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.

Structure of a mammalian ryanodine receptor

Abstract

Ryanodine receptors (RyRs) mediate the rapid release of calcium (Ca2+) from intracellular stores into the cytosol, which is essential for numerous cellular functions including excitation–contraction coupling in muscle. Lack of sufficient structural detail has impeded understanding of RyR gating and regulation. Here we report the closed-state structure of the 2.3-megadalton complex of the rabbit skeletal muscle type 1 RyR (RyR1), solved by single-particle electron cryomicroscopy at an overall resolution of 4.8 Å. We fitted a polyalanine-level model to all 3,757 ordered residues in each protomer, defining the transmembrane pore in unprecedented detail and placing all cytosolic domains as tertiary folds. The cytosolic assembly is built on an extended α-solenoid scaffold connecting key regulatory domains to the pore. The RyR1 pore architecture places it in the six-transmembrane ion channel superfamily. A unique domain inserted between the second and third transmembrane helices interacts intimately with paired EF-hands originating from the α-solenoid scaffold, suggesting a mechanism for channel gating by Ca2+.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: The architecture of RyR1 at 4.8 Å.
Figure 2: RyR1 transmembrane pore and CTD.
Figure 3: The RyR1 conduction pathway.
Figure 4: The Ca2+-sensing machinery.
Figure 5: Intra- and inter-protomer interactions formed by cytosolic domains.

Accession codes

Primary accessions

Electron Microscopy Data Bank

Protein Data Bank

Data deposits

Cryo-EM reconstructions of RyR1 have been deposited in the Electron Microscopy Data Bank under the accession numbers EMD-6106 (EGTA-treated RyR1) and EMD-6107 (EGTA- and CIP-treated RyR1). The Cα coordinates of the model have been deposited in the Protein Data Bank (PDB) under accession number 3J8E.

References

  1. Zalk, R., Lehnart, S. E. & Marks, A. R. Modulation of the ryanodine receptor and intracellular calcium. Annu. Rev. Biochem. 76, 367–385 (2007)

    CAS  PubMed  Article  Google Scholar 

  2. Marx, S. O. et al. PKA phosphorylation dissociates FKBP12.6 from the calcium release channel (ryanodine receptor): defective regulation in failing hearts. Cell 101, 365–376 (2000)

    CAS  PubMed  Article  Google Scholar 

  3. Paolini, C., Protasi, F. & Franzini-Armstrong, C. The relative position of RyR feet and DHPR tetrads in skeletal muscle. J. Mol. Biol. 342, 145–153 (2004)

    CAS  PubMed  Article  Google Scholar 

  4. Meissner, G. & Lu, X. Dihydropyridine receptor-ryanodine receptor interactions in skeletal muscle excitation-contraction coupling. Biosci. Rep. 15, 399–408 (1995)

    CAS  PubMed  Article  Google Scholar 

  5. Stern, M. D., Pizarro, G. & Rios, E. Local control model of excitation-contraction coupling in skeletal muscle. J. Gen. Physiol. 110, 415–440 (1997)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  6. Marx, S. O., Ondrias, K. & Marks, A. R. Coupled gating between individual skeletal muscle Ca2+ release channels (ryanodine receptors). Science 281, 818–821 (1998)

    ADS  CAS  PubMed  Article  Google Scholar 

  7. Wehrens, X. H. et al. FKBP12.6 deficiency and defective calcium release channel (ryanodine receptor) function linked to exercise-induced sudden cardiac death. Cell 113, 829–840 (2003)

    CAS  PubMed  Article  Google Scholar 

  8. Liu, X. et al. Role of leaky neuronal ryanodine receptors in stress-induced cognitive dysfunction. Cell 150, 1055–1067 (2012)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  9. Andersson, D. C. et al. Ryanodine receptor oxidation causes intracellular calcium leak and muscle weakness in aging. Cell Metab. 14, 196–207 (2011)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  10. Bellinger, A. M. et al. Hypernitrosylated ryanodine receptor calcium release channels are leaky in dystrophic muscle. Nature Med. 15, 325–330 (2009)

    CAS  PubMed  Article  Google Scholar 

  11. Marks, A. R. Calcium cycling proteins and heart failure: mechanisms and therapeutics. J. Clin. Invest. 123, 46–52 (2013)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. Andersson, D. C. & Marks, A. R. Fixing ryanodine receptor Ca leak — a novel therapeutic strategy for contractile failure in heart and skeletal muscle. Drug Discov. Today Dis. Mech. 7, e151–e157 (2010)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  13. Serysheva, I. I. et al. Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc. Natl Acad. Sci. USA 105, 9610–9615 (2008)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  14. Fernández, I. S. et al. Molecular architecture of a eukaryotic translational initiation complex. Science 342, 1240585 (2013)

    PubMed  Article  CAS  Google Scholar 

  15. Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  16. Groves, M. R. & Barford, D. Topological characteristics of helical repeat proteins. Curr. Opin. Struct. Biol. 9, 383–389 (1999)

    CAS  PubMed  Article  Google Scholar 

  17. Xiong, L., Zhang, J. Z., He, R. & Hamilton, S. L. A. Ca2+-binding domain in RyR1 that interacts with the calmodulin binding site and modulates channel activity. Biophys. J. 90, 173–182 (2006)

    ADS  CAS  PubMed  Article  Google Scholar 

  18. Tung, C. C., Lobo, P. A., Kimlicka, L. & Van Petegem, F. The amino-terminal disease hotspot of ryanodine receptors forms a cytoplasmic vestibule. Nature 468, 585–588 (2010)

    ADS  CAS  PubMed  Article  Google Scholar 

  19. Holm, L. & Rosenstrom, P. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545–W549 (2010)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  20. Groves, M. R. & Barford, D. Topological characteristics of helical repeat proteins. Curr. Opin. Struct. Biol. 9, 383–389 (1999)

    CAS  PubMed  Article  Google Scholar 

  21. Huber, A. H., Nelson, W. J. & Weis, W. I. Three-dimensional structure of the armadillo repeat region of β-catenin. Cell 90, 871–882 (1997)

    CAS  PubMed  Article  Google Scholar 

  22. Yu, F. H., Yarov-Yarovoy, V., Gutman, G. A. & Catterall, W. A. Overview of molecular relationships in the voltage-gated ion channel superfamily. Pharmacol. Rev. 57, 387–395 (2005)

    CAS  PubMed  Article  Google Scholar 

  23. Payandeh, J., Scheuer, T., Zheng, N. & Catterall, W. A. The crystal structure of a voltage-gated sodium channel. Nature 475, 353–358 (2011)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  24. Liao, M., Cao, E., Julius, D. & Cheng, Y. Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504, 107–112 (2013)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  25. Owsianik, G., Talavera, K., Voets, T. & Nilius, B. Permeation and selectivity of TRP channels. Annu. Rev. Physiol. 68, 685–717 (2006)

    CAS  PubMed  Article  Google Scholar 

  26. Tripathy, A., Xu, L., Mann, G. & Meissner, G. Calmodulin activation and inhibition of skeletal muscle Ca2+ release channel (ryanodine receptor). Biophys. J. 69, 106–119 (1995)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  27. Volkov, A. G., Paula, S. & Deamer, D. W. Two mechanisms of permeation of small neutral molecules and hydrated ions across phospholipid bilayers. Bioelectrochem. Bioenerg. 42, 153–160 (1997)

    CAS  Article  Google Scholar 

  28. Jiang, Y. et al. X-ray structure of a voltage-dependent K+ channel. Nature 423, 33–41 (2003)

    ADS  CAS  PubMed  Article  Google Scholar 

  29. Bezprozvanny, I., Watras, J. & Ehrlich, B. E. Bell-shaped calcium-response curves of Ins(1,4,5)P3- and calcium-gated channels from endoplasmic reticulum of cerebellum. Nature 351, 751–754 (1991)

    ADS  CAS  Article  PubMed  Google Scholar 

  30. Ludtke, S. J., Serysheva, I. I., Hamilton, S. L. & Chiu, W. The pore structure of the closed RyR1 channel. Structure 13, 1203–1211 (2005)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  31. Samsó, M., Wagenknecht, T. & Allen, P. D. Internal structure and visualization of transmembrane domains of the RyR1 calcium release channel by cryo-EM. Nature Struct. Mol. Biol. 12, 539–544 (2005)

    Article  CAS  Google Scholar 

  32. Yuchi, Z., Lau, K. & Van Petegem, F. Disease mutations in the ryanodine receptor central region: crystal structures of a phosphorylation hot spot domain. Structure 20, 1201–1211 (2012)

    CAS  PubMed  Article  Google Scholar 

  33. Sharma, P. et al. Structural determination of the phosphorylation domain of the ryanodine receptor. FEBS J. 279, 3952–3964 (2012)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  34. Marks, A. R., Fleischer, S. & Tempst, P. Surface topography analysis of the ryanodine receptor/junctional channel complex based on proteolysis sensitivity mapping. J. Biol. Chem. 265, 13143–13149 (1990)

    CAS  PubMed  Article  Google Scholar 

  35. Yin, C. C., Han, H., Wei, R. & Lai, F. A. Two-dimensional crystallization of the ryanodine receptor Ca2+ release channel on lipid membranes. J. Struct. Biol. 149, 219–224 (2005)

    CAS  PubMed  Article  Google Scholar 

  36. Woo, J.-S. et al. Structural and functional insights into the B30.2/SPRY domain. EMBO J. 25, 1353–1363 (2006)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  37. Brillantes, A. B. et al. Stabilization of calcium release channel (ryanodine receptor) function by FK506-binding protein. Cell 77, 513–523 (1994)

    CAS  PubMed  Article  Google Scholar 

  38. Gaburjakova, M. et al. FKBP12 binding modulates ryanodine receptor channel gating. J. Biol. Chem. 276, 16931–16935 (2001)

    CAS  PubMed  Article  Google Scholar 

  39. Lau, K. & van Petegem, F. Crystal structures of wild type and disease mutant forms of the ryanodine receptor SPRY2 domain. Nature Comm. 5, 5937 (2014)

    Article  CAS  Google Scholar 

  40. Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60, 2256–2268 (2004)

    CAS  PubMed  Article  Google Scholar 

  41. Xin, H. B., Timerman, A. P., Onoue, H., Wiederrecht, G. J. & Fleischer, S. Affinity purification of the ryanodine receptor/calcium release channel from fast twitch skeletal muscle based on its tight association with FKBP12. Biochem. Biophys. Res. Commun. 214, 263–270 (1995)

    CAS  PubMed  Article  Google Scholar 

  42. Dubochet, J. et al. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129–228 (1988)

    CAS  PubMed  Article  Google Scholar 

  43. Wagenknecht, T., Frank, J., Boublik, M., Nurse, K. & Ofengand, J. Direct localization of the tRNA–anticodon interaction site on the Escherichia coli 30 S ribosomal subunit by electron microscopy and computerized image averaging. J. Mol. Biol. 203, 753–760 (1988)

    CAS  PubMed  Article  Google Scholar 

  44. Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005)

    CAS  PubMed  Article  Google Scholar 

  45. Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nature Methods 10, 584–590 (2013)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  46. Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 http://dx.doi.org/10.1006/jsbi.1996.0030 (1996)

    CAS  PubMed  Article  Google Scholar 

  47. Langlois, R. et al. Automated particle picking for low-contrast macromolecules in cryo-electron microscopy. J. Struct. Biol. 186, 1–7 (2014)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  48. Scheres, S. H. A Bayesian view on cryo-EM structure determination. J. Mol. Biol. 415, 406–418 (2012)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. Reiken, S. et al. PKA phosphorylation activates the calcium release channel (ryanodine receptor) in skeletal muscle: defective regulation in heart failure. J. Cell Biol. 160, 919–928 (2003)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  50. Chen, S. et al. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135, 24–35 (2013)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003)

