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:

Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2

Nature volume 477, pages 495–498 (2011)Cite this article

Subjects

Abstract

The regulation of ion channel activity by specific lipid molecules is widely recognized as an integral component of electrical signalling in cells1,2. In particular, phosphatidylinositol 4,5-bisphosphate (PIP2), a minor yet dynamic phospholipid component of cell membranes, is known to regulate many different ion channels2,3,4,5,6,7,8. PIP2 is the primary agonist for classical inward rectifier (Kir2) channels, through which this lipid can regulate a cell’s resting membrane potential2,7,8,9. However, the molecular mechanism by which PIP2 exerts its action is unknown. Here we present the X-ray crystal structure of a Kir2.2 channel in complex with a short-chain (dioctanoyl) derivative of PIP2. We found that PIP2 binds at an interface between the transmembrane domain (TMD) and the cytoplasmic domain (CTD). The PIP2-binding site consists of a conserved non-specific phospholipid-binding region in the TMD and a specific phosphatidylinositol-binding region in the CTD. On PIP2 binding, a flexible expansion linker contracts to a compact helical structure, the CTD translates 6 Å and becomes tethered to the TMD and the inner helix gate begins to open. In contrast, the small anionic lipid dioctanoyl glycerol pyrophosphatidic acid (PPA) also binds to the non-specific TMD region, but not to the specific phosphatidylinositol region, and thus fails to engage the CTD or open the channel. Our results show how PIP2 can control the resting membrane potential through a specific ion-channel-receptor–ligand interaction that brings about a large conformational change, analogous to neurotransmitter activation of ion channels at synapses.

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: Effect of a short-chain PIP 2 on Kir2.2.
Figure 2: PIP 2 -binding site.
Figure 3: Conserved non-specific lipid-binding site in Kir channels.
Figure 4: A proposed mechanism of Kir2.2 activation by PIP2.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structures have been deposited into the Protein Data Bank under accession codes 3SPI (wild-type PIP2), 3SPC (wild-type PPA), 3SPH (PIP2(I223L)), 3SPJ (apo(I223L)) and 3SPG (PIP2(R186A)).

References

  1. Dart, C. Lipid microdomains and the regulation of ion channel function. J. Physiol. (Lond.) 588, 3169–3178 (2010)

    Article  CAS  Google Scholar 

  2. Hilgemann, D. W., Feng, S. & Nasuhoglu, C. The complex and intriguing lives of PIP2 with ion channels and transporters. Sci. STKE 2001, re19 (2001)

    CAS  PubMed  Google Scholar 

  3. Suh, B. C. & Hille, B. Regulation of ion channels by phosphatidylinositol 4,5-bisphosphate. Curr. Opin. Neurobiol. 15, 370–378 (2005)

    Article  CAS  Google Scholar 

  4. Fujiwara, Y. & Kubo, Y. Regulation of the desensitization and ion selectivity of ATP-gated P2X2 channels by phosphoinositides. J. Physiol. (Lond.) 576, 135–149 (2006)

    Article  CAS  Google Scholar 

  5. Logothetis, D. E., Jin, T., Lupyan, D. & Rosenhouse-Dantsker, A. Phosphoinositide-mediated gating of inwardly rectifying K+ channels. Pflügers Arch. Eur. J. Physiol. 455, 83–95 (2007)

    Article  CAS  Google Scholar 

  6. Vaithianathan, T. et al. Direct regulation of BK channels by phosphatidylinositol 4,5-bisphosphate as a novel signaling pathway. J. Gen. Physiol. 132, 13–28 (2008)

    Article  CAS  Google Scholar 

  7. Gamper, N. & Shapiro, M. S. Regulation of ion transport proteins by membrane phosphoinositides. Nature Rev. Neurosci. 8, 921–934 (2007)

    Article  CAS  Google Scholar 

  8. Huang, C. L., Feng, S. & Hilgemann, D. W. Direct activation of inward rectifier potassium channels by PIP2 and its stabilization by Gβγ. Nature 391, 803–806 (1998)

    Article  ADS  CAS  Google Scholar 

  9. Lopes, C. M. B. et al. Alterations in conserved Kir channel-PIP2 interactions underlie channelopathies. Neuron 34, 933–944 (2002)

    Article  CAS  Google Scholar 

  10. Berridge, M. J. Inositol trisphosphate and calcium signalling. Nature 361, 315–325 (1993)

    Article  ADS  CAS  Google Scholar 

  11. Monserrate, J. P. & York, J. D. Inositol phosphate synthesis and the nuclear processes they affect. Curr. Opin. Cell Biol. 22, 365–373 (2010)

