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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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Cites
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
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Roe, D. R., & Cheatham, T. E. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400341p · Cited by 7,466
In situ click chemistry generation of cyclooxygenase-2 inhibitors
Bhardwaj, A., Kaur, J., Wuest, M., & Wuest, F. (2017) · Nature Communications · doi:10.1038/s41467-016-0009-6 · Cited by 7,448
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2016) · Nature Methods · doi:10.1038/nmeth.4067 · Cited by 7,334
Electrostatics of nanosystems: Application to microtubules and the ribosome
Baker, N., Sept, D., Joseph, S., Holst, M., & McCammon, J. A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.181342398 · Cited by 7,125
Deciphering key features in protein structures with the new ENDscript server
Robert, X., & Gouet, P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku316 · Cited by 7,053
UCSF ChimeraX: Meeting modern challenges in visualization and analysis
Goddard, T. D., Huang, C. C., Meng, E. C., Pettersen, E. F., Couch, G. S., Morris, J. H., & Ferrin, T. E. (2018) · Protein Science · doi:10.1002/pro.3235 · Cited by 5,267
Automated electron microscope tomography using robust prediction of specimen movements
Mastronarde, D. N. (2005) · Journal of Structural Biology · doi:10.1016/j.jsb.2005.07.007 · Cited by 5,136
CTFFIND4: Fast and accurate defocus estimation from electron micrographs
Rohou, A. L., & Grigorieff, N. (2015) · Journal of Structural Biology · doi:10.1016/j.jsb.2015.08.008 · Cited by 4,759
New tools for automated high-resolution cryo-EM structure determination in RELION-3
Zivanov, J., Nakane, T., Forsberg, B., Kimanius, D., Hagen, W., Lindahl, E., & Scheres, S. (2018) · eLife · doi:10.7554/elife.42166 · Cited by 4,377
Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types
Klauda, J. B., Venable, R., Freites, J. A., O'Connor, J. W., Tobias, D., Mondragon-Ramirez, C., Vorobyov, I., MacKerell, A. D., & Pastor, R. (2010) · Journal of Physical Chemistry B · doi:10.1021/jp101759q · Cited by 4,369
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
Dolinsky, T. J., Nielsen, J. E., McCammon, J. A., & Baker, N. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh381 · Cited by 3,517
Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025
Channelrhodopsin-2, a directly light-gated cation-selective membrane channel
Nagel, G., Szellas, T., Huhn, W., Kateriya, S., Adeishvili, N., Berthold, P. R., Ollig, D., Hegemann, P., & Bamberg, E. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1936192100 · Cited by 2,730
Independent optical excitation of distinct neural populations
Klapoetke, N. C., Murata, Y., Kim, S. S., Pulver, S. R., Birdsey-Benson, A., Cho, Y. K., Morimoto, T. K., Chuong, A. S., Carpenter, E. J., Tian, Z., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2836 · Cited by 2,344
Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps
Levin, L. A., Mendoza, G., Grupe, B., Gonzalez, J. P., Jellison, B. M., Rouse, G. W., Thurber, A. R., & Warén, A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0131080 · Cited by 2,166
No evidence that carotenoid pigments boost either immune or antioxidant defenses in a songbird
Koch, R. E., Kavazis, A. N., Hasselquist, D., Hood, W. R., Zhang, Y., Toomey, M. B., & Hill, G. E. (2018) · Nature Communications · doi:10.1038/s41467-018-02974-x · Cited by 1,924
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction
Bkhetan, Z. A., & Plewczyński, D. (2018) · Scientific Reports · doi:10.1038/s41598-018-23276-8 · Cited by 1,672
Optogenetics: 10 years of microbial opsins in neuroscience
Deisseroth, K. A. (2015) · Nature Neuroscience · doi:10.1038/nn.4091 · Cited by 1,335
Self-citationLong-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning.
