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TCID	Name	Domain	Kingdom/Phylum	Protein(s)
3.E.1.1.1	Bacteriorhodopsin. Proton efflux occurs via a transient linear water-molecule chain in a hydrophobic section of the Brho channel between Asp96 and Asp85 (Freier et al., 2011). Local-global conformational coupling in brho has been proposed as a transport mechanism from crystal structures of the nine states in the bacteriorhodopsin photocycle (Lanyi and Schobert 2004). The protein can be converted into a chloride uptake pump by a single amino acid substitution at position 85. However, halorhodopsin (3.E.1.2.1), which pumps chloride ions (Cl^-) into the cell, apparently does not use hydrogen-bonded water molecules for Cl^- transport (Muroda et al. 2012). Nango et al. 2016 used time-resolved serial femtosecond crystallography and an x-ray free electron laser to visualize conformational changes in bRho from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bRho transports protons uphill against a transmembrane concentration gradient. Nango et al. 2016 have created a 3-d movie of structural changes in the protein showing that an initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. Brho has light-independent lipid scramblase activity (Verchère et al. 2017). This activity occurs at a rate >10,000 per trimer per second, comparable to that of other scramblases including bovine rhodopsin and fungal TMEM16 proteins. BR scrambles fluorescent analogues of common phospholipids but does not transport a glycosylated diphosphate isoprenoid lipid. In silico analyses suggested that membrane-exposed polar residues in transmembrane helices 1 and 2 of BR may provide the molecular basis for lipid translocation by coordinating the polar head-groups of transiting phospholipids. Consistent with this possibility, extensive coarse-grained molecular dynamics simulations of a BR trimer in a phospholipid membrane revealed water penetration along transmembrane helix 1 with the cooperation of a polar residue (Y147 in transmembrane helix 5) in the adjacent protomer. These findings suggest that the lipid translocation pathway may lie at or near the interface of the protomers of the BR trimer (Verchère et al. 2017). Retinal isomerization has been observed in the using a femtosecond x-ray laser (Nogly et al. 2018). S-TGA-1, a halobacterium-derived glycolipid, has the highest specificity to bRho, with a nanomolar dissociation constant (Inada et al. 2019). Weinert et al. 2019 recorded the structural changes in bacteriorhodopsin over 200 milliseconds in time. The snapshot from the first 5 milliseconds after photoactivation shows structural changes associated with proton release. From 10 to 15 milliseconds onwards, large additional structural rearrangements, up to 9 Å on the cytoplasmic side. Rotation of leucine-93 and phenylalanine-219 opens a hydrophobic barrier, leading to the formation of a water chain connecting the intracellular aspartic acid-96 with the retinal Schiff base. The formation of this proton wire recharges the membrane pump with a proton for the next cycle (Weinert et al. 2019). The effect of membrane composition on the orientation and activity of bR has been reported (Palanco et al. 2017). Efficient transfer of bRho from native membranes to covalently circularized nanodiscs has been accomplished (Yeh et al. 2018). The oligomeric status of BRho plays a role in the photocycle associated with short-range processes, such as retinal isomerization and deprotonation of the protonated Schiff base at the retinal pocket (Kao et al. 2019). Functional bacteriorhodopsin is efficiently solubilized and delivered to membranes by the chaperonin, GroEL (Deaton et al. 2004). Thirty one unfolded bR states in the presence of the retinal chromophore have been identified during denaturation (Jacobson et al. 2020). A transient protonic capacitor explains the bacteriorhodopsin membrane experiment of Heberle et al. 1994. Thus, after proton release by an integral membrane protein, long-range proton transfer along the membrane surface is faster than proton exchange with the bulk water phase as predicted by the TELP theory (Lee 2023). The head groups and alkyl chains of phospholipids are essential for boundary lipids and greatly influence the biological function of bRho (Umegawa et al. 2023).	Archaea	Euryarchaeota	Bacteriorhodopsin of Halobacterium salinarum
3.E.1.1.2	Archaerhodopsin-2 (aR2) (a retinal protein-carotenoid complex) (Yoshimura and Kouyama, 2007).	Archaea	Euryarchaeota	aR2 of Halorubrum sp. aus-2 (P29563)
3.E.1.1.3	"Middle" rhodopsin or bacteriorhodopsin 1 (Brhol); it has 11-cis-retinal and shows intermediate properties between Brho and sensory rhodopsin II (Sudo et al., 2011). Its structure is known to 2.0 Å resolution following crystalization using polymer-bounded lipid nanodiscs (Broecker et al. 2017). It may pump Cl^- and Br^- into the cell (Kikukawa 2021). See also Ko et al. 2022.	Archaea	Euryarchaeota	Middle rhodopsin of Haloquadratum walsbyi (G0LFX8)
3.E.1.1.4	Archaerhodopsin 3, archaerhodopsin-3, AR3, Aop3, BACR3 of 258 aas and 7 TMSs. It pumps protons in response to light absorption (Saint Clair et al. 2012) and is 86% identical to 3.E.1.1.2. Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization (Bada Juarez et al. 2021). Opsin-based transmembrane voltage sensors (OTVSs) are membrane proteins increasingly used in optogenetic applications to measure voltage changes across cellular membranes (Mei et al. 2021). Khangholi et al. 2021 studied photoactivation of cell-free expressed archaerhodopsin-3 in a model cell membrane and concluded that it functions as a channel with open and closed states and a pore radius of 0.3 nm.	Archaea	Euryarchaeota	AR3 of Halorubrum sodomense
