Skip to main content

Thank you for visiting 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.

  • Article
  • Published:

Crystal structure of the channelrhodopsin light-gated cation channel


Channelrhodopsins (ChRs) are light-gated cation channels derived from algae that have shown experimental utility in optogenetics; for example, neurons expressing ChRs can be optically controlled with high temporal precision within systems as complex as freely moving mammals. Although ChRs have been broadly applied to neuroscience research, little is known about the molecular mechanisms by which these unusual and powerful proteins operate. Here we present the crystal structure of a ChR (a C1C2 chimaera between ChR1 and ChR2 from Chlamydomonas reinhardtii) at 2.3 Å resolution. The structure reveals the essential molecular architecture of ChRs, including the retinal-binding pocket and cation conduction pathway. This integration of structural and electrophysiological analyses provides insight into the molecular basis for the remarkable function of ChRs, and paves the way for the precise and principled design of ChR variants with novel properties.

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

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Structure of C1C2 and comparison with BR.
Figure 2: Structural comparison of the retinal-binding pocket between C1C2 and BR.
Figure 3: The protonated Schiff base and its counterions in C1C2 and BR.
Figure 4: Cation-conducting pathway formed by TM1, 2, 3 and 7.
Figure 5: Two constriction sites on the cytoplasmic side of C1C2 in the closed state.
Figure 6: Distribution of known mutations and possible candidates for future mutations.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Data have been deposited at the Protein Data Bank under accession number 3UG9.


  1. Oesterhelt, D. & Stoeckenius, W. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat. New Biol. 233, 149–152 (1971)

    Article  CAS  Google Scholar 

  2. Matsuno-Yagi, A. & Mukohata, Y. Two possible roles of bacteriorhodopsin; a comparative study of strains of Halobacterium halobium differing in pigmentation. Biochem. Biophys. Res. Commun. 78, 237–243 (1977)

    Article  CAS  Google Scholar 

  3. Nagel, G. et al. Channelrhodopsin-1: a light-gated proton channel in green algae. Science 296, 2395–2398 (2002)

    Article  ADS  CAS  Google Scholar 

  4. Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G. & Deisseroth, K. Millisecond-timescale, genetically targeted optical control of neural activity. Nature Neurosci. 8, 1263–1268 (2005)

    Article  CAS  Google Scholar 

  5. Li, X. et al. Fast noninvasive activation and inhibition of neural and network activity by vertebrate rhodopsin and green algae channelrhodopsin. Proc. Natl Acad. Sci. USA 102, 17816–17821 (2005)

    Article  ADS  CAS  Google Scholar 

  6. Nagel, G. et al. Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses. Curr. Biol. 15, 2279–2284 (2005)

    Article  MathSciNet  CAS  Google Scholar 

  7. Ishizuka, T., Kakuda, M., Araki, R. & Yawo, H. Kinetic evaluation of photosensitivity in genetically engineered neurons expressing green algae light-gated channels. Neurosci. Res. 54, 85–94 (2006)

    Article  CAS  Google Scholar 

  8. Bi, A. et al. Ectopic expression of a microbial-type rhodopsin restores visual responses in mice with photoreceptor degeneration. Neuron 50, 23–33 (2006)

    Article  CAS  Google Scholar 

  9. Zhang, F., Wang, L. P., Boyden, E. S. & Deisseroth, K. Channelrhodopsin-2 and optical control of excitable cells. Nature Methods 3, 785–792 (2006)

    Article  CAS  Google Scholar 

  10. Yizhar, O., Fenno, L. E., Davidson, T. J., Mogri, M. & Deisseroth, K. Optogenetics in neural systems. Neuron 71, 9–34 (2011)

    Article  CAS  Google Scholar 

  11. Fenno, L., Yizhar, O. & Deisseroth, K. The development and application of optogenetics. Annu. Rev. Neurosci. 34, 389–412 (2011)

    Article  CAS  Google Scholar 

  12. Muller, M., Bamann, C., Bamberg, E. & Kuhlbrandt, W. Projection structure of channelrhodopsin-2 at 6 Å resolution by electron crystallography. J. Mol. Biol. 414, 86–95 (2011)

