Structural Research of Rhodopsins

Rhodopsins, a class A member of the G protein-coupled receptor (GPCR) superfamily 2, is found in optic rod photoreceptor cells of the retina and converts light signals into chemical signals that stimulate biological processes in the nervous system of humans and other vertebrates. It is the first GPCR to have its 3D structure resolved by X-ray crystallography, and its structure is an essential model for understanding the structural and functional characteristics of other GPCRs.

Overall structure of bovine rhodopsin

The first data on the 3D structure of bovine rhodopsin came from circular dichroism (CD) studies of sonicated disks and purified proteins, and FTIR data provided information on the rhodopsin helix. The structure shows that the bovine rhodopsin has a seven-transmembrane (7TM) helical core with three loop regions on both sides of the membrane. The N-terminus is located on the outer cell side and consists of a double-stranded β-fold extending from Gly4 to Pro11. Its C-terminus is located on the cytoplasmic side. It extends from residue Met309 at the C-terminus of helix 7 to the last residue of the receptor and has a short amphipathic helix perpendicular to helix 7 (helix 8).

Structural analysis of fungal rhodopsin

Researchers have crystallized the proton pumping type 1 rhodopsin, the light-driven proton pump LR, from the unicellular fungus Leptosphaeria maculans using an endocyclization method and demonstrated its high-resolution (2.2 Å) crystal structure. The structure shows that the retinal chromophore is fixed in an all-trans conformation, with the protonated retinal Schiff base (RSB) pointing extracellularly and providing hydrogen bonding to the w8 molecule. The LR consists of seven transmembrane helices TM1-TM7 connected by three intracellular (ICL 1-3) and three extracellular (ECL 1-3) loops, with the retinal chromophore covalently attached to K270 on TM7.

Figure 1. The overall architecture of fungal rhodopsin (LR). (Zabelskii D, et al., 2021)

Protein	Organism	Method	Resolution	PDB Entry ID
Light-driven proton pump LR (Mac)	Plenodomus lingam	X-ray diffraction	2.2 Å	7BMH
Viral rhodopsin OLPVRII	Organic Lake phycodnavirus	X-ray diffraction	1.9 Å	6SQG
Cyanorhodopsin (CyR) N2098R	Calothrix sp. NIES-2098	X-ray diffraction	2.65 Å	6LM0
The transmembrane domain of rhodopsin phosphodiesterase	Salpingoeca rosetta	X-ray diffraction	2.6 Å	7CJ3
The transmembrane domain and linker region of rhodopsin phosphodiesterase	Salpingoeca rosetta	X-ray diffraction	3.5 Å	7D7Q
Microbial rhodopsin	Sphingomonas paucimobilis	X-ray diffraction	2.8 Å	8ANQ
Schizorhodopsin 4	Asgard group archaeon	X-ray diffraction	2.1 Å	7E4G
Blue light-absorbing proteorhodopsin	uncultured bacterium	X-ray diffraction	2.31 Å	4JQ6
Cyanorhodopsin (CyR) N4075R	Tolypothrix sp. NIES-4075	X-ray diffraction	1.9 Å	6LM1
Gloeobacter rhodopsin	Gloeobacter violaceus PCC 7421	X-ray diffraction	2 Å	6NWD
Sensory rhodopsin II	Natronomonas pharaonis	X-ray diffraction	2.1 Å	1H68
Sensory rhodopsin	Nostoc sp. PCC 7120 = FACHB-418	X-ray diffraction	2 Å	1XIO
Green-light absorbing proteorhodopsin	uncultured Gammaproteobacteria bacterium	Cryo-EM single particle analysis	2.93 Å	7B03
Sensory Rhodopsin Determined	Nostoc sp. PCC 7120 = FACHB-418	SOLID-STATE NMR	/	2M3G
Rhodopsin	Exiguobacterium sibiricum	X-ray diffraction	2.3 Å	4HYJ
Viral rhodopsin OLPVR1	Organic Lake phycodnavirus	X-ray diffraction	1.4 Å	7AKY
Xanthorhodopsin, a Light-Driven Ion Pump with Dual Chromophore	Salinibacter ruber	X-ray diffraction	1.9 Å	3DDL
Cruxrhodopsin-3	Haloarcula vallismortis	X-ray diffraction	2.3 Å	4JR8
Viral rhodopsins chimera O1O2	Organic Lake phycodnavirus	X-ray diffraction	1.96 Å	7AKW
Archaerhodopsin-1	Halorubrum ezzemoulense	X-ray diffraction	3.4 Å	1UAZ
The proton-pumping rhodopsin AR2	Acetabularia acetabulum	X-ray diffraction	3.2 Å	3AM6
Proteorhodopsin	uncultured marine gamma proteobacterium EBAC31A08	SOLUTION NMR	/	2L6X
The Closed State of Channelrhodopsin	Chlamydomonas reinhardtii	X-ray diffraction	2.3 Å	3UG9
The light-driven chloride ion-pumping rhodopsin, ClP	Nonlabens marinus S1-08	X-ray diffraction	1.581 Å	5B2N
Thermophilic rhodopsin	Thermus thermophilus JL-18	X-ray diffraction	2.8 Å	5AZD
The red light-activated channelrhodopsin Chrimson.	Chlamydomonas noctigama	X-ray diffraction	2.6 Å	5ZHI
N24Q/C128T mutant of Channelrhodopsin 2	Chlamydomonas reinhardtii	X-ray diffraction	2.7 Å	6EIG
Proton pump MAR rhodopsin pressurized with krypton	Candidatus Actinomarina minuta	X-ray diffraction	2.25 Å	7Q37
Halorhodopsin, a light-driven chloride pump	Halobacterium salinarum	X-ray diffraction	1.8 Å	1E12
wild-type Channelrhodopsin 2	Chlamydomonas reinhardtii	X-ray diffraction	2.39 Å	6EID

Table 1. Structural research of rhodopsins.

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References

Zabelskii D, et al. Structure-based insights into evolution of rhodopsins. Commun Biol. 2021. 4(1): 821.
Zhou XE, et al. Structure and activation of rhodopsin.Acta Pharmacol Sin. 2012. 33(3): 291-299.

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