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Crystal structure of the channelrhodopsin light-gated cation channel

Abstract

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.

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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.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

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

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Acknowledgements

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.

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Authors

Contributions

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.

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Correspondence to Karl Deisseroth or Osamu Nureki.

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The authors declare no competing financial interests.

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Kato, H., Zhang, F., Yizhar, O. et al. Crystal structure of the channelrhodopsin light-gated cation channel. Nature 482, 369–374 (2012). https://doi.org/10.1038/nature10870

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