Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Comparison of X-ray and NMR structures for the Antennapedia homeodomain–DNA complex

Nature Structural Biology volume 5, pages 692–697 (1998)Cite this article

Abstract

Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for studying protein–DNA interactions. We have crystallized the Antennapedia homeodomain–DNA complex and solved this structure at 2.4 Å resolution. NMR and molecular dynamics studies had implied that this homeodomain achieves specificity through an ensemble of rapidly fluctuating DNA contacts. The crystal structure is in agreement with the underlying NMR data, but our structure reveals a well-defined set of contacts and also reveals the locations and roles of water molecules at the protein–DNA interface. The synthesis of X-ray and NMR studies provides a unified, general model for homeodomain–DNA interactions.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: a, Comparison of the protein and DNA fragments used in this study and in the NMR experiments3,4.
Figure 2: Stereo view of the experimental 2.4 Å MIR map for complex A after solvent flattening and histogram matching.
Figure 3: a, Stereo view of the protein–DNA interface in complex A.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Gehring, W.J., Affolter, M. & Bürglin, T. Annu. Rev. Biochem. 63, 487– 526 (1994).

    Article  CAS  Google Scholar 

  2. Wolberger, C. Curr. Opin. Struct. Biol. 6, 62– 68 ( 1996).

    Article  CAS  Google Scholar 

  3. Qian, Y.Q. et al. J. Mol. Biol. 234, 1070– 1083 (1993).

    Article  CAS  Google Scholar 

  4. Billeter, M. et al. J Mol Biol 234, 1084– 1093 (1993).

    Article  CAS  Google Scholar 

  5. Qian, Y.Q., Otting, G. & Wüthrich, K. J. Am. Chem. Soc. 115, 1189– 1190 (1993).

    Article  CAS  Google Scholar 

  6. Billeter, M., Guntert, P., Luginbuhl, P. & Wuthrich, K. Cell 85, 1057– 1065 (1996).

    Article  CAS  Google Scholar 

  7. Billeter, M. Prog. Biophys. Molec. Biol. 66, 211– 225 (1996).

    Article  CAS  Google Scholar 

  8. Qian, Y.Q. et al. Cell 59, 573– 580 ( 1989).

    Article  CAS  Google Scholar 

  9. Hodel, A., Kim, S.et al. et al. & Brünger, A.T. Acta Crystallogr. A48, 851– 858 (1992).

    Article  CAS  Google Scholar 

  10. Wagner, G., Hyberts, S.G. & Havel, T.F. Annu. Rev. Biophys. Biomol. Struct. 21, 167– 198 (1992).

    Article  CAS  Google Scholar 

  11. Wüthrich, K. NMR of proteins and nucleic acids, (John Wiley & Sons, New York; 1986).

    Book  Google Scholar 

  12. Botfield, M.C., Jancso, A. & Weiss, M.A. Biochemistry 33, 6177– 6185 (1994).

    Article  CAS  Google Scholar 

  13. Botfield, M.C., Jancso, A. & Weiss, M.A. Biochemistry 33, 8113– 8121 (1994).

    Article  CAS  Google Scholar 

  14. Ades, S.E. & Sauer, R.T. Biochemistry 34, 14601– 14608 (1995).

    Article  CAS  Google Scholar 

  15. Pomerantz, J.L. & Sharp, P.A. Biochemistry 33, 10851– 10858 (1994).

    Article  CAS  Google Scholar 

  16. Gruschus, J.M., Tsao, D.H.H., Wang, L.H., Nirenberg, M. & Ferretti, J.A. Biochemistry 36, 5372– 5380 (1997).

    Article  CAS  Google Scholar 

  17. Bürglin, T.R. A comprehensive classification of homeobox genes. in Guidebook to the homeobox genes (ed. Duboule, D.) 25– 71 (Oxford University Press, Oxford, England; 1994).

    Google Scholar 

  18. Wilson, D.S., Guenther, B., Desplan, C. & Kuriyan, J. Cell 82, 709– 719 (1995).

    Article  CAS  Google Scholar 

  19. Hirsch, J.A. & Aggarwal, A.K. EMBO J. 14, 6280– 6291 (1995).

    Article  CAS  Google Scholar 

  20. Fraenkel, E., Rould, M.A., Chambers, K.A. & Pabo, C.O. J. Mol. Biol., in the press (1998).

  21. Tucker-Kellogg, L. et al. Structure 5, 1047– 1054 (1997).

    Article  CAS  Google Scholar 

  22. Li, T., Stark, M.R., Johnson, A.D. & Wolberger, C. Science 270, 262– 269 (1995).

    Article  CAS  Google Scholar 

  23. Klemm, J.D., Rould, M.A., Aurora, R., Herr, W. & Pabo, C.O. Cell 77, 21– 32 (1994).

    Article  CAS  Google Scholar 

  24. Otwinowski, Z. & Minor, W. Processing of X-ray Diffraction Data Collected in Oscillation Mode. Meth. Enz. 276 307– 326 (1997).

    Article  CAS  Google Scholar 

  25. Rould, M.A. Meth. Enz.. 276, 461– 472 (1997).

    Article  CAS  Google Scholar 

  26. Otwinowski, Z. Maximum likelihood refinement of heavy atom parameters. In Isomorphous replacement and anomalous scattering, proceedings of the CCP4 study weekend (eds Wolf, W., Evans, P.R. & Leslie, A.G.W.) 80– 86 (SERC Daresbury Laboratory: Warrington, UK; 1991).

    Google Scholar 

  27. CCP4. Acta Crystallogr. D 50, 760– 776 (1994).

  28. Cowtan, K. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31, 34– 38 (1994).

    Google Scholar 

  29. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. Acta Crystallogr. A 47, 110– 119 ( 1991).

    Article  Google Scholar 

  30. Brünger, A.T. Nature 355, 472– 474 ( 1992).

    Article  Google Scholar 

  31. Read, R.J. Acta Crystallogr. A 47, 110– 119 ( 1986).

    Google Scholar 

  32. Brünger, A.T. XPLOR Manual Version 3.1, (Yale University Press, New Haven, Connecticut; 1992).

    Google Scholar 

  33. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. J. Appl. Crystallogr. 26, 283– 291 (1993).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by a National Institutes of Health grant to C.O.P. who is also in the Howard Hughes Medical Institute. Crystallographic data were collected with equipment purchased with support from the PEW Charitable Trusts and at the W. M. Keck Foundation X-ray Crystallography Facility at the Whitehead Institute (Cambridge, Massachusetts). We thank T. Benson, J. Hoch, P. Kim, M. Rould, M. Summers and S. Wolfe for helpful discussions; D. King for mass spectrometry analysis; and L. Nekludova for assistance in comparison of homeodomain structures.

Author information

Author notes

  1. Ernest Fraenkel

    Present address: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, 02138, USA

Authors and Affiliations

  1. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Ernest Fraenkel & Carl O. Pabo

  2. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, 02139 , Massachusetts, USA

    Carl O. Pabo

Authors
  1. Ernest Fraenkel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Carl O. Pabo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Carl O. Pabo.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fraenkel, E., Pabo, C. Comparison of X-ray and NMR structures for the Antennapedia homeodomain–DNA complex. Nat Struct Mol Biol 5, 692–697 (1998). https://doi.org/10.1038/1382

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/1382

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing