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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The AF2 ChRmine model captures the overall fold, but its N-terminal region and extracellular loops differ from the cryo-EM structure, likely because of ChRmine's unique covalent Schiff base.
“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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ChR2 Mutants at L132 and T159 with Improved Operational Light Sensitivity for Vision Restoration
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Self-citationStructurally Distinct Cation Channelrhodopsins from Cryptophyte Algae
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Ion Channel Properties of a Cation Channelrhodopsin, Gt_CCR4
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Self-citationCrystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis
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Self-citationKalium rhodopsins: Natural light-gated potassium channelsPreprint
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- Govorunova EG Gou Y Sineshchekov OA Li H Wang Y Brown LS Xue M Spudich JL Kalium rhodopsins: natural lightgated potassium channels bioRxiv 2021 2021.09.17.460684
- Kishi KE Kim YS Fukuda M Kusakizako T Thadhani E Byrne EFX Paggi JM Ramakrishnan C Matsui TE Yamashita K Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine bioRxiv 2021 2021.08.15.456392 bioRxiv PMC7612760 35114111
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Self-citationProtein design accelerates the development and application of optogenetic tools
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Potassium-selective channelrhodopsins
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Practical considerations in an era of multicolor optogenetics
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Closed-loop experiments and brain machine interfaces with multiphoton microscopy
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Tetherless Optical Neuromodulation: Wavelength from Orange-red to Mid-infrared
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Kalium rhodopsins: Natural light-gated potassium channelsPreprint
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Structural insights into light-gating of potassium-selective channelrhodopsin
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Channel Gating in Kalium Channelrhodopsin Slow Mutants
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Self-citationOptogenetic Generation of Neural Firing Patterns with Temporal Shaping of Light Pulses
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Sensory photoreceptors in Chlamydomonas
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Cryo-EM structures of kalium channelrhodopsins KCRsPreprint
Zhang, M., Shan, Y., Li, X., Zhao, L., & Pei, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.09.515798 · Cited by 8 · see citing works
Integrated Bioelectronic and Optogenetic Methods to Study Brain–Body Circuits
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Optogenetic restoration of high-sensitivity vision using ChRmine- and ChroME-based channelrhodopsins
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Cryo-EM structure of a blue-shifted channelrhodopsin from Klebsormidium nitens
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Self-citationPump-like channelrhodopsins: Not just bridging the gap between ion pumps and ion channels
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A thin-film optogenetic visual prosthesisPreprint
Knudsen, E. B., Zappitelli, K. M., Brown, J., Reeder, J. T., Smith, K. S., Rostov, M., Choi, J., Rochford, A. E., Slager, N., Miura, S. K., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.31.526482 · Cited by 7 · see citing works
Optogenetics for light control of biological systems
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High-Speed All-Optical Neural Interfaces with 3D Temporally Focused Holography
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Channelrhodopsins: From Phototaxis to Optogenetics
Govorunova, E. G., & Sineshchekov, O. A. (2023) · Biochemistry (Moscow) · doi:10.1134/s0006297923100115 · Cited by 6 · see citing works
Optogenetic Neuromodulation in Inflammatory Pain
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Channelrhodopsins with distinct chromophores and binding patterns
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AlphaFold2 transmembrane protein structure prediction shinesPreprint
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Optogenetics: Pinpoint Light on Precise Neuromodulation
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A software platform for real-time and adaptive neuroscience experiments
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Self-citationAdvantages of human opsins in optogenetic visual restoration
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HulaCCR1, a pump-like cation channelrhodopsin discovered in a lake microbiome
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A large-scale curated and filterable dataset for cryo-EM foundation model pre-training
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Unique hydrogen-bonding network in a viral channelrhodopsin
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Direct Stimulation of Gastric Smooth Muscle Cells via Gq Proteins With Light
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- 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 · 2021: 4
- 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
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