Hopkins, C. W., Grand, S. M. L., Walker, R. C., & Roitberg, A. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct5010406 · Cited by 1,317
PROMALS3D: a tool for multiple protein sequence and structure alignments
Pei, J., Kim, B., & Grishin, N. V. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn072 · Cited by 1,286
Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms
Ernst, O. P., Lodowski, D. T., Elstner, M., Hegemann, P., Brown, L. S., & Kandori, H. (2013) · Chemical Reviews · doi:10.1021/cr4003769 · Cited by 1,171
Channelrhodopsin-1: A Light-Gated Proton Channel in Green Algae
Nagel, G., Ollig, D., Fuhrmann, M., Kateriya, S., Musti, A. M., Bamberg, E., & Hegemann, P. (2002) · Science · doi:10.1126/science.1072068 · Cited by 1,166
Mariani, V., Biasini, M., Barbato, A., & Schwede, T. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt473 · Cited by 1,138
Beglov, D., & Roux, B. (1994) · The Journal of Chemical Physics · doi:10.1063/1.466711 · Cited by 990
A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis
Zivanov, J., Nakane, T., & Scheres, S. H. W. (2018) · IUCrJ · doi:10.1107/s205225251801463x · Cited by 879
Pebay‐Peyroula, E., Rummel, G., Rosenbusch, J. P., & Landau, E. M. (1997) · Science · doi:10.1126/science.277.5332.1676 · Cited by 861
Self-Assembly of Discoidal Phospholipid Bilayer Nanoparticles with Membrane Scaffold Proteins
Bayburt, T. H., Grinkova, Y. V., & Sligar, S. G. (2002) · Nano Letters · doi:10.1021/nl025623k · Cited by 810
Zivanov, J., Nakane, T., & Scheres, S. H. W. (2020) · IUCrJ · doi:10.1107/s2052252520000081 · Cited by 804
Sievers, F., & Higgins, D. G. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0313s48 · Cited by 784
Gunaydin, L. A., Yizhar, O., Berndt, A., Sohal, V. S., Deisseroth, K., & Hegemann, P. (2010) · Nature Neuroscience · doi:10.1038/nn.2495 · Cited by 757
Self-citationHighly confined ions store charge more efficiently in supercapacitors
Merlet, C., Péan, C., Rotenberg, B., Madden, P. A., Daffos, B., Taberna, P., Simon, P., & Salanne, M. (2013) · Nature Communications · doi:10.1038/ncomms3701 · Cited by 746
Kawate, T., & Gouaux, E. (2006) · Structure · doi:10.1016/j.str.2006.01.013 · Cited by 732
Partial recovery of visual function in a blind patient after optogenetic therapy
Sahel, J.-A., Boulanger-Scemama, E., Pagot, C., Arleo, A., Galluppi, F., Martel, J. N., Esposti, S. D., Delaux, A., de Saint Aubert, J.-B., de Montleau, C., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01351-4 · Cited by 700
Cortical layer-specific critical dynamics triggering perception
Marshel, J. H., Kim, Y. S., Machado, T. A., Quirin, S., Benson, B., Kadmon, J., Raja, C., Chibukhchyan, A., Ramakrishnan, C., Inoue, M., et al. (2019) · Science · doi:10.1126/science.aaw5202 · Cited by 652
Self-citationStructure of the Light-Driven Chloride Pump Halorhodopsin at 1.8 Å Resolution
Kolbe, M., Besir, H., Essen, L., & Oesterhelt, D. (2000) · Science · doi:10.1126/science.288.5470.1390 · Cited by 543
Crystal structure of the channelrhodopsin light-gated cation channel
KATO, H. E., Zhang, F., Yizhar, O., Ramakrishnan, C., Nishizawa, T., Hirata, K., Ito, J., Aita, Y., Tsukazaki, T., Hayashi, S., et al. (2012) · Nature · doi:10.1038/nature10870 · Cited by 543
Self-citationRed-shifted optogenetic excitation: a tool for fast neural control derived from Volvox carteri
Zhang, F., Prigge, M., Beyrière, F., Tsunoda, S. P., Mattis, J., Yizhar, O., Hegemann, P., & Deisseroth, K. A. (2008) · Nature Neuroscience · doi:10.1038/nn.2120 · Cited by 540
Self-citationNanodiscs for structural and functional studies of membrane proteins
