Structures of the calcium-activated, non-selective cation channel TRPM4

Abstract

TRPM4 is a calcium-activated, phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) -modulated, non-selective cation channel that belongs to the family of melastatin-related transient receptor potential (TRPM) channels. Here we present the electron cryo-microscopy structures of the mouse TRPM4 channel with and without ATP. TRPM4 consists of multiple transmembrane and cytosolic domains, which assemble into a three-tiered architecture. The N-terminal nucleotide-binding domain and the C-terminal coiled-coil participate in the tetrameric assembly of the channel; ATP binds at the nucleotide-binding domain and inhibits channel activity. TRPM4 has an exceptionally wide filter but is only permeable to monovalent cations; filter residue Gln973 is essential in defining monovalent selectivity. The S1–S4 domain and the post-S6 TRP domain form the central gating apparatus that probably houses the Ca2+- and PtdIns(4,5)P2-binding sites. These structures provide an essential starting point for elucidating the complex gating mechanisms of TRPM4 and reveal the molecular architecture of the TRPM family.

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Figure 1: Overall structure of TRPM4.
Figure 2: Bottom-tier NBD and ARD.
Figure 3: Ion conduction pore and channel selectivity.
Figure 4: S1–S4 and TRP domains.
Figure 5: C-terminal stretcher and coiled-coil helices.

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Change history

  • 07 December 2017

    In the HMTL, authors Xiao-chen Bai and Youxing Jiang were reversed in the author list.

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Acknowledgements

We thank N. Nguyen for manuscript preparation, J. M. Simard and J. Bryan for providing the TRPM4 clones. Single particle cryo-EM data were collected at the University of Texas Southwestern Medical Center (UTSW) Cryo-Electron Microscopy Facility. We thank D. Nicastro and Z. Chen for support in facility access and data acquisition. Negatively stained sample screening was performed at UTSW Electron Microscopy core. This work was supported in part by the Howard Hughes Medical Institute (Y.J.) and by grants from the National Institutes of Health (GM079179 to Y. J.) and the Welch Foundation (grant I-1578 to Y. J.). X.B. is supported by the Cancer Prevention and Research Initiative of Texas and Virginia Murchison Linthicum Scholar in Medical Research fund.

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J.G. and J.S. prepared the samples; J.G., J.S., Q.C. and X.B. performed data acquisition, image processing and structure determination; W.Z. performed electrophysiology; all authors participated in research design, data analysis, and manuscript preparation.

Corresponding authors

Correspondence to Xiao-chen Bai or Youxing Jiang.

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The authors declare no competing financial interests.

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Reviewer Information Nature thanks R. Penner and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Figure 1 Gating properties of mouse TRPM4 overexpressed in HEK293 cells.

a, Macroscopic currents of TRPM4 at ±100 mV in an inside-out patch in the presence or absence of various ligands in the bath (cytosolic). b, IV curves of TRPM4 at the time points indicated in a. c, Sample traces of single channel recordings of TRPM4 in the Ca2+-desensitized state (with 300 μM Ca2+) at 100 mV (top), 0 mV (middle) and −100 mV (bottom), revealing the voltage-dependent, single-channel-open probability. d, Sample IV curves of TRPM4 recorded with various cytosolic (bath solution) Ca2+ concentrations in the presence (right) or absence (left) of 10 μM PtdIns(4,5)P2. e, Concentration-dependent Ca2+-activation of TRPM4 channels in the presence or absence of PtdIns(4,5)P2. I/Imax values were measured at 100 mV from IV curves shown in d. Data were reported as mean ± s.e.m. of five independent biological replicates. Curves are least-square fits to a Hill equation and the result indicates that Ca2+ has much lower apparent affinity for desensitized TRPM4. All electrophysiological recordings were repeated at least five times using different patches. Source data

Extended Data Figure 2 Structure determination of apo TRPM4.

a, Purification of TRPM4 reconstituted in nanodiscs by size-exclusion chromatography. b, Negatively stained micrograph of TRPM4 in nanodiscs. c, Representative cryo-EM micrograph of TRPM4 in nanodiscs. d, Flowchart of image processing for apo TRPM4 particles. e, Gold-standard FSC curve of the final 3D reconstruction of the apo TRPM4 and the density map coloured by local resolution. f, Gold-standard FSC curve of particles from the focused 3D classification at the coiled-coil region and the density map coloured by local resolution.

Extended Data Figure 3 Structure determination of ATP-bound TRPM4.

a, Flow chart of image processing for ATP-bound TRPM4 particles. b, Gold-standard FSC curve of the final 3D reconstruction of the TRPM4–ATP complex and the density map coloured by local resolution. c, Gold-standard FSC curve of particles from the focused 3D classification at the coiled-coil region of TRPM4–ATP complex and the density map coloured by local resolution.

