HulaCCR1, a pump-like cation channelrhodopsin discovered in a lake microbiome: Figure Data

This repository contains figure data for the paper Takaramoto et al (2024) HulaCCR1, a pump-like cation channelrhodopsin discovered in a lake microbiome J Mol Biol 168844: 436.
The files are as follows:
Figure_1a_alignment.csv: Alignment of transmembrane helix 3Figure_1b_for_phylogenetic_tree.meg: Alignment used to generate the treeFigure_2b_rhodopsin_phylogeny.newick: Phylogeny of the stramenopile (and other heterotrophic flagellate) CCRsFigure_2c_clade_distrbution.csv: Distribution of BCCRs in the different environmental datasets containing ChRs from the mgCCR1-3 clade. CSV file with three columns: JGI GOLD analysis accession (or HulaCCR1 for our Hula Lake dataset), BCCR (sub)clade, number of genesFigure_3a_difference_absorption_spectra.csv: Difference UV-visible absorption spectra between before and after the hydroxylamine bleach of HulaCCR1Figure_3c_photocurrents_standard_vs_NMG+.csv: Photocurrents of HulaCCR1 with standard solutions and NMG+ solutionsFigure_3d_I-V_plot.csv: I-V plot of HulaCCR1 photocurrents with different extracellular solutionsFigure_3e_pH_dependence.csv: pH dependence of the I-V plotFigure_4a_representative_traces.csv: Representative photocurrent traces of HulaCCR1 with different cationsFigure_4b_I-V_plots.csv: I-V plots of HulaCCR1 photocurrents with different extracellular cationsFigure_4c_Erev_permeability.csv: Difference in Erev between different cations and H+ (ΔErev) and relative permeability of different cations against H+Figure_5b_action_spectra.csv: Normalized action spectra of the HulaCCR1 WT and E176DFigure_5c_photocurrent_traces_E176.csv: Photocurrent traces of the WT and E176D upon nanosecond laser flash excitationFigure_5d_time_constants.csv: Time constants of channel opening and closing of the HulaCCR1 WT and E176DFigure_5e_photocurrent_traces_C181.csv: Photocurrent traces of the HulaCCR1 WT, C181A, and C181S upon nanosecond laser flash excitationFigure_5f_off-kinetics.csv: Photocurrent offkinetics of HulaCCR1 WT, C303A, and ChRmineFigure_5g_light-power_dependence.csv: Light-power dependence of the photocurrent of HulaCCR1 WT, C303A, and ChRmineFigure_6c_membrane_localization.csv: Quantification of plasma membrane localizationFigure_6d_I-V_plot.csv: I-V plot of the full length and truncated variants of HulaCCR1Figure_7b_voltage_traces.csv: Light stimulation of HulaCCR1-expressing hippocampal neurons: voltage tracesFigure_S1a_transposon_phylogeny.newick: Phylogenetic tree of transposon sequences found in reference genomes and in the flanks of the contigs containing genes from the mgCCR1-3 cladeFigure_S1a_transposon_subclades.csv: Summary of the transposon subclades identified in contigs with the genes from the mgCCR1-3 clade. For each representative sequence, numbers of fragments from each mgCCR1-3 subclade that cluster together with the representative are listed.Figure_S1b_cryptist_phylogeny.newick: 18S phylogeny of the CryptistaFigure_S2_sintax.tsv: Aggregated results of the sintax analysisFigure_S4a_photocurrent_traces.csv: Representative photocurrent traces of the HulaCCR1 WT and mutantsFigure_S4b_time_constants_E176.csv: Time constants of channel opening and closing of the WT HulaCCR1 and E176DFigure_S4d_action_spectra.csv: Normalized action spectra of the HulaCCR1 WT and mutantsFigure_S4e_light-power_dependence.csv: Light-power dependence of photocurrent traces of the HulaCCR1 WT, C303A, and ChRmineFigure_S5b_photocurrent_traces.csv: Representative photocurrent traces of the HulaCCR1 WT, E319Q, and E322QFigure_S5c_photocurrent_amplitude.csv: Mean photocurrent amplitude recorded at −80 mVFigure_S5d_photocurrent_traces_D2O.csv: Photocurrent traces of the HulaCCR1 WT and E322Q upon nanosecond laser-flash excitation recorded in H2O/D2O solutionsFigure_S5e_time_constants.csv: Time constants of channel opening and closing of the HulaCCR1 WT and E322QFigure_S6b_I-V_plots.csv: I-V plots of the full-length HulaCCR1 and truncated variant 13-428Figure_S6c_photocurrent_traces.csv: Representative photocurrent traces of the full-length HulaCCR1 and truncated variant 13-428Figure_S7a_fluorescence_profiles_HulaCCR1.csv: Normalized fluorescence profiles of the full-length protein and the truncated variantsFigure_S7b_GtACR1.csv: Normalized fluorescence profiles of GtACR1 WT and GtACR1 with residues 1-43 from HulaCCR1 at the N-terminusFigure_S7c_photocurrent_traces.csv: Representative photocurrent trances of truncated variantsHulaCCR1_fromColabFold.zip and mgCCR1_fromColabFold.zip: structures of HulaCCR1 and mgCCR1 predicted with ColabFold