    Article  Google Scholar 

  13. Gunaydin, L. A. et al. Ultrafast optogenetic control. Nature Neurosci. 13, 387–392 (2010)

    Article  CAS  Google Scholar 

  14. Berndt, A., Yizhar, O., Gunaydin, L. A., Hegemann, P. & Deisseroth, K. Bi-stable neural state switches. Nature Neurosci. 12, 229–234 (2009)

    Article  CAS  Google Scholar 

  15. Berndt, A. et al. High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels. Proc. Natl Acad. Sci. USA 108, 7595–7600 (2011)

    Article  ADS  CAS  Google Scholar 

  16. Kleinlogel, S. et al. Ultra light-sensitive and fast neuronal activation with the Ca2+-permeable channelrhodopsin CatCh. Nature Neurosci. 14, 513–518 (2011)

    Article  CAS  Google Scholar 

  17. Yizhar, O. et al. Neocortical excitation/inhibition balance in information processing and social dysfunction. Nature 477, 171–178 (2011)

    Article  ADS  CAS  Google Scholar 

  18. Wen, L. et al. Opto-current-clamp actuation of cortical neurons using a strategically designed channelrhodopsin. PLoS ONE 5, e12893 (2010)

    Article  ADS  Google Scholar 

  19. Lin, J. Y., Lin, M. Z., Steinbach, P. & Tsien, R. Y. Characterization of engineered channelrhodopsin variants with improved properties and kinetics. Biophys. J. 96, 1803–1814 (2009)

    Article  ADS  CAS  Google Scholar 

  20. Wang, H. et al. Molecular determinants differentiating photocurrent properties of two channelrhodopsins from Chlamydomonas. J. Biol. Chem. 284, 5685–5696 (2009)

    Article  CAS  Google Scholar 

  21. Kawate, T. & Gouaux, E. Fluorescence-detection size-exclusion chromatography for precrystallization screening of integral membrane proteins. Structure 14, 673–681 (2006)

    Article  CAS  Google Scholar 

  22. Tsunoda, S. P. & Hegemann, P. Glu 87 of channelrhodopsin-1 causes pH-dependent color tuning and fast photocurrent inactivation. Photochem. Photobiol. 85, 564–569 (2009)

    Article  CAS  Google Scholar 

  23. Matsui, Y. et al. Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin. J. Mol. Biol. 324, 469–481 (2002)

    Article  CAS  Google Scholar 

  24. Stenkamp, R. E. Alternative models for two crystal structures of bovine rhodopsin. Acta Crystallogr. D 64, 902–904 (2008)

    Article  CAS  Google Scholar 

  25. Mittelmeier, T. M., Boyd, J. S., Lamb, M. R. & Dieckmann, C. L. Asymmetric properties of the Chlamydomonas reinhardtii cytoskeleton direct rhodopsin photoreceptor localization. J. Cell Biol. 193, 741–753 (2011)

    Article  CAS  Google Scholar 

  26. Nack, M. et al. The DC gate in Channelrhodopsin-2: crucial hydrogen bonding interaction between C128 and D156. Photochem. Photobiol. Sci. 9, 194–198 (2010)

    Article  CAS  Google Scholar 

  27. Lanyi, J. K. Proton transfers in the bacteriorhodopsin photocycle. Biochim. Biophys. Acta 1757, 1012–1018 (2006)

    Article  CAS  Google Scholar 

  28. Bas, D. C., Rogers, D. M. & Jensen, J. H. Very fast prediction and rationalization of pKa values for protein–ligand complexes. Proteins 73, 765–783 (2008)

    Article  CAS  Google Scholar 

  29. Sugiyama, Y. et al. Photocurrent attenuation by a single polar-to-nonpolar point mutation of channelrhodopsin-2. Photochem. Photobiol. Sci. 8, 328–336 (2009)

    Article  CAS  Google Scholar 

  30. Ruffert, K. et al. Glutamate residue 90 in the predicted transmembrane domain 2 is crucial for cation flux through channelrhodopsin 2. Biochem. Biophys. Res. Commun. 410, 737–743 (2011)

    Article  CAS  Google Scholar 

  31. Plazzo, A. P. et al. Bioinformatic and mutational analysis of channelrhodopsin-2 cation conducting pathway. J. Biol. Chem. (2011)