    CAS  PubMed  Article  Google Scholar 

  52. Pintilie, G. D., Zhang, J., Goddard, T. D., Chiu, W. & Gossard, D. C. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J. Struct. Biol. 170, 427–438 (2010)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  53. Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)

    CAS  PubMed  Article  Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  55. McGuffin, L. J., Bryson, K. & Jones, D. T. The PSIPRED protein structure prediction server. Bioinformatics 16, 404–405 (2000)

    CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgements

We thank R. Axel for discussions and M. Thomas for assistance with the preparation of illustrations. This work was supported by grants from the National Institutes of Health (R01AR060037 and R01HL061503 to A.R.M., U54GM095315 to W.A.H., R01GM29169 to J.F.), and the Howard Hughes Medical Institute (to J.F.). R.Z. was a fellow of the American Heart Association (0625919T), and O.B.C. was supported by an overseas biomedical fellowship (NHMRC; Australia) and a Charles H. Revson Senior Fellowship (Charles H. Revson Foundation).

Author information

Authors and Affiliations

Authors

Contributions

A.R.M. conceived the project, designed experiments, analysed data and wrote the manuscript. W.A.H. conceived the project, designed experiments, analysed data and wrote the manuscript. J.F. designed the cryo-EM experiments, analysed data and wrote the manuscript. R.Z. designed experiments, isolated the RyR1 used in this work, analysed data and wrote the manuscript. O.B.C. designed experiments, analysed data, built the atomic model and wrote the manuscript. F.M. designed experiments. A.G. designed experiments and conducted the cryo-EM experiments, including data acquisition and processing, and wrote the manuscript. R.A.G. conducted the cryo-EM experiments. S.R. conducted phospho-RyR immunoblot experiments.

Corresponding authors

Correspondence to Wayne A. Hendrickson, Joachim Frank or Andrew R. Marks.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Skeletal muscle RyR1 purification.

a, Coomassie blue staining of SDS–PAGE showing molecular weight standards (MWS), CHAPS-solubilized sarcoplasmic reticulum membrane (SR), RyR1 eluted with calstabin2 from a glutathione S-transferase (GST)–calstabin1 affinity chromatography column (AC), the eluted RyR1 from fast protein liquid chromatography (FPLC) size-exclusion chromatograph (SEC). b, FPLC plot showing the RyR1 peak at 7 ml elution and the excess calstabin2 (Cs2) peak at 12 ml elution. c, Immunoblot analysis of CIP-treated RyR1 probed at indicated time points with (from bottom) anti-RyR1 (34C) antibody, anti-phosphotyrosine antibody (pTyr; Abcam ab10321), anti-phosphothreonine antibody (pThr; Abcam ab79851), anti-phosphoserine antibody (pSer; Abcam ab9332) and anti-RyR phospho-specific antibody (RyR1-pS2843) that recognizes the PKA phosphorylated site on RyR1.

Extended Data Figure 2 Particle picking and two-dimensional class averages.

a, Sample micrograph of the RyR1-CIP-EGTA data set after motion correction, with red boxes around the particles picked by Autopicker47. Scale bar, 500 Å. b, Sample power spectrum of a twice-decimated micrograph after motion correction. c, Euler angle distribution before symmetry was imposed of the particles that went into the CIP-treated data set final reconstruction. Latitude (radial distance) corresponds to θ from 0 to 90°. Longitude (position on the circle) corresponds to ϕ, from 0 to 360°. The dots colour and area represent the number of particles in each view. d, Two-dimensional projections of the final CIP-treated map (upper rows; red lines) compared to their respective reference-free two-dimensional class averages (lower rows).

