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.

Crystal structure of a zinc-finger–RNA complex reveals two modes of molecular recognition

Abstract

Zinc-finger proteins of the classical Cys2His2 type are the most frequently used class of transcription factor and account for about 3% of genes in the human genome1,2. The zinc-finger motif was discovered3 during biochemical studies on the transcription factor TFIIIA, which regulates the 5S ribosomal RNA genes of Xenopus laevis4,5. Zinc-fingers mostly interact with DNA, but TFIIIA binds not only specifically to the promoter DNA, but also to 5S RNA itself6,7,8,9. Increasing evidence indicates that zinc-fingers are more widely used to recognize RNA10,11,12,13. There have been numerous structural studies on DNA binding14, but none on RNA binding by zinc-finger proteins. Here we report the crystal structure of a three-finger complex with 61 bases of RNA, derived15 from the central regions of the complete nine-finger TFIIIA–5S RNA complex. The structure reveals two modes of zinc-finger binding, both of which differ from that in common use for DNA: first, the zinc-fingers interact with the backbone of a double helix; and second, the zinc-fingers specifically recognize individual bases positioned for access in otherwise intricately folded ‘loop’ regions of the RNA.

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

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Components of the zinc-finger–RNA complex.
Figure 2: Interactions of the three-finger peptide with the RNA.
Figure 3: Recognition of loop E by finger 4.
Figure 4: Recognition of loop A by finger 6.

References

  1. Clamp, M. et al. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res. 31, 38–42 (2003)

    Article  CAS  Google Scholar 

  2. Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 30, 276–280 (2002)

    Article  CAS  Google Scholar 

  3. Miller, J., McLachlan, A. D. & Klug, A. Repetitive zinc-binding domains in the protein transcriptional factor IIIA from Xenopus oocytes. EMBO J. 4, 1609–1615 (1985)

    Article  CAS  Google Scholar 

  4. Sakonju, S. & Brown, D. D. Contact points between a positive transcription factor and the Xenopus 5S RNA gene. Cell 31, 395–405 (1982)

    Article  CAS  Google Scholar 

  5. Engelke, D., Ng, S.-Y., Shastry, B. & Roeder, R. Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes. Cell 19, 717–728 (1980)

    Article  CAS  Google Scholar 

  6. Picard, B. & Wegnez, M. Isolation of a 7S particle from Xenopus laevis oocytes: a 5S RNA–protein complex. Proc. Natl Acad. Sci. USA 76, 241–245 (1979)

    Article  ADS  CAS  Google Scholar 

  7. Pelham, H. & Brown, D. A specific transcription factor that can bind to either the 5S RNA gene or 5S RNA. Proc. Natl Acad. Sci. USA 77, 4170–4174 (1980)

    Article  ADS  CAS  Google Scholar 

  8. Bogenhagen, D. F. & Sands, M. S. Binding of TFIIIA to derivatives of 5S RNA containing sequence substitutions or deletions defines a minimal TFIIIA binding site. Nucleic Acids Res. 20, 2639–2645 (1992)

    Article  CAS  Google Scholar 

  9. Theunissen, O., Rudt, F., Guddat, U., Mentzel, H. & Pieler, T. RNA and DNA binding zinc fingers in Xenopus TFIIIA. Cell 71, 679–690 (1992)

    Article  CAS  Google Scholar 

  10. Nagai, K. et al. Structure and assembly of the spliceosomal snRNPs. Biochem. Soc. Trans. 29, 15–26 (2001)

    Article  CAS  Google Scholar 

  11. Finerty, P. J. & Bass, B. L. A Xenopus zinc finger protein that specifically binds dsRNA and RNA–DNA hybrids. J. Mol. Biol. 271, 195–208 (1997)

    Article  CAS  Google Scholar 

  12. Mendez-Vidal, C., Wilhelm, M. T., Hellborg, F., Qian, W. & Wiman, K. G. The p53-induced mouse zinc finger protein wig-1 binds double-stranded RNA with high affinity. Nucleic Acids Res. 30, 1991–1996 (2002)

