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:

Structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with its ligand

Nature volume 420, pages 696–700 (2002)Cite this article

Abstract

In a variety of cells, the Ca2+ signalling process is mediated by the endoplasmic-reticulum-membrane-associated Ca2+ release channel, inositol 1,4,5-trisphosphate (InsP3) receptor (InsP3R)1. Being ubiquitous and present in organisms ranging from humans to Caenorhabditis elegans, InsP3R has a vital role in the control of cellular and physiological processes as diverse as cell division, cell proliferation, apoptosis, fertilization, development, behaviour, memory and learning2. Mouse type I InsP3R (InsP3R1), found in high abundance in cerebellar Purkinje cells, is a polypeptide with three major functionally distinct regions: the amino-terminal InsP3-binding region, the central modulatory region and the carboxy-terminal channel region2. Here we present a 2.2-Å crystal structure of the InsP3-binding core of mouse InsP3R1 in complex with InsP3. The asymmetric, boomerang-like structure consists of an N-terminal β-trefoil domain and a C-terminal α-helical domain containing an ‘armadillo repeat’-like fold. The cleft formed by the two domains exposes a cluster of arginine and lysine residues that coordinate the three phosphoryl groups of InsP3. Putative Ca2+-binding sites are identified in two separate locations within the InsP3-binding core.

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

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

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

Figure 1: Overall domain architecture of InsP3R and sequence alignment of the InsP3-binding core between members of the InsP3R family.
Figure 2: Structure of mouse InsP3R1c in complex with InsP3.
Figure 3: β-Trefoil and ‘armadillo repeat’-like folds in mouse InsP3R1c.
Figure 4: Coordination of InsP3 by mouse InsP3R1c.

Similar content being viewed by others

References

  1. Berridge, M. J., Lipp, P. & Bootman, M. D. The versatility and universality of calcium signalling. Nature Rev. Mol. Cell Biol. 1, 11–21 (2000)

    Article  CAS  Google Scholar 

  2. Furuichi, T. & Mikoshiba, K. Inositol 1,4,5-trisphosphate receptor-mediated Ca2+ signaling in the brain. J. Neurochem. 64, 953–960 (1995)

    Article  CAS  Google Scholar 

  3. Uchiyama, T., Yoshikawa, F., Hishida, A., Furuichi, T. & Mikoshiba, K. A novel recombinant hyperaffinity inositol 1,4,5-trisphosphate (IP3) absorbent traps IP3, resulting in specific inhibition of IP3-mediated calcium signaling. J. Biol. Chem. 277, 8106–8113 (2002)

    Article  CAS  Google Scholar 

  4. Overduin, M., Cheever, M. L. & Kutateladze, T. G. Signaling with phoshoinositides: better than binary. Mol. Interventions 1, 151–159 (2001)

    Google Scholar 

  5. Hamada, K., Shimizu, T., Matsui, T., Tsukita, S. & Hakoshima, T. Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain. EMBO J. 19, 4449–4462 (2000)

    Article  CAS  Google Scholar 

  6. Ferguson, K. M., Lemmon, M. A., Schlessinger, J. & Sigler, P. B. Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain. Cell 83, 1037–1046 (1995)

    Article  CAS  Google Scholar 

  7. Hyvonen, M. et al. Structure of the binding site for inositol phosphates in a PH domain. EMBO J. 14, 4676–4685 (1995)

    Article  CAS  Google Scholar 

  8. Hotoda, H. et al. Molecular recognition of adenophostin, a very potent Ca2+ inducer, at the d-myo-inositol 1,4,5-trisphosphate receptor. Biochemistry 38, 9234–9241 (1999)

    Article  CAS  Google Scholar 

  9. Murzin, A. G., Lesk, A. M. & Chothia, C. beta-Trefoil fold. Patterns of structure and sequence in the Kunitz inhibitors interleukins-1β and 1α and fibroblast growth factors. J. Mol. Biol. 223, 531–543 (1992)

    Article  CAS  Google Scholar 

  10. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123–138 (1993)

    Article  CAS  Google Scholar 

  11. Huber, A. H., Nelson, W. J. & Weis, W. I. Three-dimensional structure of the armadillo repeat region of β-catenin. Cell 90, 871–882 (1997)

    Article  CAS  Google Scholar 

  12. Cingolani, G., Petosa, C., Weis, K. & Muller, C. W. Structure of importin-β bound to the IBB domain of importin-α. Nature 399, 221–229 (1999)

    Article  ADS  CAS  Google Scholar 

  13. Peifer, M., Berg, S. & Reynolds, A. B. A repeating amino acid motif shared by proteins with diverse cellular roles. Cell 76, 789–791 (1994)

    Article  CAS  Google Scholar 

  14. Rost, B., Sander, C. & Schneider, R. PHD—an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10, 53–60 (1994)

    CAS  PubMed  Google Scholar 

  15. Jones, D. T. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797–815 (1999)

    Article  CAS  Google Scholar 

  16. Hamada, K., Miyata, T., Mayanagi, K., Hirota, J. & Mikoshiba, K. Two-state conformational changes in inositol 1,4,5-trisphosphate receptor regulated by calcium. J. Biol. Chem. 277, 21115–21118 (2002)

