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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

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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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