3.E.1.1.5	Bacteriorhodopsin I (HmBRI) of 250 aas and 7 TMSs. The structure is known to 2.5 Å resolution, revealing the usual BRI fold but with several modifications (Shevchenko et al. 2014). Expression in E. coli membranes does not affect the overall structure.	Archaea	Euryarchaeota	Bacteriorhodopsin I of Haloarcula marismortui
3.E.1.1.6	Sensory rhodopsin (green-light-activated photoreceptor; does not transport ions) (Jung et al., 2003). Has all-trans-retinal when dark adapted, but 11-cis-retinal when light adapted due to reversible interconversion (Sineshchekov et al., 2005). Anabaena sensory rhodopsin, a photochromic sensor that interacts with a soluble 14-kDa cytoplasmic transducer that is encoded on the same operon, interconverts between all-trans-15-anti and 13-cis-15-syn retinal forms depending on the wavelength of illumination, although only the former participates in a photocycle with a signaling M intermediate (Dong et al. 2016). A mutation in the cytoplasmic half-channel of the protein, replacing Asp217 with Glu (D217E), results in the creation of a light-driven, single- photon, inward proton transporter. Dong et al. 2016 presented the 2.3 A structure of dark-adapted D217E ASR, which reveals changes in the water network surrounding Glu217, as well as a shift in the carbon backbone near retinal-binding Lys210, illustrating a possible pathway leading to the protonation of Glu217 in the cytoplasmic half-channel, located 15 A from the Schiff base.	Bacteria	Cyanobacteriota	Sensory rhodopsin of Anabaena (Nostoc) sp. PCC7120
3.E.1.1.7	H⁺-pumping electrogenic bacteriorhodopsin of 250 aas and 7 TMSs (Kamo et al. 2006). The delta rhodopsin (dR), a microbial light-driven proton-pumping rhodopsin from Haloterrigena turkmenica, was expressed and localized in the vacuolar membrane of Saccharomyces cerevisiae by conjugation with a vacuolar membrane-localized protein. Vacuoles with dR were isolated from S. cerevisiae, and the light-driven proton pumping activity was evaluated based on the pH change outside the vacuoles. A light-induced increase in the intracellular ATP content was observed in yeast harboring vacuoles with dR (Daicho et al. 2024).	Archaea	Euryarchaeota	Brho of Haloterrigena turkmenica
3.E.1.1.8	Inward H⁺ pumping xenorhodopsin (bacteriorhodopsin) of 228 aas and 7 TMSs.	Archaea	Euryarchaeota	Xenorhodopsin of Nanosalina sp. (strain J07AB43)
3.E.1.1.9	Rhodopsin, RxR, of 239 aas and 7 TMSs. This rhodopsin is from the thermophilic eubacterium Rubrobacter xylanophilus DSM 9941(T) and was isolated from thermally polluted water. Although R. xylanophilus rhodopsin (RxR) is from an Actinobacterium, it is located between eukaryotic and archaeal rhodopsins in the phylogenetic tree (Kanehara et al. 2017). E. coli cells expressing RxR showed a light-induced decrease in environmental pH and inhibition by a protonophore, indicating that it works as a light-driven outward proton pump. Purified RxR has an absorption maximum at 541 nm and binds all-trans retinal. The pKa values for the protonated retinal Schiff base and its counterion were 10.7 and 1.3, respectively. Of note, RxR showed an extremely high thermal stability in comparison with other proton pumping rhodopsins such as thermophilic rhodopsin TR (by 16-times) and bacteriorhodopsin from Halobacterium salinarum (HsBR, by 4-times) (Kanehara et al. 2017). Hayashi et al. 2020 showed how RxR realizes its exceptionally high stability while retaining its original proton pumping function. Biochemical synthesis of membrane-spanning lipids is one adaptation that organisms such as thermophilic archaea have evolved to prevent membrane leakiness (Kim et al. 2019).	Bacteria	Actinomycetota	Rhodoopsin of Rubrobacter xylanophilus
3.E.1.1.10	Schizorhodopsin of 202 aas and 7 TMSs. The crystal structure reveals the mechanism of inward proton pumping (Higuchi et al. 2021). Schizorhodopsins (SzRs), a new rhodopsin family identified in Asgard archaea, are phylogenetically located at an intermediate position between type-1 microbial rhodopsins and heliorhodopsins. SzRs work as light-driven inward H⁺ pumps (Higuchi et al. 2021). Strongly hydrogen-bonded Schiff base and adjoining polyene twisting in the retinal chromophore of schizorhodopsins has been observed (Shionoya et al. 2021).	Archaea	Candidatus Lokiarchaeota	Szr of Candidatus Lokiarchaeota archaeon
3.E.1.1.11	Mastigocladopsis repens rhodopsin chloride pump (inward pumping). The 3-d structure is known to 3.3 Å resolution (Besaw et al. 2020). It may transport both Cl^- and Br^- (Kikukawa 2021).	Bacteria	Cyanobacteriota	Rhodopsin chloried pump of Mastigocladopsis repens
3.E.1.1.13	Xenorhodopsinof 229 aas and 7 TMSs. The structures have been determined for all intermediates of the photocycle; 7ZNB, C, D, E, G, H and I, all A - C. Thus, a comprehensive function-structure study of the light-driven bacterial inward proton pump, xenorhodopsin from Bacillus coahuilensis, in all major proton-conducting states was carried out (Kovalev et al. 2023). The structures revealed that proton translocation is based on proton wires regulated by internal gates. The wires serve as both selectivity filters and the translocation pathways for protons. The cumulative results suggest a general concept of proton translocation. Kovalev et al. 2023 demonstrated the use of serial time-resolved crystallography at a synchrotron source with sub-millisecond resolution for rhodopsin studies, opening the door for principally new applications.	Bacteria	Bacillota	Xenorhodopsin of Bacillus coahuilensis
