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Structures of TRPV2 in distinct conformations provide insight into role of the pore turret

Abstract

Cation channels of the transient receptor potential (TRP) family serve important physiological roles by opening in response to diverse intra- and extracellular stimuli that regulate their lower or upper gates. Despite extensive studies, the mechanism coupling these gates has remained obscure. Previous structures have failed to resolve extracellular loops, known in the TRPV subfamily as ‘pore turrets’, which are proximal to the upper gates. We established the importance of the pore turret through activity assays and by solving structures of rat TRPV2, both with and without an intact turret at resolutions of 4.0 Å and 3.6 Å, respectively. These structures resolve the full-length pore turret and reveal fully open and partially open states of TRPV2, both with unoccupied vanilloid pockets. Our results suggest a mechanism by which physiological signals, such as lipid binding, can regulate the lower gate and couple to the upper gate through a pore-turret-facilitated mechanism.

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Fig. 1: Effects of pore turret deletions and phosphoinositides on channel activity.
Fig. 2: TRPV2 constructs and cryo-EM density maps.
Fig. 3: Structure and orientation of pore turret domain.
Fig. 4: Cation pathway of WT and mutant variants of TRPV2.
Fig. 5: Comparisons of TRPV2 structures.
Fig. 6: Model alignments of S3–S6.
Fig. 7: Model mechanism for agonist-independent TRPV2 activation.

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Data availability

The rat TRPV2 models (PDB 6BO4 (WT) and PDB 6BO5 (mutant)) and cryo-EM density maps (EMD-7118 (WT) and EMD-7119 (mutant)) have been deposited in the PDB (http://www.rcsb.org/) and the Electron Microscopy Data Bank (https://www.ebi.ac.uk/pdbe/emdb/). Other data are available from the corresponding authors upon reasonable request.

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Acknowledgements

We thank C. Hryc for providing his expertise in modeling cryo-EM density maps and helping to validate the models. We thank M. Agosto, J. Gonzalez, and other members of the Wensel laboratory for helpful discussions and suggestions and M. Zhou for helpful comments. We thank the National Center for Macromolecular Imaging for providing the cryo-EM and computational resources. This work was supported by the Robert Welch Foundation (grant nos. Q0035 and Q-1967-20180324) and a training fellowship from the Houston Area Molecular Biophysics Program of the Keck Center of the Gulf Coast Consortia, National Institute of General Medical Sciences (grant no. T32GM008280). Further support was provided by National Institutes of Health grants (nos. P41GM103832, R01GM072804, R01EY007981, R01EY026545) and the American Heart Association (grant no. 16GRNT29720001).

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Contributions

T.L.D. designed the project, designed and performed all biochemistry and molecular biology experiments, processed cryo-EM data, constructed and optimized the molecular models, prepared figures and animations, and wrote the manuscript. Z.W. and G.F. collected cryo-E.M. data, and Z.W. reconstructed, refined, and validated the maps. Z.Z. collected and processed preliminary cryo-EM data to optimize cryo-specimen preparation for high-resolution imaging. T.G.W., W.C., and I.I.S. supervised personnel, provided laboratory resources and facilities, participated in structure interpretations, and edited the manuscript.

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Correspondence to Wah Chiu or Theodore G. Wensel.

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Integrated supplementary information

Supplementary Figure 1 Comparisons of the TRPV2 pore conformations and S6 registers and rearrangements of the upper gates for TRPV2 and TRPV1.

a,b, Van der Waals space filling representation of the pores for the previously deposited TRPV2 structures PDB 5HI9 (dark gray) and PDB 5AN8 (light gray), both showing fully closed conformations. c, Selectivity filter and pore loop region of the WT (blue) and mutant (purple) models fit to cryo-EM densities (mesh) indicating side chain positions. Included is a zoomed view of the M607 side chain responsible for blocking conduction at the upper gate. d, Cell-based TRPV2 activity assay showing that alanine substitution at L610 and F618 results in greatly diminished channel activity in response to 2-APB. e, Superimposition of closed TRPV1 (orange) (PDB 5IRZ) and open TRPV1 (pink) (PDB 5IRX). f, Superimposition of the open upper gates for our WT TRPV2 (blue) cryo-EM structure and the TRPV2 crystal structure (yellow) (PDB 6BWM).

