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

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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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  2. Simpson Joseph
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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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