3.E.1.1.14	Synechocystis halorhodopsin of 234 aas and 7 TMSs. The 3-D structure is known (Astashkin et al. 2022). MRs can pump various monovalent ions like Na⁺, K⁺, Cl^-, I-, and NO₃^-. The only characterized MR proposed to pump sulfate in addition to halides belongs to the cyanobacterium Synechocystis sp. PCC 7509 and is named Synechocystis halorhodopsin (SyHR). Astashkin et al. 2022 presented the crystal structure of SyHR in the ground state, the structure of its sulfate-bound form as well as two photoreaction intermediates, the K and O states. The data reveal the molecular origin of the unique properties of the protein (exceptionally strong chloride binding and proposed pumping of divalent anions) and sheds light on the mechanism of anion release and uptake in cyanobacterial halorhodopsins. The unique properties of SyHR highlight its potential as an optogenetics tool and may help engineer different types of anion pumps with applications in optogenetics (Astashkin et al. 2022).	Bacteria	Cyanobacteriota	SyHR of Synechocystis sp. PCC 7509
3.E.1.1.15	Schizorhodopsin 4 of 110 aas and 7 TMSs. The protein pumps H⁺ into the cytoplasm of the cell. Cis-trans reisomerization preceding reprotonation of the retinal chromophore Is common to the schizorhodopsin family. A simple and rational mechanism for inward proton pumping has been proosed (Urui et al. 2024), and the 3-D structure is known (Higuchi et al. 2021).	Archaea		Schizorhodopsin 4 of an Asgard group archaeon
3.E.1.1.16	Microbial (bacterial) rhodopsin, Bop2, of 246 aas and 7 TMSs. It has no proton-pumping activity but is potentially capable of functioning as a sensory SRII-like protein. The chromophore contains 36.5% all-trans-, 7.6% 11-cis- and 56.4% 13-cis-retinal in the dark and 30.1% 11-cis- and 47.7% 13-cis-retinal upon illumination with >460 nm light (Sudo et al. 2011). Haloquadratum walsbyi (Hw) survives at high MgCl₂ concentrations, with a total of three MRhos identified, including (1) a high-acid-tolerance light-driven proton outward pump, HwBR, (2) a chloride-insensitive chloride pump, HwHR, and (3) HwMR, the sole magnesium-sensitive MRho among all tested MRho proteins from Haloarchaea. D84 is one of the key residues mediating such magnesium ion association in HwMR. Sequence analysis and molecular modeling suggested HwMR to have an extra H8 helix in the cytosolic region like those in signal-transduction-type MRho of deltarhodopsin-3 (dR-3) and Anabaena sensory rhodopsin (ASR) (Ko et al. 2022).	Archaea	Euryarchaeota	Bop2 of Haloquadratum walsbyi
3.E.1.1.17	Cyanorhodopsin, CyR, of 254 aas and 7 TMSs. These proteins are found in non-marine cyanobacterial strains. They catalyze light-driven outward H+ pumping (Hasegawa et al. 2020).	Bacteria	Cyanobacteriota	CyR of Calothrix sp. NIES-2098
3.E.1.2.1	Halorhodopsin Cl^- uptake pump; homologous to bacteriorhodopsin (3.E.1.1.1) which can be converted from a proton pump with outwardly directed polarity into a chloride pump with inwardly directed polarity via a single amino acid substitution at position 85. Cl^- transport does not depend on water hydrogen bonded to the chromophore as in the case of bacteriorhodopsin (Muroda et al. 2012). However, inter-helical hydrogen bonds, mediated by a key arginine residue, largely govern the dynamics of the protein and water groups coordinating the chloride ion (Jardón-Valadez et al. 2014). Helices E and F probably move considerable during chloride binding and ion transport (Schreiner et al. 2016).	Archaea	Euryarchaeota	Halorhodopsin of Halobacterium salinarum
3.E.1.2.2	Chloride-pumping halorhodopsin (a trimer with the carotenoid, bacterioruberin, binding to crevices between adjacent protein subunits in the trimeric assembly; Sasaki et al., 2012). Structure known to 2.0 Å resolution (Kouyama et al., 2010) (PDB# 3A7K)). In addition to Cl^-, it pumps Br^-, I^- and NO₃^- (Kikukawa 2021).	Archaea	Euryarchaeota	Halorhodopsin of Natronomonas pharaonis (P15647)
3.E.1.3.1	Sensory rhodopsin I	Archaea	Euryarchaeota	Sensory rhodopsin I of Halobacterium salinarum
3.E.1.3.2	Sensory rhodopsin II or photoreceptor phoborhodopsin (ppR). The 3-d structure has been solved by NMR (Gautier and Nietlispach 2012). The dynamics of light induced conformational changes have been studied (Taniguchi et al. 2007).	Archaea	Euryarchaeota	Sensory rhodopsin II (phoborhodopsin) of Halobacterium salinarum
3.E.1.3.3	Sensory rhodopsin II, SR2 (Sop2; ppR), also called Pharaonis phoborhodopsin. The NMR solution structure of the detergent solubilized protein is in good agreement with the x-ray structure (Gautier et al. 2010). The onformational dynamics of Sensory Rhodopsin II in nanolipoprotein and styrene-maleic acid lipid particles has been studied (Mosslehy et al. 2019). The retinal configuration of ppR intermediates have been studied (Makino et al. 2018).	Archaea	Euryarchaeota	SRII of Natronomonas (Natronobacterium) pharaonis (P42196)
3.E.1.3.4	Sensory rhodopsin III, SRIII, of 232 aas and 7 TMSs (Fu et al. 2010).	Archaea	Euryarchaeota	SRIII of Haloarcula marismortui
