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Molecular mechanism of ATP binding and ion channel activation in P2X receptors

Nature volume 485, pages 207–212 (2012)Cite this article

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Abstract

P2X receptors are trimeric ATP-activated ion channels permeable to Na+, K+ and Ca2+. The seven P2X receptor subtypes are implicated in physiological processes that include modulation of synaptic transmission, contraction of smooth muscle, secretion of chemical transmitters and regulation of immune responses. Despite the importance of P2X receptors in cellular physiology, the three-dimensional composition of the ATP-binding site, the structural mechanism of ATP-dependent ion channel gating and the architecture of the open ion channel pore are unknown. Here we report the crystal structure of the zebrafish P2X4 receptor in complex with ATP and a new structure of the apo receptor. The agonist-bound structure reveals a previously unseen ATP-binding motif and an open ion channel pore. ATP binding induces cleft closure of the nucleotide-binding pocket, flexing of the lower body β-sheet and a radial expansion of the extracellular vestibule. The structural widening of the extracellular vestibule is directly coupled to the opening of the ion channel pore by way of an iris-like expansion of the transmembrane helices. The structural delineation of the ATP-binding site and the ion channel pore, together with the conformational changes associated with ion channel gating, will stimulate development of new pharmacological agents.

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Figure 1: The architectures of zebrafish P2X4.
Figure 2: Analysis of conformational difference between ΔP2X4-C and ΔP2X4-B2.
Figure 3: ATP-binding site.
Figure 4: The transmembrane pore.
Figure 5: Structural transitions in the transmembrane domain.
Figure 6: Mechanism of activation.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

The coordinates and structure factors for the zebrafish apo DP2X4-B2 and ATP-bound DP2X4-C have been deposited in the Protein Data Bank under the accession codes 4DW0 and 4DW1, respectively.

Change history

  • 09 May 2012

    A typographical error was corrected in the abstract; an addition was made to Acknowledgements.

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Acknowledgements

We thank C. Alexander and D. C. Dawson for providing Xenopus oocytes, K. L. Dürr and T. Friedrich for providing the pCNA3.1x vector, L. Vaskalis for assistance with figure illustrations, K. J. Swartz and M. P. Kavanaugh for advice related to the oocyte experiments, and Gouaux laboratory members for discussions. We are also grateful to the staff at the Advanced Photon Source beamline 24-ID-C for help with X-ray data collection. This work was supported by a Japan Society for the Promotion of Science Postdoctoral Fellowship for Research Abroad (M.H.), and by the American Asthma Foundation (E.G.) and the NIH (E.G.). E.G. is an investigator with the Howard Hughes Medical Institute.

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Authors and Affiliations

  1. Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA,

    Motoyuki Hattori & Eric Gouaux

  2. Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA,

    Eric Gouaux

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  1. Motoyuki Hattori
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  2. Eric Gouaux
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M.H. and E.G. contributed to all aspects of the project.

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Correspondence to Eric Gouaux.

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Supplementary information

Supplementary Information

This file contains Supplementary Table 1, Supplementary Figures 1-16 and an additional reference. (PDF 11145 kb)

Supplementary Movie 1

This movie shows the structural conformational changes in the TM region of zfP2X4 between the apo, closed (ΔzfP2X4-B2) and the ATP-bound, open (ΔzfP2X4-C) states, viewed from the intracellular side. The colouring of scheme is the same as Fig 1a. (MOV 6040 kb)

Supplementary Movie 2

This movie shows the structural conformational changes of zfP2X4 between the apo, closed (ΔzfP2X4-B) and the ATP-bound, open (ΔzfP2X4-C) states, viewed perpendicular to the membrane plane. The couloring of scheme of the head (A), dorsal fin (B), left flipper (A), body and TM domains (A, B) is the same as in Fig. 2a. (MOV 7128 kb)

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Hattori, M., Gouaux, E. Molecular mechanism of ATP binding and ion channel activation in P2X receptors. Nature 485, 207–212 (2012). https://doi.org/10.1038/nature11010

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