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Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit

Nature volume 400, pages 841–847 (1999)Cite this article

Abstract

We have calculated at 5.0 Å resolution an electron-density map of the large 50S ribosomal subunit from the bacterium Haloarcula marismortui by using phases derived from four heavy-atom derivatives, intercrystal density averaging and density-modification procedures. More than 300 base pairs of A-form RNA duplex have been fitted into this map, as have regions of non-A-form duplex, single-stranded segments and tetraloops. The long rods of RNA crisscrossing the subunit arise from the stacking of short, separate double helices, not all of which are A-form, and in many places proteins crosslink two or more of these rods. The polypeptide exit channel was marked by tungsten cluster compounds bound in one heavy-atom-derivatized crystal. We have determined the structure of the translation-factor-binding centre by fitting the crystal structures of the ribosomal proteins L6, L11 and L14, the sarcin–ricin loop RNA, and the RNA sequence that binds L11 into the electron density. We can position either elongation factor G or elongation factor Tu complexed with an aminoacylated transfer RNA and GTP onto the factor-binding centre in a manner that is consistent with results from biochemical and electron microscopy studies.

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Figure 1: The 5Å-resolution electron-density map of the 50S ribosomal subunit.
Figure 2: Visualization of the tunnel in which tungsten clusters are located.
Figure 3: A variety of interactions between RNA duplexes.
Figure 4: The fitting of previously solved protein and nucleic acid structures to the 5Å-resolution electron density map.
Figure 5: The proteins (in white backbone ribbons) and RNAs (in coloured ribbon) of the factor-binding site that have been fitted to the density.
Figure 6: Packing diagrams of the 50S subunits in the orthorhombic, monoclinic and twinned monoclinic unit cells.

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Acknowledgements

We thank E. Freeborn for biochemical support; R. Sweet for helping us with data collection at the National Synchrotron Light Source; and I.Tanaka, M. Garber and S. Al-Karadaghi for providing coordinates before publication. This investigation was supported by grants from NIH to T.A.S. and P.B.M. N.B. was a Damon Runyon-Walter Winchell Postdoctoral Fellow during part of this study, and P.N. is supported by the Danish Research Council. The coordinates of all identified RNA and protein structures have been deposited in the protein data bank with accession number IC04.

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  1. Departments of Molecular Biophysics & Biochemistry Yale University, New Haven, 06520-8114, Connecticut, USA

    Nenad Ban, Poul Nissen, Jeffrey Hansen & Thomas A. Steitz

  2. Departments of Chemistry, Yale University, New Haven, 06520-8114, Connecticut, USA

    Peter B. Moore & Thomas A. Steitz

  3. Howard Hughes Medical Institute, New Haven, 06520-8114, Connecticut, USA

    Nenad Ban, Jeffrey Hansen & Thomas A. Steitz

  4. Department of Biology, Brookhaven National Laboratory, Upton, 11973, New York, USA

    Malcolm Capel

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Ban, N., Nissen, P., Hansen, J. et al. Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature 400, 841–847 (1999). https://doi.org/10.1038/23641

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