3.E.1.3.5	Phoborhodopsin (sensory rhodopsin II) of 249 aas and 7 TMSs. The photochemistry and proton transport have been reviewed (Kamo et al. 2001) and the crystal structure is known (Kandori and Kamo 2002). Rhodopsins have been reviewed (Kandori 2020).	Archaea	Euryarchaeota	Phoborhodopsin of Halorubrum chaoviator
3.E.1.4.1	Heat shock protein HSP30	Eukaryota	Fungi, Ascomycota	HSP30 of Saccharomyces cerevisiae
3.E.1.4.2	Retinal binding protein, Neurospora Opsin-1, NOP-1 (Bieszke et al. 1999; Bieszke et al. 2007).	Eukaryota	Fungi, Ascomycota	NOP-1 of Neurospora crassa
3.E.1.4.3	H⁺ pumping rhodopsin (opsin; Ops), of 313 aas and 7 TMSs (Idnurm and Howlett 2001; Waschuk et al., 2005). Its 3-d strcuture has been solved, and it resembles archaeal rhodopsins more than bacterial rhodopsins (Zabelskii et al. 2021).	Eukaryota	Fungi, Ascomycota	Rhodopsin of Leptosphaeria maculans (AAG01180)
3.E.1.4.4	Acetaularia rhodopsin I, ARI or c102333 of 246 aas. It exhibits outward H⁺ pumping activity, and D89 and D100 are essential for pumping activity (Lee et al. 2015). Blue-light causes a shunt of the photocycle under H⁺ reuptake from the extracellular side (Tsunoda et al. 2006). Similarities and differences of AR with BR have been revealed by detailed electrophysiological studies, revealing among other things, the voltage dependencies of the pump (Tsunoda et al. 2006).	Eukaryota	Viridiplantae, Chlorophyta	c102333 of Acetabularia acetabulum (Q1AJZ3)
3.E.1.4.5	Opsin 1, Bacteriorhodopsin-like protein	Eukaryota		Opsin 1 of Guillardia theta (Q2QCJ4)
3.E.1.4.6	Possible chaperone membrane protein related to Hsp30, Mrh1 (320 aas; 33% identical to Hsp30p). This protein and its two paralogues, Hsp30 and YR02, are induced by heat shock and are present primarily in the plasma membrane (Wu et al. 2000). It plays a role in acetic acid tolerance and may be an acetic acid exporter (Takabatake et al. 2015).	Eukaryota	Fungi, Ascomycota	Mrh1p of Saccharomyces cerevisiae (Q12117)
3.E.1.4.7	Cyanorhodopsin of 334 aas and 7 TMSs, Ops1 (Frassanito et al. 2010).	Eukaryota		Cyanorhodopsin of Cyanophora paradoxa
3.E.1.4.8	Yro2 of 344 aas and 7 TMSs. Plays a role in acetic acid tolereance and is induced by acetic acid stress and by entry into the stationary phase. It is 72% identical to Mrh1 (TC# 3.E.1.4.6) which is also believed to be involved in the acetic acid stress response (Takabatake et al. 2015).	Eukaryota	Fungi, Ascomycota	Yro2 of Saccharomyces cerevisiae
3.E.1.4.9	Pentachlorophenone-induced protein, FDD123	Eukaryota	Fungi, Basidiomycota	FDD123 of Coriolus versicolor
3.E.1.5.1	Bacterio-rhodopsin/guanylyl cyclase 1 fusion protein of 626 aas; light-activated enzyme, RhCG, Gc1 or Cyc1Op. The central bacteriorhodopsin domain with 7 TMSs is linked via an additional TMS to the C-terminal adenylate/guanylate cyclase catalytic domain. CyclOp enables precise and rapid optogenetic manipulation of cGMP levels in cells and animals (Gao et al. 2015).	Eukaryota	Fungi, Blastocladiomycota	Gc1 of Blastocladiella emersonii (Aquatic fungus)
3.E.1.5.2	Learning/memory process protein of 704 aas and 7 N-terminal TMSs as the rhodopsin (Rh) domain with a C-terminal cyclic nucleotide phosphodiesterase (PDE) domain. The Rh-PDE enzyme light-dependently decreases the concentrations of cyclic nucleotides such as cGMP and cAMP. Photoexcitation of purified full-length Rh-PDE yields an "M" intermediate with a deprotonated Schiff base; its recovery is much faster than that of the enzyme domain (Watari et al. 2019). Mechanistic insights into rhodopsin-mediated, light-dependent regulation of second-messenger levels have thus been revealed (Watari et al. 2019).	Eukaryota		Rh-PDE fusion protein of Salpingoeca rosetta
3.E.1.5.3	Rhodopsin-containing uncharacterized protein of 2205 aas with the rhodopsin domain at the N-terminus with 7 or 8 TMSs. Additional TMSs may exist in the remainder of the protein. It may be a light inhibited guanlyate cyclase (Tian et al. 2022). The guanylate cyclase domain may be within residues 1120 and 1350.	Eukaryota	Viridiplantae, Chlorophyta	UP of Volvox reticuliferus
3.E.1.6.1	Green-light-absorbing H⁺ pumping proteorhopdopsin of 249 aas and 8 TMSs. It exhibits variable vectorality: H⁺ is pumped out at basic pH but not at acidic pH; see Friedrich et al., 2002). It presents a fast proton release and an alkaliphilic photocycle, consistent with its marine origin and the near-surface environment where this bacterium was collected. This proteorhodopsin has been used to measure membrane potentials and electrical spiking in E. coli (Kralj et al., 2011; Ward et al., 2011). 3-d structures of three proteorhodopsins show that they can exist as pentamers or hexamers, depending on the protein (Ran et al. 2013). Protonation states of several carboxylic acids, the boundaries and distortions of transmembrane α-helices, and secondary structural elements in the loops have been identified (Shi et al. 2009). Proteorhodopsin molecules incorporated into mesostructured silica films exhibit native-like function, as well as enhanced thermal stability compared to surfactant or lipid environments (Jahnke et al. 2018).	Bacteria	Pseudomonadota	Green-light-absorbing proteorhodopsin from an uncultured γ-proteobacterium EOAC 31A08
3.E.1.6.2	Xanthorhodopsin, a proton pump with a carotenoid antenna, salinixanthin (Lanyi and Balashov 2008). A crystal structure (1.9 Å resolution) is available (Luecke et al., 2008).	Bacteria	Rhodothermota	Xanthorhodopsin with a salinixanthin chromophore of Salinibacter ruber (Q2S2F8)