Denisov, I. G., & Sligar, S. G. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3195 · Cited by 526
Projections from neocortex mediate top-down control of memory retrieval
Rajasethupathy, P., Sankaran, S., Marshel, J. H., Kim, C. K., Ferenczi, E., Lee, S. Y., Berndt, A., Ramakrishnan, C., Jaffe, A., Lo, M., et al. (2015) · Nature · doi:10.1038/nature15389 · Cited by 509
Self-citationThe Microbial Opsin Family of Optogenetic Tools
Zhang, F., Vierock, J., Yizhar, O., Fenno, L. E., Tsunoda, S. P., Kianianmomeni, A., Prigge, M., Berndt, A., Cushman, J. C., Polle, J. E. W., et al. (2011) · Cell · doi:10.1016/j.cell.2011.12.004 · Cited by 507
Self-citationBraiman, M. S., Mogi, T., Marti, T., Stern, L. J., Khorana, H. G., & Rothschild, K. J. (1988) · Biochemistry · doi:10.1021/bi00423a002 · Cited by 491
A three-dimensional movie of structural changes in bacteriorhodopsin
Nango, E., Royant, A., Kubo, M., Nakane, T., Wickstrand, C., Kimura, T., Tanaka, T. U., Tono, K., Song, C., Tanaka, R., et al. (2016) · Science · doi:10.1126/science.aah3497 · Cited by 443
Self-citationSimultaneous fast measurement of circuit dynamics at multiple sites across the mammalian brain
Kim, C. K., Yang, S., Pichamoorthy, N., Young, N. P., Kauvar, I., Jennings, J. H., Lerner, T. N., Berndt, A., Lee, S. Y., Ramakrishnan, C., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3770 · Cited by 439
Self-citationA light-driven sodium ion pump in marine bacteria
Inoue, K., Ono, H., Abe‐Yoshizumi, R., Yoshizawa, S., Ito, H., Kogure, K., & Kandori, H. (2013) · Nature Communications · doi:10.1038/ncomms2689 · Cited by 410
Self-citationMolecular basis of transmembrane signalling by sensory rhodopsin II–transducer complex
Gordeliy, V., Labahn, J., Moukhametzianov, R., Efremov, R. G., Granzin, J., Schlesinger, R., Büldt, G., Savopol, T., Scheidig, A. J., Klare, J. P., et al. (2002) · Nature · doi:10.1038/nature01109 · Cited by 395
Structure-Guided Transformation of Channelrhodopsin into a Light-Activated Chloride Channel
Berndt, A., Lee, S. Y., Ramakrishnan, C., & Deisseroth, K. A. (2014) · Science · doi:10.1126/science.1252367 · Cited by 381
Self-citationConversion of Channelrhodopsin into a Light-Gated Chloride Channel
Wietek, J., Wiegert, J. S., Adeishvili, N., Schneider, F., Watanabe, H. C., Tsunoda, S. P., Vogt, A., Elstner, M., Oertner, T. G., & Hegemann, P. (2014) · Science · doi:10.1126/science.1249375 · Cited by 348
Fivenson, E. M., & Bernhardt, T. G. (2020) · mBio · doi:10.1128/mbio.00939-20 · Cited by 322
Cryo-EM single-particle structure refinement and map calculation using Servalcat
Yamashita, K., Palmer, C. M., Burnley, B. T., & Murshudov, G. N. (2021) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798321009475 · Cited by 321
Self-citationThe form and function of channelrhodopsin
Deisseroth, K. A., & Hegemann, P. (2017) · Science · doi:10.1126/science.aan5544 · Cited by 297
Self-citationGerwert, K. B., Souvignier, G., & Hess, B. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.24.9774 · Cited by 268
Inoue, M., Takeuchi, A., Manita, S., Horigane, S., Sakamoto, M., Kawakami, R., Yamaguchi, K., Otomo, K., Yokoyama, H., Kim, R., et al. (2019) · Cell · doi:10.1016/j.cell.2019.04.007 · Cited by 245
Self-citationCrystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore
Luecke, H., Schobert, B., Stagno, J. R., Imasheva, E. S., Wang, J. M., Balashov, S. P., & Lanyi, J. Κ. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807162105 · Cited by 235
Structural basis for Na+ transport mechanism by a light-driven Na+ pump