    Article  CAS  Google Scholar 

  17. Jiang, Q. X., Thrower, E. C., Chester, D. W., Ehrlich, B. E. & Sigworth, F. J. Three-dimensional structure of the type 1 inositol 1,4,5-trisphosphate receptor at 24 Å resolution. EMBO J. 21, 3575–3581 (2002)

    Article  CAS  Google Scholar 

  18. Wilcox, R. A., Primrose, W. U., Nahorski, S. R. & Challiss, R. A. New developments in the molecular pharmacology of the myo-inositol 1,4,5-trisphosphate receptor. Trends Pharmacol. Sci. 19, 467–475 (1998)

    Article  CAS  Google Scholar 

  19. Kozikowski, A. P., Ognyanov, V. I., Fauq, A. H., Nahorski, A. R. & Wilcox, R. A. Synthesis of 1d-3-deoxy-, 1d-2,3-dideoxy-, and 1d-2,3,6-trideoxy-myo-inositol 1,4,5-trisphosphate from quebrachitol, their binding affinities, and calcium release activity. J. Am. Chem. Soc. 115, 4429–4434 (1993)

    Article  CAS  Google Scholar 

  20. Yoshikawa, F. et al. Mutational analysis of the ligand binding site of the inositol 1,4,5-trisphosphate receptor. J. Biol. Chem. 271, 18277–18284 (1996)

    Article  CAS  Google Scholar 

  21. Marchant, J. S. & Taylor, C. W. Cooperative activation of IP3 receptors by sequential binding of IP3 and Ca2+ safeguards against spontaneous activity. Curr. Biol. 7, 510–518 (1997)

    Article  CAS  Google Scholar 

  22. Sienaert, I. et al. Molecular and functional evidence for multiple Ca2+-binding domains in the type 1 inositol 1,4,5-trisphosphate receptor. J. Biol. Chem. 272, 25899–25906 (1997)

    Article  CAS  Google Scholar 

  23. Sienaert, I. et al. Localization and function of a calmodulin/apocalmodulin binding domain in the N-terminal part of the type 1 inositol 1,4,5-trisphosphate receptor. Biochem. J. 365, 269–277 (2002)

    Article  CAS  Google Scholar 

  24. Yoshikawa, F. et al. High efficient expression of the functional ligand binding site of the inositol 1,4,5-triphosphate receptor in Escherichia coli. Biochem. Biophys. Res. Commun. 257, 792–797 (1999)

    Article  CAS  Google Scholar 

  25. Van Duyne, G. D., Standaert, R. F., Karplus, P. A., Schreiber, S. L. & Clardy, J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229, 105–124 (1993)

    Article  CAS  Google Scholar 

  26. Pflugrath, J. W. The finer things in X-ray diffraction data collection. Acta Crystallogr. D 55, 1718–1725 (1999)

    Article  CAS  Google Scholar 

  27. Terwillinger, T. C., Kim, S. H. & Eisenberg, J. Generalized method of determining heavy-atom positions using the difference Patterson function. Acta Crystallogr. A 43, 1–5 (1987)

    Article  Google Scholar 

  28. La Fortelle, E. D. & Bricogne, G. Maximum-likelihood heavy atom parameter refinement in the MIR and MAD methods. Methods Enzymol. 276, 472–494 (1997)

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

Download references

Acknowledgements

We thank A. Nakagawa, A. Miyazaki and K.T. Chong for their assistance at the beamline BL44XU at SPring-8, Japan; the staff at the X8-C and X25 beamline of Brookhaven National Laboratory and the BioCars beamline at Advanced Photon Source for their assistance; D. Jones and M. Swindells for mGenTHREADER analysis; and members of our division for discussions. This work was supported by grants from the Canadian Institutes of Health Research (CIHR) to I.B. and M.I., and by grants from RIKEN (to K.M.) and the Ministry of Education, Science, Sports, and Culture of Japan (to K.M. and T.M.). M.I. is a CIHR Investigator.

Author information

Authors and Affiliations

  1. Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, Ontario, M5G 2M9, Canada

    Ivan Bosanac, Jean-René Alattia, Tapas K. Mal, Jenny Chan, Susanna Talarico, Frances K. Tong, Kit I. Tong & Mitsuhiko Ikura

  2. Laboratory for Developmental Neurobiology and Molecular Neurogenesis, Brain Science Institute, RIKEN, Saitama, 351-0198, Japan

    Fumio Yoshikawa, Teiichi Furuichi & Katsuhiko Mikoshiba

  3. Department of Molecular Neurobiology, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan

    Miwako Iwai, Takayuki Michikawa & Katsuhiko Mikoshiba

  4. Calcium Oscillation Project, ICORP, Japan Science and Technology Corporation (JST), 108-0071, Tokyo, Japan

    Takayuki Michikawa & Katsuhiko Mikoshiba

Authors
  1. Ivan Bosanac
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jean-René Alattia
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tapas K. Mal
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jenny Chan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Susanna Talarico
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Frances K. Tong
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Kit I. Tong
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Fumio Yoshikawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Teiichi Furuichi
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Miwako Iwai
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Takayuki Michikawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Katsuhiko Mikoshiba
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Mitsuhiko Ikura
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mitsuhiko Ikura.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bosanac, I., Alattia, JR., Mal, T. et al. Structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with its ligand. Nature 420, 696–700 (2002). https://doi.org/10.1038/nature01268

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature01268

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

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