Extended Data Figure 4 Data collection, structure refinement and model validation.

a, Data collection and model refinement statistics. b, FSC curves for cross-validation between the maps and the models. Curves for model versus summed map in green (sum), for model versus half map in black (work), and for model versus half map not used for refinement in red (free).

Extended Data Figure 5 Sample EM density maps of TRPM4.

a, Sample maps at various regions of apo TRPM4. The maps are low-pass filtered to 3.1 Å and sharpened with a temperature factor of −120 Å2. b, EM density of coiled-coil region in the apo TRPM4 after focused 3D classification. The map is low-pass filtered to 3.5 Å and sharpened with a temperature factor of −91 Å2. c, Electron microscopy density of ATP and its surrounding residues in the ATP-bound TRPM4. The map is low-pass filtered to 2.9 Å and sharpened with a temperature factor of −91 Å2.

Extended Data Figure 6 Sequence alignment of mouse TRPM4 (MmTRPM4) and human TRPM (HsTRPM1–8) channels.

Secondary structure assignments are based on the mouse TRPM4 structure. Only the sequences up to the end of the coiled-coil domain are included in the alignment. Red triangles mark the key residues for ATP binding.

Extended Data Figure 7 NBD structure and ATP inhibition.

a, Structural comparison between the NBD of ATP-bound TRPM4 and AMP-bound LOG protein (PDB accession number 3SBX). The NBD region in the dotted box shares a similar fold to that of LOG protein. The ATP-binding site in the TRPM4 NBD is distinct from AMP in LOG. b, Superposition of TRPM4 structures in the apo (green) and ATP-bound (purple) states. The top two tiers are virtually identical in both states. Major conformational change occurs at the NBD. c. Sample IV curves of TRPM4 and its mutants at various concentrations of cytosolic free ATP. Channels were activated by 300 μM Ca2+ and 10 μM PtdIns(4,5)P2 in the bath solution. Normalized currents (I/Imax) at 100 mV were used to generate the inhibition curves shown in Fig. 2e. Imax is the current at 100 mV without ATP. d, Recovery of wild-type TRPM4 and H160A mutant activities from Ca2+-desensitization by cytosolic ATP·Mg. Currents were recorded at −100 mV. Note that ATP was washed out before Ca2+ activation to avoid ATP inhibition. All electrophysiological recordings were repeated at least five times using different patches.

Extended Data Figure 8 The middle-tier LHD mediates inter-domain interactions within the subunit.

a, Structure of the LHD (cyan) and its interactions with the ARD (lower right inset), the TRP domain (upper right inset) and S1 helix (left inset). Between the middle and bottom tiers, the linker helices of LH1, LH4 and LH5 stack on top of AKR2 and form extensive hydrophobic interactions (lower right inset). The C-terminal region of the LHD mediates direct contacts with the top-tier transmembrane domain: the U-shaped LH9–LH11 grip the bottom side of TRP helix 1 (upper right inset); LH12 and the loops on its two ends clamp around the S0 and N terminus of S1 (left inset). b, Four linker domains encircle a wide open, fenestrated court at the centre of the channel. LH6–LH8 helices from each subunit frame the open central court and form head-to-tail packing with their neighbouring counterparts in a channel tetramer, providing the only inter-subunit contact at the middle tier.

Extended Data Figure 9 The Q973D mutant remains non-selective among monovalent cations similar to the wild-type TRPM4 channel.

Shown are sample IV curves recorded in bi-ionic conditions with 150 mM Na+ in the pipette and 150 mM X+ (X = Li, Na, K or Cs) in the bath. Currents were recorded when channels reached desensitized steady state after activation with 300 μM cytosolic (bath) Ca2+. All recordings were repeated at least five times using different patches.

Extended Data Figure 10 S1–S4 domain of TRPM4.

a, Structural comparison of the S1–S4 domain between TRPM4 (green) and TRPV1 (blue, PDB accession number 5IRX). b, Voltage dependence of wild-type TRPM4 and R901A mutant at Ca2+-desensitized state (top). The membrane was stepped from the holding potential (0 mV) to various testing potentials (−100 mV to +100 mV) for one second and then stepped to −100 mV. The peak tail currents were used to plot the GV curves (bottom). Data were reported as mean ± s.e.m. from five independent patches (biological replicates). Source Data are available in with the online version of the paper. V1/2 and Z values were obtained from fits of the data to the Boltzmann equation. Source data

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Guo, J., She, J., Zeng, W. et al. Structures of the calcium-activated, non-selective cation channel TRPM4. Nature 552, 205–209 (2017). https://doi.org/10.1038/nature24997

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