    Article  CAS  Google Scholar 

  12. Martin, T. F. PI(4,5)P2 regulation of surface membrane traffic. Curr. Opin. Cell Biol. 13, 493–499 (2001)

    Article  CAS  Google Scholar 

  13. Cho, W. & Stahelin, R. V. Membrane-protein interactions in cell signaling and membrane trafficking. Annu. Rev. Biophys. Biomol. Struct. 34, 119–151 (2005)

    Article  CAS  Google Scholar 

  14. Heo, W. D. et al. PI(3,4,5)P3 and PI(4,5)P2 lipids target proteins with polybasic clusters to the plasma membrane. Science 314, 1458–1461 (2006)

    Article  ADS  CAS  Google Scholar 

  15. Hilgemann, D. W. & Ball, R. Regulation of cardiac Na+,Ca2+ exchange and KATP potassium channels by PIP2 . Science 273, 956–959 (1996)

    Article  ADS  CAS  Google Scholar 

  16. Stanfield, P. R., Nakajima, S. & Nakajima, Y. Constitutively active and G-protein coupled inward rectifier K+ channels: Kir2.0 and Kir3.0. Rev. Physiol. Biochem. Pharmacol. 145, 47–179 (2002)

    Article  CAS  Google Scholar 

  17. Rohács, T. et al. Specificity of activation by phosphoinositides determines lipid regulation of Kir channels. Proc. Natl Acad. Sci. USA 100, 745–750 (2003)

    Article  ADS  Google Scholar 

  18. Enkvetchakul, D., Jeliazkova, I. & Nichols, C. G. Direct modulation of Kir channel gating by membrane phosphatidylinositol 4,5-bisphosphate. J. Biol. Chem. 280, 35785–35788 (2005)

    Article  CAS  Google Scholar 

  19. Tao, X., Avalos, J. L., Chen, J. & MacKinnon, R. Crystal structure of the eukaryotic strong inward-rectifier K+ channel Kir2.2 at 3.1 Å resolution. Science 326, 1668–1674 (2009)

    Article  ADS  CAS  Google Scholar 

  20. Zhang, H., He, C., Yan, X., Mirshahi, T. & Logothetis, D. E. Activation of inwardly rectifying K+ channels by distinct PtdIns(4,5)P2 interactions. Nature Cell Biol. 1, 183–188 (1999)

    Article  CAS  Google Scholar 

  21. Cheng, W. W., D’Avanzo, N., Doyle, D. A. & Nichols, C. G. Dual-mode phospholipid regulation of human inward rectifying potassium channels. Biophys. J. 100, 620–628 (2011)

    Article  ADS  CAS  Google Scholar 

  22. Clarke, O. B. et al. Domain reorientation and rotation of an intracellular assembly regulate conduction in Kir potassium channels. Cell 141, 1018–1029 (2010)

    Article  CAS  Google Scholar 

  23. Pegan, S. et al. Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification. Nature Neurosci. 8, 279–287 (2005)

    Article  CAS  Google Scholar 

  24. Vagin, A. & Teplyakov, A. An approach to multi-copy search in molecular replacement. Acta Crystallogr. D 56, 1622–1624 (2000)

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  26. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010)

    Article  CAS  Google Scholar 

  27. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    Article  CAS  Google Scholar 

  28. Xie, L.-H., John, S., a, Ribalet, B. & Weiss, J. N. Activation of inwardly rectifying potassium (Kir) channels by phosphatidylinosital-4,5-bisphosphate (PIP2): interaction with other regulatory ligands. Prog. Biophys. Mol. Biol. 94, 320–335 (2007)

    Article  CAS  Google Scholar 

  29. Cohen, S. X. et al. Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr. D 60, 2222–2229 (2004)

    Article  Google Scholar 

  30. Delano, W. L. PyMOL. 〈http://www.pymol.org〉 (Delano Scientific, 2002)

Download references

Acknowledgements

We thank staff members at NSLS X29 and X25, Brookhaven National Laboratory for beamline assistance, members of the Gadsby laboratory (Rockefeller University) for help in Xenopus oocyte preparation, R. Molday (University of British Columbia) for providing the anti-1D4 tag cell line and members of the MacKinnon laboratory for helpful suggestions. R.M. is an investigator in the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

  1. Laboratory of Molecular Neurobiology & Biophysics, The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10065, USA,

    Scott B. Hansen, Xiao Tao & Roderick MacKinnon

Authors
  1. Scott B. Hansen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiao Tao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Roderick MacKinnon
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

S.B.H. purified and crystallized the protein; collected, processed and refined crystallographic data, and performed electrophysiology experiments. X.T. aided in experimental design and provided assistance in all aspects of the project. R.M. designed the study and analysed data. All authors wrote and discussed the manuscript.

Corresponding author

Correspondence to Roderick MacKinnon.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-7 with legends and Supplementary Table 1. (PDF 894 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hansen, S., Tao, X. & MacKinnon, R. Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2. Nature 477, 495–498 (2011). https://doi.org/10.1038/nature10370

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature10370

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