  32. Radu, I. et al. Conformational changes of channelrhodopsin-2. J. Am. Chem. Soc. 131, 7313–7319 (2009)

    Article  CAS  Google Scholar 

  33. Lasogga, L., Rettig, W., Otto, H., Wallat, I. & Bricks, J. Model systems for the investigation of the opsin shift in bacteriorhodopsin. J. Phys. Chem. A 114, 2179–2188 (2010)

    Article  CAS  Google Scholar 

  34. Ritter, E., Stehfest, K., Berndt, A., Hegemann, P. & Bartl, F. J. Monitoring light-induced structural changes of Channelrhodopsin-2 by UV-visible and Fourier transform infrared spectroscopy. J. Biol. Chem. 283, 35033–35041 (2008)

    Article  CAS  Google Scholar 

  35. Bamann, C., Kirsch, T., Nagel, G. & Bamberg, E. Spectral characteristics of the photocycle of channelrhodopsin-2 and its implication for channel function. J. Mol. Biol. 375, 686–694 (2008)

    Article  CAS  Google Scholar 

  36. Bamann, C., Gueta, R., Kleinlogel, S., Nagel, G. & Bamberg, E. Structural guidance of the photocycle of channelrhodopsin-2 by an interhelical hydrogen bond. Biochemistry 49, 267–278 (2010)

    Article  CAS  Google Scholar 

  37. Petřek, M. et al. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7, 316 (2006)

    Article  Google Scholar 

  38. Hirata, K. et al. New micro-beam beamline at SPring-8, targeting at protein microcrystallography. AIP Conference Proceedings 1234, 893–896 (2010)

    ADS  Google Scholar 

  39. Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)

    Article  CAS  Google Scholar 

  40. Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2006)

    Article  Google Scholar 

  41. Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772–1779 (2002)

    Article  Google Scholar 

  42. de La Fortelle, E. & Bricogne, G. Maximumlikelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472–494 (1997)

    Article  CAS  Google Scholar 

  43. Kelley, L. A. & Sternberg, M. J. Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 4, 363–371 (2009)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  45. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    Article  CAS  Google Scholar 

Download references


We thank Y. Tanaka, T. Higuchi, M. Hattori and H. Nishimasu for useful discussions; T. Hino for technical support; and the beamline staff members at BL32XU of SPring-8 (Hyogo, Japan) and at X06SA of the Swiss Light Source (Villigen, Switzerland) for technical help during data collection. This work was supported by the Japan Society for the Promotion of Science (JSPS) through its “Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST program)” to O.N., by a grant for the National Project on Protein Structural and Functional Analyses from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) to O.N., and by a Grant-in-Aid for Scientific Research (S) from MEXT to O.N. F.Z. is supported by the McKnight Foundation. K.D. is supported by the Gatsby Charitable Foundation and the Keck, Snyder, Woo, and Yu Foundations, as well as by the National Institutes of Health, and the Defense Advanced Research Project Agency Reorganization and Plasticity to Accelerate Injury Recovery (DARPA REPAIR) program.

Author information

Authors and Affiliations



H.E.K. performed the structural determination of C1C2, prepared the mutants, measured the spectral property of C1C2 and wrote the paper. A.D.M. performed the electrophysiological analyses of C1C2. J.I. helped A.D.M. to take pictures of C1C2 and to determine membrane expression. Y.A. helped A.D.M. to perform patch-clamp experiments. T.T., T.N., R.I. and O.N. assisted with the structural determination. K.H. assisted with the data collection of C1C2. O.N., F.Z. and K.D. conceived the study; F.Z., O.Y. and K.D. helped to organize the project; S.H. and P.H. provided input on structural considerations; and C.R. with K.D. constructed the final C1C2 that enabled crystal structure determination. All authors discussed the results and commented on the manuscript. O.N. and K.D. supervised all aspects of the work and wrote/edited the manuscript.

Corresponding authors

Correspondence to Karl Deisseroth or Osamu Nureki.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Notes, Supplementary Figures 1-15 with legends and Supplementary Tables 1-2. (PDF 3187 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kato, H., Zhang, F., Yizhar, O. et al. Crystal structure of the channelrhodopsin light-gated cation channel. Nature 482, 369–374 (2012).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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.


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