3.E.1.6.3	Gloeobacter rhodopsin (GT) of 298 aas and 7 TMSs (associates with salinixanthin, the light-harvesting carotenoid antenna of xanthorhodopsin) (Imasheva et al., 2009; Hashimoto et al., 2010). Expression in a chemotrophic E. coli enabled light-driven phototrophic energy generation (Kim et al. 2017). The X-ray crystallographic structure and oligomeric state have been described (Morizumi et al. 2019). The structural characteristics of GR's hydrogen bonding network in the transmembrane domain as well as the displacement of extracellular sides of the TMS resemble those of XR. The pH-dependent pentamer form of GR was documented. Structural motifs (extended helices, 3-omega motif and flipped B-C loop) typical of other characterized rhodopsins, were also identified (Morizumi et al. 2019). This proton outward pumping rhodopsin interacts with a helix-turn-helix transcriptional regulator and regulats gene expression. ATP-binding cassette (ABC) transporters and the self-regulation of G. violaceus transcriptional regulator (GvTcR) are regulated by light, and gene regulation was observed in G. violaceus using the real-time PCR (Shim et al. 2024).	Bacteria	Cyanobacteriota	Rhodopsin of Gloeobacter violaceus (Q7NP59)
3.E.1.6.4	Bacteriorhodopsin-like circadian clock related protein (Okamoto and Hastings, 2003)	Eukaryota		BacRhodopsin of Pyrocystis lunula (Q8GZE7)
3.E.1.6.5	H⁺-pumping bacteriorhodopsin, Brho or ESR (Petrovskaya et al. 2010). Photoelectric potential generation correlates with the ESR structure and proposed mechanism of proton transfer (Siletsky et al. 2016). Proteoliposomes with unidirectional orientation using ESR from Exiguobacterium sibiricum have been prepared. Three ESR hybrids with soluble protein domains (mCherry or thioredoxin at the C-terminus and Caf1M chaperone at the N-terminus) were obtained and characterized (Petrovskaya et al. 2023).	Bacteria	Bacillota	Brho of Exiguobacterium sibiricum (B1YFV8)
3.E.1.6.6	Proton pumping proteorhodopsin of 253 aas (Kimura et al. 2011).	Bacteria	Bacteroidota	Proteorhodopsin of Nonlabens dokdonensis (Donghaeana dokdonensis)
3.E.1.6.7	Na⁺ or H⁺ pumping bacteriorhodopsin, NaR, Kr2 or KR2 (Krokinobacter rhodopsin 2), of 280 aas and 7 TMSs. It uses light to pump protons or sodium ions from the cell depending on the ionic composition of the medium. In cells suspended in a KCl solution, NaR functions as a light-driven proton pump, whereas in a NaCl solution, it exhibits light-driven sodium ion pumping, a novel activity within the rhodopsin family (da Silva et al. 2015). A cation switch controls its conformations, and specific interactions of Na⁺ with the half-channels open an appropriate path for ion translocation (da Silva et al. 2015). Several high resolution x-ray structures have been solved (4XTO, Kato et al. 2015). Putative Na⁺ binding sites have been identified, and it was shown how protonation and conformational changes gate the ion through these sites toward the extracellular side (Suomivuori et al. 2017). Evidence for homology of this and other microbial rhodopsin with GPCR receptors including mamalian rhodopsins has been presented (Yee et al. 2013; Shalaeva et al. 2015). The 3-d structures have been determined by different groups (3X3B_A,B, 4XT0_A-E; 5JRF_A, and 6RF4_A-E). A covalent bond between Lys-255 and the polypeptide chain is responsible for stable retinal chromophore binding and sodium-pumping activity of KR2,but not for transport activity (Ochiai et al. 2023). Light-driven Na⁺-pumping rhodopsin (NaR) has been reviewed with an overview of structural and functional studies encompassing ground/intermediate-state structures and photocycle kinetics (Yang and Chen 2023). The review focuses on (1) unraveling the translocation pathway of Na⁺; (2) examining the role of structural changes within the photocycle, particularly in the O state, in facilitating Na⁺ transport; and (3) investigating the timing of Na⁺ uptake/release.	Bacteria	Bacteroidota	NaR of Dokdonia eikasta (Krokinobacter eikastus)
3.E.1.6.8	Proteorhodopsin of 246 aas and 7 TMSs, Pro. A light-driven Na⁺ pump (Bertsova et al. 2015).	Bacteria	Bacteroidota	Proteorhodopsin of Dokdonia sp. PRO95
3.E.1.6.9	Bacteriorhodopsin (thermophilic rhodopsin; TR) of 260 aas and 7 TMSs. 53% identical to xanthorhodopsin (TC# 3.E.1.6.2). It is a photoreceptor protein with extremely high thermal stability and a light-driven electrogenic proton pump. The x-ray crystal structure revealed the presence of a putative binding site for a carotenoid antenna and a larger number of hydrophobic residues and aromatic-aromatic interactions than in most microbial rhodopsins (Tsukamoto et al. 2016). The structural changes upon thermal stimulation involved a thermally induced structure in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. An extracellular LPGG motif between helices F and G may play an important role in thermal stability, acting as a "thermal sensor" (Tsukamoto et al. 2016).	Bacteria	Deinococcota	Bacteriorhodopsin of Thermus thermophilus
3.E.1.6.10	Uncharaacterized bacteriorhodopsin of 289 aas and 7 TMSs.	Bacteria	Pseudomonadota	UP of Parvularcula oceani
3.E.1.6.11	Uncharacterized bacteriorhodopsin of 321 aas and 7 TMSs.	Bacteria	Pseudomonadota	UP of Parvularcula oceani
