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Molecular insights into lipid-assisted Ca2+ regulation of the TRP channel Polycystin-2

Nature Structural & Molecular Biology volume 24, pages 123–130 (2017)Cite this article

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Abstract

Polycystin-2 (PC2), a calcium-activated cation TRP channel, is involved in diverse Ca2+ signaling pathways. Malfunctioning Ca2+ regulation in PC2 causes autosomal-dominant polycystic kidney disease. Here we report two cryo-EM structures of distinct channel states of full-length human PC2 in complex with lipids and cations. The structures reveal conformational differences in the selectivity filter and in the large exoplasmic domain (TOP domain), which displays differing N-glycosylation. The more open structure has one cation bound below the selectivity filter (single-ion mode, PC2SI), whereas multiple cations are bound along the translocation pathway in the second structure (multi-ion mode, PC2MI). Ca2+ binding at the entrance of the selectivity filter suggests Ca2+ blockage in PC2MI, and we observed density for the Ca2+-sensing C-terminal EF hand in the unblocked PC2SI state. The states show altered interactions of lipids with the pore loop and TOP domain, thus reflecting the functional diversity of PC2 at different locations, owing to different membrane compositions.

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Figure 1: Segmented map volumes showing PC2 protomers of the 4.2-Å-resolution structure (PC2MI) and the 4.3-Å-resolution structure (PC2SI).
Figure 2: Ion-translocation pathway in PC2MI and PC2SI.
Figure 3: Cation-binding sites in PC2.
Figure 4: N-glycosylation and tetramer interactions of PC2MI and PC2SI.
Figure 5: Lipid and fatty acid coordination in PC2.
Figure 6: Schematic representation of the multi-ion mode of PC2MI and single-ion mode of PC2SI.

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Acknowledgements

Work in the laboratory of C.Z. was supported by SFB699 and SFB807 from the Deutsche Forschungsgemeinschaft. We are thankful to D. Mills, J. Vonck, E. d'Imprima and R. Rachel for assistance with electron microscopy and data processing. We thank R. Krämer and C. Wetzel for critical reading of the manuscript and C. Loland for valuable suggestions.

M.G., A.C.W.P. and E.P.C. are funded by the SGC, a registered charity (number 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, the Canada Foundation for Innovation, Genome Canada, GlaxoSmithKline, Janssen, Lilly Canada, Merck & Co., the Novartis Research Foundation, the Ontario Ministry of Economic Development and Innovation, Pfizer, the São Paulo Research Foundation–FAPESP, Takeda, EU/EFPIA Innovative Medicines Initiative (IMI) Joint Undertaking (ULTRA-DD grant 115766) and the Wellcome Trust (092809/Z/10/Z). The OPIC electron microscopy facility was founded through a Wellcome Trust JIF award (060208/Z/00/Z) and is supported by a WT equipment grant (093305/Z/10/Z).

Work in the laboratory of J.T.H. is supported by Wellcome Trust Core Award grant 090532/Z/09/Z and by the European Research Council under the European Union Horizon 2020 Research and Innovation Programme (649053).

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  1. Lydia Kreuter

    Present address: Present address: Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA.,

Authors and Affiliations

  1. Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany

    Martin Wilkes, Daniel Rhinow, Friederike Joos & Werner Kühlbrandt

  2. Biophysics II, Faculty of Biology and Preclinical Medicine, Regensburg, Germany

    M Gregor Madej, Lydia Kreuter, Veronika Heinz, Silvia De Sanctis, Sabine Ruppel, Rebecca M Richter & Christine Ziegler

  3. Structural Genomics Consortium, University of Oxford, Oxford, UK

    Marina Grieben, Ashley C W Pike & Elisabeth P Carpenter

  4. Division of Structural Biology, Oxford Particle Imaging Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

    Juha T Huiskonen

  5. Department of Anatomy, Faculty of Biology and Preclinical Medicine, Regensburg, Germany

    Ralph Witzgall

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Contributions

C.Z. directed research; M.W. performed cloning, established the expression systems, and collected and processed cryo-EM data; M.W., L.K., R.M.R. and S.R. expressed and purified PC2; D.R. performed FIB-SEM tomography; F.J. carried out freeze fracture, thin sectioning and immunogold labeling; M.W. and V.H. performed negative-stain single-particle analysis; M.G.M. and S.D.S. carried out homology modeling; M.G., A.C.W.P., J.T.H. and E.P.C. contributed the structure of the closed conformation of PC2; M.G.M. and C.Z. performed structure determination and refinement and analyzed the data; and M.G.M., W.K., M.W., R.W., E.P.C. and C.Z. wrote the manuscript.

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Correspondence to Christine Ziegler.

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Integrated supplementary information

Supplementary Figure 1 PC2 expression in HEK293 GnTI– cells.