KATO, H. E., Inoue, K., Abe‐Yoshizumi, R., Kato, Y., Ono, H., Konno, M., Hososhima, S., Ishizuka, T., Hoque, M. R., Kunitomo, H., et al. (2015) · Nature · doi:10.1038/nature14322 · Cited by 234
Self-citationDeep brain optogenetics without intracranial surgery
Chen, R., Gore, F., Nguyen, Q.-A., Ramakrishnan, C., Patel, S., Kim, S. H., Raffiee, M., Kim, Y. S., Hsueh, B., Krook-Magnuson, E. I., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0679-9 · Cited by 233
Self-citationReal-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy
Shibata, M., Nishimasu, H., Kodera, N., Hirano, S., Ando, T., Uchihashi, T., & Nureki, O. (2017) · Nature Communications · doi:10.1038/s41467-017-01466-8 · Cited by 215
Self-citationStructural foundations of optogenetics: Determinants of channelrhodopsin ion selectivity
Berndt, A., Lee, S. Y., Wietek, J., Ramakrishnan, C., Steinberg, E. E., Rashid, A. J., Kim, H., Park, S., Santoro, A., Frankland, P. W., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1523341113 · Cited by 214
Self-citationStructural insights into ion conduction by channelrhodopsin 2
Volkov, O., Kovalev, K., Polovinkin, V., Borshchevskiy, V. I., Bamann, C., Astashkin, R., Marin, E., Popov, A. N., Balandin, T. G., Willbold, D., et al. (2017) · Science · doi:10.1126/science.aan8862 · Cited by 196
High frequency neural spiking and auditory signaling by ultrafast red-shifted optogenetics
Mager, T., de la Morena, D. L., Senn, V., Paladini, J., D’Errico, A., Feldbauer, K., Wrobel, C., Jung, S., Bodensiek, K., Rankovic, V., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04146-3 · Cited by 188
Fenno, L. E., Ramakrishnan, C., Kim, Y. S., Evans, K. E., Lo, M., Vesuna, S. S., Inoue, M., Cheung, K. Y. M., Yuen, E., Pichamoorthy, N., et al. (2020) · Neuron · doi:10.1016/j.neuron.2020.06.003 · Cited by 180
Self-citationFabs Enable Single Particle cryoEM Studies of Small Proteins
Wu, S., Avila-Sakar, A., Kim, J., Booth, D. S., Greenberg, C. H., Rossi, A., Liao, M., Li, X., Alian, A., Griner, S. L., et al. (2012) · Structure · doi:10.1016/j.str.2012.02.017 · Cited by 178
Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography
Weinert, T., Skopintsev, P., James, D., Dworkowski, F., Panepucci, E., Kekilli, D., Furrer, A., Brünle, S., Mous, S. T., Ozerov, D., et al. (2019) · Science · doi:10.1126/science.aaw8634 · Cited by 171
Color-tuned Channelrhodopsins for Multiwavelength Optogenetics
Prigge, M., Schneider, F., Tsunoda, S. P., Shilyansky, C., Wietek, J., Deisseroth, K. A., & Hegemann, P. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.391185 · Cited by 165
Self-citationTransient protonation changes in channelrhodopsin-2 and their relevance to channel gating
Lorenz, V., Resler, T., Krause, N., Nack, M., Gossing, M., von Mollard, G. F., Bamann, C., Bamberg, E., Schlesinger, R., & Heberle, J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219502110 · Cited by 163
Kühlbrandt, W. (2000) · Nature · doi:10.1038/35020654 · Cited by 162
Crystal structure of the red light-activated channelrhodopsin Chrimson
Oda, K., Vierock, J., Oishi, S., Rodriguez-Rozada, S., Taniguchi, R., Yamashita, K., Wiegert, J. S., Nishizawa, T., Hegemann, P., & Nureki, O. (2018) · Nature Communications · doi:10.1038/s41467-018-06421-9 · Cited by 152
Self-citationCrystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis
Kouyama, T., Kanada, S., Takeguchi, Y., Narusawa, A., Murakami, M., & Ihara, K. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.11.061 · Cited by 151
Structure of the bacteriorhodopsin mutant F219L N intermediate revealed by electron crystallography