3.E.1.6.12	Blue-light absorbing proteorhodopsin (BPR) of 251 aas and 8 TMSs including a cleavable N-terminal TMS. BPR does not rely on the Sec pathway for inner membrane integration (Soto-Rodríguez and Baneyx 2018). The BPR signal sequence is recognized by the signal recognition particle (SRP; a protein that orchestrates the cotranslational biogenesis of inner membrane proteins) and serves as a beneficial "pro" domain rather than a traditional secretory peptide. It is a light-driven proton pump that may have a regulatory rather than energy harvesting function, based on light-induced opening of proton channels to modulate cell physiology depending on light intensity variations. It could therefore be a sensory rhodopsin, potentially associated with a transducer component. It presents a much slower photocycle than that of the green-absorbing proteorhodopsin, probably an adaptation to the intensity of solar illumination at a depth of 75m, where this bacterium was collected. Transport occurs only at pHs above 7 and is unidirectional.	Bacteria	Pseudomonadota	BPR of Gamma-proteobacterium Hot 75m4
3.E.1.6.13	Viral rhodopsin II (RhoII) of 211 aas and 7 TMSs, OLPVRII, a VirChR1, a Na⁺/K⁺ channel that does not transport Ca²⁺. It forms a pentamer, with a symmetrical, bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of 5 arginines, whereas 5 phenylalanines form a hydrophobic barrier in its exit (Bratanov et al. 2019). The proton donor, E42, is in helix B. The structure is unique among known rhodopsins. Structural and functional data and molecular dynamics suggest that OLPVRII might be a light-gated pentameric ion channel analogous to pentameric ligand-gated ion channels. A photon (hν) causes neural firing. The 1.4 Å structure has been determined revealing a unique ion transport pathway through the protein (Zabelskii et al. 2020).	Viruses	Bamfordvirae, Nucleocytoviricota	OLPVR1 of Organic Lake phycodnavirus
3.E.1.6.14	Chloride (Cl^-) pumping rhodopsin of 272 aas and 7 TMSs. It may pump Cl^-, Br^-, I^-, and NO3^-(Kikukawa 2021).	Bacteria	Bacteroidota	NTQ rhodopsin of Nonlabens marinus
3.E.1.6.15	Bellilinea Na⁺-pumping rhodopsin, BeNaR, of 269 aas and 7 TMSs. Kurihara et al. 2023 identified and characterized a rhodopsin from a thermophilic bacterium, Bellilinea sp. Recombinant Escherichia coli cells expressing this rhodopsin showed light-induced alkalization of the medium only in the presence of Na⁺, and the alkalization signal was enhanced by addition of a protonophore, indicating an outward Na⁺ pump function across the cellular membrane. Its Na⁺-pumping activity is greater than that of the known Na⁺-pumping rhodopsin, KR2. Its photochemical properties included: (i) Visible spectroscopy and HPLC revealed that BeNaR had an absorption maximum at 524 nm with predominantly (>96%) the all-trans retinal conformer. (ii) Time-dependent thermal denaturation experiments revealed that BeNaR showed high thermal stability. (iii) The time-resolved flash-photolysis in the nanosecond to millisecond time domains revealed the presence of four kinetically distinctive photointermediates, K, L, M and O. (iv) Mutational analysis revealed that Asp101, which acts as a counterion, and Asp230 around the retinal were essential for the Na⁺-pumping activity. Kurihara et al. 2023 proposed a model for the outward Na⁺-pumping mechanism of BeNaR.	Bacteria	Chloroflexota	BeNaR of Bellilinea caldifistulae
3.E.1.7.1	Channelrhodopsin-1 (chlamyrhodopsin-3) (ChR1; Cop3; CSOA) (light-gated cation (H⁺, Na⁺, K⁺, and Ca²⁺) channel) (Nagel et al., 2003). TMSs 1 and 2 are the main structures involved in desensitization involving the stabilization of the protein's conformation and the alteration of the charge distribution around the retinal-Schiff base (Zamani et al. 2017). Replacing the glutamate located at the central gate of the ion channel with positively charged amino acyl residues reverses the ion selectivity and allows anion (chloride, Cl^-) conduction (Zhang et al. 2019). zlight-gated channelrhodopsin sparks proton-induced calcium release in guard cells (Huang et al. 2023). The mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2 (ChR1/ChR2), in the high- and low-conducting open states have been examined (Prignano et al. 2024). Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca²⁺ permeability vs. Na⁺ by nearly two-fold at peak current, but less so at stationary current. Molecular models of dimeric wild-type C1C2 and N297D mutant channels were examined in both open states and the PMF profiles for Na⁺ and Ca²⁺ permeation through each protein using well-tempered/multiple-walker metadynamics were determined. Results of these studies agree well with experimental measurements and demonstrated that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by side chain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca²⁺ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and side chain swinging. Prignano et al. 2024 also found that altered cation binding affinities at both the extracellular entrance and the central binding sites underlie the distinct transport properties of the low-conducting open state. This facilitates an understanding of ion selectivity and permeation in cation channelrhodopsins.	Eukaryota	Viridiplantae, Chlorophyta	Channelrhodopsin-1 of Chlamydomonas reinhardtii