Extended Data Figure 3 Classification and protomer boundaries.

a, Classification of the RyR1-EGTA data set. First row, refined volume with all particles. Second row, primary classification with a number of classes (K = 10) giving rise to two major classes, one refined to 4.8 Å (blue box) and one refined to 5.0 Å (green box). This class (green box) was subclassified with K = 10 (third row), and yielded one class with a missing or disordered cytosolic portion of a protomer (red box). b, Classification of the RyR1-EGTA-CIP-treated data set with K = 8. Class 8 (purple box) was refined to 5.0 Å. c, Views from the cytosol, membrane plane and lumen of the RyR1 model superimposed with a difference map between the full tetramer map (blue box) and the map with the cytosolic region of one protomer missing or disordered (red box).

Extended Data Figure 4 RyR1 cryo-EM local resolution map.

a, Gold-standard FSC curve for the three-dimensional reconstructions, marked with resolutions corresponding to FSC = 0.143. b, Cytosolic, membrane plane and luminal views of RyR1 (EGTA- and CIP-treated data set) local resolution distribution from 4 (blue) to 6 (red) Å resolution. c, Local resolution distribution through a slab of density coincident with channel axis. d, Same slab as c for the EGTA-treated without CIP. e, Slices through the volume of the CIP-EGTA data set (top) and EGTA data set (bottom). Slice direction and number are indicated on the images.

Extended Data Figure 5 Representative densities of RyR1-selected regions.

ae, Representative density (grey mesh) in selected regions of the map. The protomers are represented as Cα traces, in different colours for clarity, with enlarged views of the following regions: calstabin2 (a), the bridge solenoid (b), NTD (c), the pore region (d) and S6 (e).

Extended Data Figure 6 RyR1 local model to map correlation.

a, Cytosolic, membrane plane and luminal views of the local correlation (calculated in a 5 × 5 voxel sliding window) between a map calculated from the model (filtered to 5 Å) and the density map of dephosphorylated RyR1, depicted in spectral colouring from 0.7 (red) to 1 (blue). b, c, Local model/density map correlation within a slab of density through the plane of the membrane, highlighting the unmodelled rod of density on the periphery of the transmembrane region (b) and a slab coinciding with the channel axis (c).

Extended Data Figure 7 α- solenoid subdomains.

RyR1 density map (grey semitransparent surface) superimposed with the α-solenoid scaffold of RyR1. a, Core of the α-solenoid scaffold (insertions and elaborations not shown). Green, bridging solenoid; blue, NTD solenoid; red, core solenoid. b, Alignment of NTD with an α-solenoid structure (PDB code 3NMX). c, Alignment of core solenoid with an α-solenoid structure (PDB code 1G3J). d, Overlay of bridging solenoid with an α-solenoid structure (PDB code 1WA5). In bd, RyR1 α-solenoid repeats are depicted in spectral colouring from blue (N terminus) to red (C terminus), and the aligned α-solenoid protein is represented in dark grey.

Extended Data Figure 8 Architecture of bridging and core solenoids.

a, Density map of RyR1 in dark blue mesh superimposed with the bridging solenoid shown in detail on right, as labelled. b, Two views of the interaction of the core solenoid (spectral colouring) containing the putative Ca2+-binding domain with CTD (grey) as labelled.

Extended Data Figure 9 Calstabin2-binding site.

Views in the membrane plane and cytosol of RyR1 with enlarged views of calstabin2 (yellow) bound to RyR1. SPRY1 is depicted in light blue, SPRY2 in cyan, the bridging solenoid in green and the calstabin binding helix in purple.

Extended Data Figure 10 Putative Ca2+-binding domain in RyR1.

a, Sequence alignment of rabbit RyR1–3 with the C-lobe of human calmodulin (hCaM). b, Structural alignment of the C-lobe of yeast calmodulin with the model of RyR1.

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Zalk, R., Clarke, O., des Georges, A. et al. Structure of a mammalian ryanodine receptor. Nature 517, 44–49 (2015). https://doi.org/10.1038/nature13950

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature13950

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

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