    Article  CAS  Google Scholar 

  13. Ladomery, M., Sommerville, J., Woolner, S., Slight, J. & Hastie, N. Expression in Xenopus oocytes shows that WT1 binds transcriptions in vivo, with a central role for zinc finger one. J. Cell Sci. 116, 1539–1549 (2003)

    Article  CAS  Google Scholar 

  14. Wolfe, S. A., Nekludova, L. & Pabo, C. O. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29, 183–212 (2000)

    Article  CAS  Google Scholar 

  15. Searles, M. A., Lu, D. & Klug, A. The role of the central zinc fingers of transcription factor IIIA in binding to 5S RNA. J. Mol. Biol. 301, 47–60 (2000)

    Article  CAS  Google Scholar 

  16. Clemens, K. R. et al. Molecular basis for specific recognition of both RNA and DNA by a zinc finger protein. Science 260, 530–533 (1993)

    Article  ADS  CAS  Google Scholar 

  17. McBryant, S. J. et al. Interaction of the RNA binding fingers of Xenopus transcription factor IIIA with specific regions of 5S ribosomal RNA. J. Mol. Biol. 248, 44–57 (1995)

    Article  CAS  Google Scholar 

  18. Setzer, D. R., Menezes, S. R., del Rio, S., Hung, V. S. & Subramanyan, G. Functional interactions between the zinc fingers of Xenopus transcription factor IIIA during 5S rRNA binding. RNA 2, 1254–1269 (1996)

    CAS  Google Scholar 

  19. Friesen, W. J. & Darby, M. K. Phage display of RNA binding zinc fingers from transcription factor IIIA. J. Biol. Chem. 272, 10994–10997 (1997)

    Article  CAS  Google Scholar 

  20. Theunissen, O., Rudt, F. & Pieler, T. Structural determinants in 5S RNA and TFIIIA for 7S RNP formation. Eur. J. Biochem. 258, 758–767 (1998)

    Article  CAS  Google Scholar 

  21. Nolte, R. T., Conlin, R. M., Harrison, S. C. & Brown, R. S. Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. Proc. Natl Acad. Sci. USA 95, 2938–2943 (1998)

    Article  ADS  CAS  Google Scholar 

  22. Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920 (2000)

    Article  ADS  CAS  Google Scholar 

  23. Wimberley, B., Varani, G. & Tinoco, I. The conformation of loop E in eukaryotic 5S ribosomal RNA. Biochemistry 32, 1078–1087 (1993)

    Article  Google Scholar 

  24. Correll, C. C. et al. Crystal structure of the ribosomal RNA domain essential for binding elongation factors. Proc. Natl Acad. Sci. USA 95, 13436–13441 (1998)

    Article  ADS  CAS  Google Scholar 

  25. Morgan, B. et al. Aiolos, a lymphoid restricted transcription factor that interacts with Ikaros to regulate lymphocyte differentiation. EMBO J. 16, 2004–2013 (1997)

    Article  CAS  Google Scholar 

  26. Collaborative Computational Project 4, The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

    Article  Google Scholar 

  27. Sheldrick, G. M. & Gould, R. O. Structure solution by iterative peaklist optimization and tangent expansion in space group P1. Acta Crystallogr. B 51, 423–431 (1995)

    Article  Google Scholar 

  28. de la Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472–494 (1997)

    Article  CAS  Google Scholar 

  29. Jones, T. A., Zou, J-Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  30. Brunger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We acknowledge the Daresbury Laboratory and the ESRF for provision of facilities. We thank P. Evans and other colleagues for advice and help. D.L. was initially supported by a grant from the Human Frontier Science Programme (to A.K.) and later by a Fellowship from the Sino-British Fellowship Trust.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Aaron Klug.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Lu, D., Alexandra Searles, M. & Klug, A. Crystal structure of a zinc-finger–RNA complex reveals two modes of molecular recognition. Nature 426, 96–100 (2003). https://doi.org/10.1038/nature02088

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature02088

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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