3.E.1.7.2	Channelrhodopsin-2 (chlamyrhodopsin-4 of 737 aas and 7 N-terminal TMSs; ChR2; CR2; Cop4; CSOB) (light-gated cation-selective ion channel (both monovalent and divalent cations (H⁺, Na⁺, K⁺, and Ca²⁺⁾are transported)) (Nagel et al., 2003). Berndt et al. (2010) showed that ChR2 has two open states with differing ion selectivities. The channel is fairly nonspecific at the beginning of a light pulse, and becomes more specific for protons during longer periods of light exposure. Residues involved in channel closure have been identified (Bamann et al. 2010). ChR2 is 712 aas long; the MR domain is N-terminal (Lee et al. 2015). The free energy profiles computed for proton transfer to the counterion, either via a direct jump or mediated by a water molecule, demonstrate that, when retinal is all-trans, water and protein electrostatic interactions largely favour the protonated retinal Schiff base state (Adam and Bondar 2018). Blue light illumination of ChR2 activates an intrinsic leak channel conductive for cations. Sequence comparison of ChR2 with the related ChR1 protein revealed a cluster of charged amino acids within the predicted transmembrane domain 2 (TM2), which includes glutamates E90, E97 and E101. Charge inversion substitutions altered ChR2 function, replacement of E90 by lysine or alanine resulted in differential effects on H+- and Na+-mediated currents. These results are consistent with this glutamate side chain within TMS2 contributing to ion flux through and the cation selectivity of ChR2 (Ruffert et al., 2011). Glutamate residue-97 lies in the outer pore where it interacts with a cation to facilitate dehydration. This residue is also the primary binding target of Gd3+(Tanimoto et al., 2012). Channelrhodopsin has been converted into a light-gated chloride channel (Wietek et al. 2014). TMSs 2, 6 and 7 reorient or rearrange during the photocycle with no major differences near TMSs 3 and 4 at the dimer interface. TMS2 plays a key role in light-induced channel opening and closing in ChR2 (Müller et al. 2015). Negative charges at the extracellular side of transmembrane domain 7 funnel cations into the pore (Richards and Dempski 2015). CrChR2, is the most widely used optogenetic tool in neuroscience. Water efflux and the cessation of the ion conductance are synchronized (Lórenz-Fonfría et al. 2015). light and pH induce changes in the structure and accessibility of TMSB (Volz et al. 2016). Residues V86, K93 and N258 form a putative barrier to ion translocation. These residues contribute to cation selectivity (V86 and N258), the transition between the two open states (V86), open channel stability, and the hydrogen-bonding network (K93I and K93N) (Richards and Dempski 2017). The x-ray structure is available and reveals much about the mechanism of channel regulation (Gerwert 2017; Volkov et al. 2017). The mechanism of formation of the ion channel of ChR2 has been studed by molecular dynamics simulation and steering (Yang et al. 2019). The effects on ion channel activities of different protonation states of E90 in channelrhodopsin-2 have been described (Cheng et al. 2021). Yang et al. 2023 have designed a TRP-like biohybrid sensor by integrating upconversion nanoparticles (UCNP) and optogenetically engineered cells on a graphene transistor for infrared sensing and imaging. They used UCNP and ChR2 within the sensor in place of TRPs. (Yang et al. 2023). Light activation of ChR2 augments an influx of Na⁺ with a consequent inhibition of cell growth. In a K⁺ uptake deficient yeast strain, growth can be rescued in selective medium by the blue light induced K⁺ conductance of ChR (Höler et al. 2023).	Eukaryota	Viridiplantae, Chlorophyta	Channelrhodopsin-2, CR2, of Chlamydomonas reinhardtii (Q8RUT8)
3.E.1.7.3	Channelrhodopsin-2 (ChR2) of light-gated ion channel. A 6 Å projection map is available (Müller et al., 2011). Glutamate residue-97 lies in the outer pore where it interacts with a cation to facilitate dehydration. This residue is also the primary binding target of Gd³⁺ (Tanimoto et al., 2012). Cardiomyocytes expressing ChR2 upon optical stimulation depolarize, resulting from alterations of membrane voltage and intracellular calcium (Keshmiri Neghab et al. 2021).	Eukaryota	Viridiplantae, Chlorophyta	Channelrhodopsin-2 of Volvox carteri (B4Y105)
3.E.1.7.4	Channelopsin, MChR1 (Govorunova et al., 2011). In another channelrhodopsin (CrChR2) of this family, an E97A mutation in TMS 2 prevents high affiinity binding of the inhibitor, Gd³⁺and interfers with photocurrent, but this ChR1 with an alanine at this position, has low affininty for Gd³⁺ but normal photocurrent (Watanabe et al. 2016).	Eukaryota	Viridiplantae, Streptophyta	MChR1 of Mesostigma viride (F8UVI5)
3.E.1.7.5	Channel rhodopsin of 829 aas and 7 N-terminal TMSs, KnChR. Channelrhodopsins (ChRs) are light-gated cation (H⁺, Na⁺, K⁺, and Ca²⁺) channels extensively applied as optogenetics tools for manipulating neuronal activity. All ChRs have a large cytoplasmic domain. The cation channel properties of KnChR from a filamentous terrestrial alga, Klebsormidium nitens, have been described (Tashiro et al. 2021). The C-terminal cytoplasmic domain has a peptidoglycan binding domain (FimV), and modulates the ion channel properties. The channel closure rate is affected by the C-terminus moiety, and truncation of the moiety to various lengths prolongs the channel open lifetime by more than 10-fold. Two Arginine residues (R287 and R291) are crucial for altering the photocurrent kinetics. Tashiro et al. 2021 proposed that electrostatic interaction between the rhodopsin domain and the C-terminal domain accelerates the channel kinetics. Maximal sensitivity was observed at 430 and 460 nm, the former making KnChR one of the most blue-shifted ChRs, serving as a novel prototype for studying the molecular mechanism of color tuning of the ChRs.	Eukaryota	Viridiplantae, Streptophyta	KnChR of Klebsormidium nitens
