallogr. 34, 33–41 (2001).

    Article  CAS  Google Scholar 

  24. Gabashvili, I.S. et al. Cell 100: 537–549 (2000).

    Article  CAS  Google Scholar 

  25. Hubbard, S.J. & Thornton, J.M. Naccess. (Department of Biochemistry and Molecular Biology, University College, London; 1993).

  26. Nadassy, K., Wodak, S.J. & Janin, J. Biochemistry 38, 1999–2017 (1999).

    Article  CAS  Google Scholar 

  27. Carter, A.P. et al. Science 291, 498–501 (2001).

    Article  CAS  Google Scholar 

  28. Noller, H.F. In The RNA World (eds Gesteland, R.F., Cech, T.R. & Atkins, J.F.) 197–219 (Cold Spring Harbor Laboratory Press, New York 1999).

    Google Scholar 

  29. Yusupova, G.Z., Yusupov, M.M., Cate, J.H.D. & Noller, H.F. Cell 106, 233–241 (2001).

    Article  CAS  Google Scholar 

  30. Benson, D.A. et al. Nucleic Acids Res. 28, 15–18 (2000).

    Article  CAS  Google Scholar 

  31. Brosius, J., Palmer, M.L., Kennedy, P.J. & Noller, H.F. Proc. Natl. Acad. Sci. USA 75, 4801–4805 (1978).

    Article  CAS  Google Scholar 

  32. Berman, H.M. et al. Nucleic Acids Res. 28, 235–242 (2000).

    Article  CAS  Google Scholar 

  33. Person, W.R., Wood, T., Zhang, Z. & Miller, W. Genomics 46, 24–36 (1997).

    Article  Google Scholar 

  34. Tatusova, T.A. & Madden, T.L FEMS Microbiol. Lett. 174, 247–250 (1999).

    Article  CAS  Google Scholar 

  35. Wittmann, H.G. Annu. Rev. Biochem. 51, 155–183 (1982).

    Article  CAS  Google Scholar 

  36. Makino, K. et al. Genes Genet. Syst. 74, 227–239 (1999).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was performed under the auspices of the Department of Energy (DOE) under contract to the University of California. C.S.T. and K.Y.S. are supported by LANL/LDRD funding. S.J. is supported by both NSF and NIH grants. The cryo-EM density map was kindly provided by J. Frank of HHMI.

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Authors and Affiliations

  1. Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, 87545, New Mexico, USA

    Chang-Shung Tung & Kevin Y. Sanbonmatsu

  2. Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, 92093-0647, California, USA

    Simpson Joseph

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  1. Chang-Shung Tung
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Correspondence to Chang-Shung Tung.

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Tung, CS., Joseph, S. & Sanbonmatsu, K. All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nat Struct Mol Biol 9, 750–755 (2002). https://doi.org/10.1038/nsb841

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