(a) Laser confocal microscopy after 48 h of PC2 expression. (b) Western blot analysis against the C‑terminal domain of PC2 of Triton-solubilized HEK 293 GnT I- cells (1) before induction, (2) 6 h, (3) 12 h, (4) 24 h, (5) 48 h, and (6) 72 h after induction. (c) Crystalloid formation in HEK 293 GnT I- cells in thin plastic sections overexpressing PC2 12 h to 72 h after induction. (d) Ion ablation tomography and 3D reconstruction reveals that crystalloids after 72 h are a honeycomb of tubular ER vesicles. (e) Immuno-gold labeling of the PC2 C‑terminal domain (C-term) in thin plastic sections of whole cells after 48 h. Gold labels are visible as small black dots.

Supplementary Figure 2 Purification and single-particle cryo-EM of human PC2.

(a) Gel filtration profile (Superose-6) of PC2 in amphipol A8-35 after purification on streptactin resin. The PC2 tetramer elutes at a retention volume of about 1.35 ml. Absorption was measured at 280 nm. (b) SDS-PAGE of amphipol reconstituted PC2. (c) Cryo-micrograph of PC2 tetramers recorded at a defocus of 2.5 μm. (d) Four representative 2D class averages.

Supplementary Figure 3 Single-particle processing.

267 010 particles were semi-automatically selected and subjected to 3D classification without symmetry imposed. The best class containing 162 074 particles was further classified with C4 symmetry, resulting in two good classes. Particles of both classes were combined and subjected to a 3D refinement, followed by particle polishing. Two distinct PC2 conformations were obtained by further 3D classification with C4 symmetry, followed by two independent 3D refinements of the two best 3D class averages.

Supplementary Figure 4 Local resolution and FSC curves of the 4.2-Å structure (PC2MI) and 4.3-Å structure (PC2SI).

Local map resolution (rainbow bar, in Å) was determined with RESMAP. (a) Exoplasmic, (b) side and (c) cytoplasmic view of PC2MI and respective views (h-g) of PC2SI. (d) Histogram of the local resolution indicates a mean resolution of ~4.0 Å for PC2MI and 4.0 - 4.5 Å PC2SI. (e) Correlation of the masked and unmasked map with the Phenix-refined model for the 4.2 Å and (k) for the 4.3 Å dataset. (f) Correlation of individual half-maps (blue and magenta) and summed map of the the 4.2 Å structure refined with Phenix (red) or REFMAC (green), compared to the respective correlation of the 4.3 Å structure (l).

Supplementary Figure 5 Cation binding in PC2 and comparison of the presumed open states to the closed PC2CL.

(a) Ca2+ (green spheres) and potential other cations (blue spheres) in PC2MI aligned with Ca2+ in CaVAB (yellow spheres, pdb entry code 4MVO) and TRPV6 (magenta, pdb entry code 5IWP). Gray spheres indicate the position of cations in PC2SI. (b) Spatial constraints in the translocation pathway of PC2 states with CaVAB (magenta, pdb entry code 4MVO). Radii along the translocation pathway of PC2MI (green) and PC2SI (blue) were calculated using the script HOLE. Residues forming narrow constrictions are indicated. Structural difference between PC2MI, PC2SI and the closed state PC2CL (Grieben et al., 2016): c) PC2MI and d) PC2SI are shown as worm models; colors and channel diameters indicate Cα r.m.s.d. relative to PC2CL (blue 0 Å, white 1.5 Å and red >3 Å, larger diameter stands for larger deviation; Cα of PC2CL is shown as black wire).

Supplementary Figure 6 Fatty acid binding affects C-terminal conformation.

Coordination of fatty acids (FA1-3) in the upper membrane leaflet and one to the lower leaflet in PC2MI (a) and PC2SI (b). The phosphatidic acid (PA) and the adjacent helices with prominent residues are indicated. (c) Cytoplasmic view on the PC2SI (4.3 Å) model. The PC2SI (4.3 Å) map contains continuous density (black mesh) that can be traced (orange pearl chain) to an additional globular density attributed to the EF-hand (transparent volume). (d) EF-hand causes a change in the coordination of the fatty acid network shown for one protomer (orange) shown as side-view of panel (c). (e) The structure of the EF-hand (pdbID: 2Y4Q) fitted into the additional density.

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Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 1559 kb)

Supplementary Video 1

Morphing between the single-ion state (PC2SI) and the closed state (PC2CL) (MOV 15270 kb)

Supplementary Video 2

Morphing between the single-ion state (PC2MI) and the closed state (PC2CL) (MOV 15484 kb)

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Wilkes, M., Madej, M., Kreuter, L. et al. Molecular insights into lipid-assisted Ca2+ regulation of the TRP channel Polycystin-2. Nat Struct Mol Biol 24, 123–130 (2017). https://doi.org/10.1038/nsmb.3357

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