3.E.1.7.6	Catonic channelrhodopsin 1 of 630 aas and probably 7 N-terminal TMSs. (see Idzhilova et al. 2022 for reference).	Eukaryota	Viridiplantae, Chlorophyta	Channelrhodopsin 1 of Tetraselmis subcordiformis (Platymonas subcordiformis) (Carteria subcordiformis)
3.E.1.7.7	Cationic channelrhodopsin 3 of 511 aas and 7 probable TMSs (see Idzhilova et al. 2022.	Eukaryota	Viridiplantae, Chlorophyta	Cationic channelrhodoopsin 3 of Tetraselmis subcordiformis (Platymonas subcordiformis) (Carteria subcordiformis)
3.E.1.7.8	Light-activated cation selective ion channel [synthetic construct] of 344 aas and 7 probable TMSs. It is also called ComV1 or Ex3mV1Co. Channelrhodopsins have been utilized in gene therapy to restore vision in patients with retinitis pigmentosa (Hatakeyama et al. 2023). Channel kinetics (tauon and tauoff) were considerably altered by the replacement of the 172nd amino acid and was dependent on the amino acid characteristics. The size of amino acids at this position correlated with tauon and decay, whereas the solubility correlated with tauon and tauoff. Molecular dynamic simulation indicated that the ion tunnel constructed by H172, E121, and R306 widened due to H172A variant, whereas the interaction between A172 and the surrounding amino acids weakened compared with H172. The bottleneck radius of the ion gate constructed with the 172nd amino acid affected the photocurrent and channel kinetics. The 172nd amino acid in ComV1 is a key residue for determining channel kinetics as its properties alter the radius of the ion gate (Hatakeyama et al. 2023).			ComsV1, synthetic construct
3.E.1.7.9	Channel rhodopsin, mVChR1, synthetic construct, of 344 aas with possibly 7 TMSs (Tomita et al. 2014). This system has been used for the development of an optogenetic gene sensitive to daylight and it use in vision restoration for people (Watanabe et al. 2021).			mVChR1, a synthetic construct
3.E.1.7.10	Kalium (potassium) channelrhodoopsin 1, KCR1, of 265 aas and 7 TMSs. It shows higher selectivity for K⁺ than for Na⁺ and therefore is used to silence neurons with light (optogenetics). Replacement of the conserved cysteine residue in the TMS 3 (Cys110) with alanine or threonine results in a >1,000-fold decrease in the channel closing rate (Sineshchekov et al. 2023).	Eukaryota		KCR1 of Hyphochytrium catenoides
3.E.1.7.11	ChRmine of 318 aas and 7 TMSs. It is a pump-like cation-conducting channelrhodopsin that 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; Kishi et al. 2022 presented 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. The authors 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 (Kishi et al. 2022).	Eukaryota	Ciliophora	ChRmine of Tiarina fusa
3.E.1.7.12	Uncharacterized protein of 931 aas with 7 N-terminal TMSs.	Eukaryota		UP of Cafeteria roenbergensis
3.E.1.7.13	Cation channelrhodopsin 1, partial [synthetic construct] of 334 aas and 7 TMSs.	None		Cation-channelrhodopsin 1 (synthetic)
3.E.1.8.1	Anion-specific light-gated channel rhodopsin of 438 aas, Acr1, lacking measurable cation transport capability (Govorunova et al. 2015). The crystal structure of the light-gated anion channel, GtACR1, revealed a continuous tunnel traversing the protein from extracellular to intracellular sides (Li et al. 2021). The tunnel is the conductance channel closed by three constrictions: C1 in the extracellular half, mid-membrane C2 containing the photoactive site, and C3 on the cytoplasmic side. The crystal structure of bromide-bound GtACR1 revealed structural changes that relax the C1 and C3 constrictions, including a novel salt-bridge switch mechanism involving C1 and the photoactive site. Thus, substrate binding induces a transition from an inactivated state to a pre-activated state in the dark that facilitates channel opening by reducing free energy in the tunnel constrictions. The results provide direct evidence that the tunnel is the closed form of the channel of GtACR1 and shed light on the light-gated channel activation mechanism (Li et al. 2021). The preferential transport of NO₃^- by full-length Guillardia theta anion channelrhodopsin 1, ACR1, is enhanced by its extended cytoplasmic domain (Ohki et al. 2023).	Eukaryota		Arc1 of Guillardia theta
3.E.1.8.2	Anion-specific light-gated channel rhodopsin of 438 aas, Acr2, lacking measurable cation transport capability (Govorunova et al. 2015). Two conserved carboxylates, E159 and D230, play roles in the anion transport activity of ACR2 (Kojima et al. 2018).	Eukaryota		Acr2 of Guillardia theta
3.E.1.8.3	Homologue of anion-specific light-gated channel rhodopsin of 461 aas and 7 putative TMSs, lacking apparent channel activity (Govorunova et al. 2015).	Eukaryota		Acr homologue of Guillardia theta
3.E.1.8.4	Synthetic anion-specific channelrhodopsin of 307 aas and 7 TMSs, derived from an anion channel of Guillardia theta (Govorunova et al. 2018).			Channelrhodopsin of Guillardia theta
3.E.1.8.5	Light-activated anion channel rhodopsin of 300 aas and 7 TMSs [synthetic construct]. It is very similar or identical to PsuACR_353, a light-gated anion-selective channel from the marine cryptophyte algae, Proteomonas sulcata, with the highest transport rate for nitrate (NO₃^-) (Kikuchi et al. 2021). A Thr residue in the third TMS, which corresponds to Cys102 in GtACR1, contributes to the preference for NO₃^-.			PsuACR_353 of Proteomonas sulcata