Vonck, J. (2000) · The EMBO Journal · doi:10.1093/emboj/19.10.2152 · Cited by 124
Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes
Ran, T., Ozorowski, G., Gao, Y., Sineshchekov, O. A., Wang, W., Spudich, J. L., & Luecke, H. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913017575 · Cited by 123
Crystal structure of the natural anion-conducting channelrhodopsin GtACR1
Kim, Y. S., KATO, H. E., Yamashita, K., Ito, S., Inoue, K., Ramakrishnan, C., Fenno, L. E., Evans, K. E., Paggi, J. M., Dror, R. O., et al. (2018) · Nature · doi:10.1038/s41586-018-0511-6 · Cited by 111
Self-citationSridharan, S., Gajowa, M. A., Ogando, M. B., Jagadisan, U. K., Abdeladim, L., Sadahiro, M., Bounds, H. A., Hendricks, W. D., Turney, T. S., Tayler, I., et al. (2022) · Neuron · doi:10.1016/j.neuron.2022.01.008 · Cited by 104
Crystal structure of heliorhodopsin
Shihoya, W., Inoue, K., Singh, M. P., Konno, M., Hososhima, S., Yamashita, K., Ikeda, K., Higuchi, A., Izume, T., Okazaki, S., et al. (2019) · Nature · doi:10.1038/s41586-019-1604-6 · Cited by 102
Self-citationAtomistic design of microbial opsin-based blue-shifted optogenetics tools
KATO, H. E., Kamiya, M., Sugo, S., Ito, J., Taniguchi, R., Orito, A., Hirata, K., Inutsuka, A., Yamanaka, A., Maturana, A. D., et al. (2015) · Nature Communications · doi:10.1038/ncomms8177 · Cited by 97
Self-citationMolecular mechanism of light-driven sodium pumping
Kovalev, K., Astashkin, R., Gushchin, I., Orekhov, P. S., Volkov, D., Zinovev, E. V., Marin, E., Rulev, M., Alekseev, A. A., Royant, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16032-y · Cited by 94
Structural mechanisms of selectivity and gating in anion channelrhodopsins
KATO, H. E., Kim, Y. S., Paggi, J. M., Evans, K. E., Allen, W. E., Richardson, C. E., Inoue, K., Ito, S., Ramakrishnan, C., Fenno, L. E., et al. (2018) · Nature · doi:10.1038/s41586-018-0504-5 · Cited by 93
Self-citationShibata, M., Inoue, K., Ikeda, K., Konno, M., Singh, M. P., Kataoka, C., Abe‐Yoshizumi, R., Kandori, H., & Uchihashi, T. (2018) · Scientific Reports · doi:10.1038/s41598-018-26606-y · Cited by 89
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Okada, T., Kato, D., Nomura, Y., Obata, N., Quan, X., Morinaga, A., Yano, H., Guo, Z., Aoyama, Y., Tachibana, Y., et al. (2021) · Science Advances · doi:10.1126/sciadv.abd8261 · Cited by 84
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Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A. D., Katayama, K., et al. (2021) · eLife · doi:10.7554/elife.62389 · Cited by 76
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Enami, N., Yoshimura, K., Murakami, M., Okumura, H., Ihara, K., & Kouyama, T. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.02.032 · Cited by 70
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Self-citationOppermann, J., Fischer, P. B., Silapētere, A., Liepe, B., Rodriguez-Rozada, S., Flores‐Uribe, J., Schiewer, E., Keidel, A., Vierock, J., Kaufmann, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11322-6 · Cited by 67
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Trehan, A., Liu, R. S. H., Shichida, Y., Imamoto, Y., Nakamura, K., & Yoshizawa, T. (1990) · Bioorganic Chemistry · doi:10.1016/0045-2068(90)90013-u · Cited by 27
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Research works printed but not linked: 1
- Kishi, 2021, Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine, bioRxiv
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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
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