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Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine
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Abstract
ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.
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“while the AF2 model of the channelrhodopsin ChRmine captures its overall fold, the modeled N-terminal region and extracellular loops deviate from its experimental high-resolution cryogenic electron microscopy (cryo-EM) structure (Fig. 2f), likely due to ChRmine’s unique covalent Schiff base feature41”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [41]
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VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Saitou, N., & Nei, M. (1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,959
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 46,047
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
Kumar, S., Stecher, G., & Tamura, K. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw054 · Cited by 43,923
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 21,430
MolProbity : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115
REFMAC 5 for the refinement of macromolecular crystal structures
Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M., Long, F., & Vagin, A. A. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911001314 · Cited by 8,415
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
Zheng, S. Q., Palovcak, E. J., Armache, J., Verba, K. A., Cheng, Y., & Agard, D. A. (2017) · Nature Methods · doi:10.1038/nmeth.4193 · Cited by 7,496
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Vogt, N. (2022) · Nature Methods · doi:10.1038/s41592-022-01433-2 · Cited by 5
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Hong, E., Glynn, C. J., Wang, Q., & Rao, S. (2022) · Biosensors · doi:10.3390/bios13010042 · Cited by 3
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Johnsen, K. A., Cruzado, N. A., Menard, Z. C., Willats, A. A., Charles, A. S., Markowitz, J. E., & Rozell, C. J. (2025) · Journal of Neuroscience · doi:10.1523/jneurosci.2239-24.2025 · Cited by 3
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Dixit, N., Pyari, G., Bansal, H., & Roy, S. (2025) · Scientific Reports · doi:10.1038/s41598-025-95355-6 · Cited by 2
Hwang, S., Utesch, T., Schattenberg, C. J., Vierock, J., & Sun, H. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c00356 · Cited by 2
Szundi, I., Muders, V., Funatogawa, C., Kliger, D. S., Schlesinger, R., & Heberle, J. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.03.019 · Cited by 2
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Sun, J., Ma, W., Li, X., Sun, Y., Hong, Q., & Zhang, J. (2025) · Nonlinear Dynamics · doi:10.1007/s11071-025-11082-7 · Cited by 2
Metadata
- Authors
- Kishi, K. E., Kim, Y. S., Fukuda, M., Inoue, M., Kusakizako, T., Wang, P. Y., Ramakrishnan, C., Byrne, E. F. X., Thadhani, E., Paggi, J. M., Matsui, T. E., Yamashita, K., Nagata, T., Konno, M., Quirin, S., Lo, M., Benster, T., Uemura, T., Liu, K., Shibata, M., Nomura, N., Iwata, S., Nureki, O., Dror, R. O., Inoue, K., Deisseroth, K., & Kato, H. E.
- Affiliations
- Komaba Institute for Science, The University of Tokyo (JP)
- Stanford University (US)
- The University of Tokyo (JP)
- MRC Laboratory of Molecular Biology (GB)
- Japan Science and Technology Agency (JP)
- Kyoto University (JP)
- Kanazawa University (JP)
- The Institute for Solid State Physics, The University of Tokyo (JP)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Deisseroth, Karl
- Kato, Hideaki E.
- ORCID
- Kim, Yoon Seok
- Fukuda, Masahiro
- Inoue, Masatoshi
- Kusakizako, Tsukasa
- Wang, Peter Y.
- Ramakrishnan, Charu
- Byrne, Eamon F.X.
- Thadhani, Elina
- Paggi, Joseph M.
- Matsui, Toshiki E.
- Yamashita, Keitaro
- Nagata, Takashi
- Konno, Masae
- Quirin, Sean
- Liu, Kehong
- Shibata, Mikihiro
- Nomura, Norimichi
- Iwata, So
- Nureki, Osamu
- Dror, Ron O.
- Inoue, Keiichi
- Deisseroth, Karl
- Kato, Hideaki E.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2022-02
- Volume
- 185
- Issue
- 4
- Pages
- 672-689.e23
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7612760
- OpenAlex
- W4221028201
- Cited by
- 149
- References
- 126
- Citations by year
- 2026: 19 · 2025: 40 · 2024: 23 · 2023: 39 · 2022: 24
- FWCI
- 13.93
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Institutional Repositories DataBase (IRDB) (submittedVersion)
- Kyoto University Research Information Repository (Kyoto University) (submittedVersion, cc-by)
- Funders
- Japan Agency for Medical Research and Development (JP18am0101079, JP20am0101115)
- UK Research and Innovation
- University of Tokyo
- Medical Research Council (MC_UP_A025_1012)
- Japan Society for the Promotion of Science (16H06294, 20K21122, 21H01771, 20K21383, 21H00247, 20K15754, 23K21092, 19H00923, JP21H01875, 19H05777, 20H05758)
- National Institute of Mental Health (R01MH075957, R37MH075957)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Photoreceptor and optogenetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ion channel regulation and function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Keywords
- channelrhodopsin, channel gating, cryo-EM structure, transmembrane helix 3, extracellular loop 1, optogenetics, protein engineering
- MeSH terms
- Channelrhodopsins, Animals, Female, Humans, Male, Mice, Inbred C57BL, Models, Molecular, Phylogeny, Schiff Bases, Structure-Activity Relationship, Ion Channel Gating, Rats, Sprague-Dawley, Cryoelectron Microscopy, Mice, Rats, HEK293 Cells, Sf9 Cells, Optogenetics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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