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Crystal structures of a series of RNA aptamers complexed to the same protein target

Nature Structural Biology volume 5, pages 970–975 (1998)Cite this article

Abstract

We have determined the crystal structures, at 2.8 Å resolution, of two different RNA aptamers, each bound to MS2 coat protein. One of the aptamers contains a non-Watson-Crick base pair, while the other is missing one of the unpaired adenines that make sequence-specific contacts in the wild-type complex. Despite these differences, the RNA aptamers bind in the same location on the protein as the wild-type translational operator. Comparison of these new structures with other MS2-RNA complexes allows us to refine further the definition of the minimal recognition elements and suggests a possible application of the MS2 system for routine structure determination of small nucleic acid motifs.

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Figure 1: Secondary structures of RNA stem-loops that bind to MS2 coat protein.
Figure 2: Overall structure of the complexes, generated by superposing the coat protein.
Figure 4: Schematic diagram of the potential protein-RNA hydrogen bonds, where atoms separated by 3.3 Å or less are considered to be within hydrogen-bonding distance.
Figure 3: Close up of the GA non-Watson-Crick base pair in the F5 aptamer complex structure with the final aptamer model in all-atom representation.

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Acknowledgements

The authors would like to thank L. Liljas and members of his laboratory at Uppsala University, Sweden, for their assistance over a number of years with the crystallography of phage particles and for comments on the manuscript. We also thank J. Jäger for helpful discussions and S. Fonseca for help with protein purification. This work was supported by grants from the U.K. B.B.S.R.C. and M.R.C., the Wellcome Trust, the Leverhulme Trust and the Howard Hughes Medical Institute. N.J.S. is an M.R.C. fellow.

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Author notes

  1. Siân Rowsell

    Present address: Zeneca Pharmaceuticals, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK

  2. Andrew D. Ellington

    Present address: ICMB A4800, University of Texas at Austin, 26th and Speedway, Austin, Texas, 78712, USA

  3. Ichiro Hirao

    Present address: Yokoyama CytoLogic Project, ERATO, Japan Science and Technology Corporation (JST), The Institute of Physical and Chemical Research (RIKEN), Hirosawa, Wako-shi, Saitama, 351-01, Japan

  4. Siân Rowsell, Nicola J. Stonehouse, Máire A. Convery, Andrew D. Ellington and Ichiro Hirao: These authors have contributed equally to this work.

Authors and Affiliations

  1. School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK

    Siân Rowsell & Simon E.V. Phillips

  2. North of England Structural Biology Centre, University of Leeds, Leeds, LS2 9JT, UK

    Siân Rowsell, Nicola J. Stonehouse, Máire A. Convery, Chris J. Adams, Peter G. Stockley & Simon E.V. Phillips

  3. Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK

    Nicola J. Stonehouse, Máire A. Convery, Chris J. Adams, Peter G. Stockley & Simon E.V. Phillips

  4. Department of Chemistry, Indiana University, Bloomington, 47405, Indiana, USA

    Andrew D. Ellington & Ichiro Hirao

  5. Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine and Cancer Research and Treatment Center, Albuquerque, 87131, New Mexico, USA

    David S. Peabody

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Rowsell, S., Stonehouse, N., Convery, M. et al. Crystal structures of a series of RNA aptamers complexed to the same protein target . Nat Struct Mol Biol 5, 970–975 (1998). https://doi.org/10.1038/2946

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