Supplementary Figure 2 Optimization of constructs for heterologous expression and purification.

a, Diagrams for the TRPV2 (blue) and TRPV4 (orange) constructs created for a S. cerevisiae heterologous expression system. b, Western blot against the 1D4 epitope tag testing the relative expression levels of the indicated TRPV2 and TRPV4 constructs. Each well was loaded with an equal amount of yeast cells. d, Coomassie-stained gels with bands indicating the approximate molecular weights for the purified TRPV2 variant monomers. e, Size exclusion chromatography profiles for the purified TRPV2 variants. Fractions under the main peak were pooled for biochemical analysis and structure determination. f, Dose responses for the final TRPV2 constructs used for structure determination compared to the responses of the minimally modified counterparts.

Supplementary Figure 3 Resolution estimation of cryo-EM structures.

a,d, Resolution maps for the full-length (a) and mutant (d) TRPV2 variants. b,e, The overall resolutions for the full-length and mutant TRPV2 maps are 4 Å and 3.6 Å, respectively, and these were determined using Fourier shell correlations with a 0.143 cutoff. c,f, Representative areas of the TRPV2 maps (mesh) superimposed with the molecular models showing resolved α-helices with clear side chains in the ankyrin-repeat domain (ARD) and in the transmembrane domains. g,h, FSC curves for WT (g) and mutant (h) models versus half maps and the whole maps.

Supplementary Figure 4 Resolution estimation of cryo-EM structures.

a,d, Resolution maps for the full-length (a) and mutant (d) TRPV2 variants. b,e, The overall resolutions for the full-length and mutant TRPV2 maps are 4 Å and 3.6 Å, respectively, and these were determined using Fourier shell correlations with a 0.143 cutoff. c,f, Representative areas of the TRPV2 maps (mesh) superimposed with the molecular models showing resolved α-helices with clear side chains in the ankyrin-repeat domain (ARD) and in the transmembrane domains. g,h, FSC curves for WT (g) and mutant (h) models versus half maps and the whole maps.

Supplementary Figure 5 Pore turret model fit to density.

Rotated views of the pore turret loop backbone (green) fit to the density (mesh). Residues P565, P568, P579, P587, and P589 are labeled.

Supplementary Figure 6 Calculated atomic displacement parameters (also known as B factors) for the TRPV2 models.

a,e, Side and top views for the WT (a) and mutant (e) TRPV2 models color-coded according to the average atomic displacement parameter at each residue. b,f, Zoomed view of the WT (b) and mutant (f) TRPV2 pore regions. c,g, Side views of the WT (c) and mutant (g) TRPV2 monomer models. d,h, Zoom view of the WT (d) and mutant (h) lower gate and vanilloid pocket regions.

Supplementary Figure 7 S6 helix registers and TRPV1/TRPV2 lower gate conformation comparisons.

a, WT (blue) and mutant (purple) TRPV2 models for the S6 helix fit to cryo-EM densities (mesh). b, Superimposition of the S6 helices of WT and mutant TRPV2. c, Superimposition of WT TRPV2 S6 helix in the open conformation with the S6 helix of TRPV2 (5AN8) (gray) in the closed conformation. d, Lower gate superimpositions of the closed TRPV1 (orange) (PDB 5IRZ) conformation with the open conformation of DkTx/RTX-bound TRPV1 (pink) (PDB 5IRX). e, Lower gate superimpositions of the closed TRPV2 (5AN8) (gray) conformation with the open conformation of RTX-bound TRPV2 (yellow) (PDB 6BWM).

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7

Reporting Summary

Supplementary Video 1

TRPV2 WT and mutant constructs and structures

Supplementary Video 2

TRPV2 pore turret structure

Supplementary Video 3

Proposed TRPV2 gating mechanism

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Dosey, T.L., Wang, Z., Fan, G. et al. Structures of TRPV2 in distinct conformations provide insight into role of the pore turret. Nat Struct Mol Biol 26, 40–49 (2019). https://doi.org/10.1038/s41594-018-0168-8

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