9JOX

Cryo-EM structure of the light-driven chloride ion-pumping rhodopsin, NM-R3

Summary for 9JOX

• Entry DOI: 10.2210/pdb9jox/pdb
• EMDB information: 61688
• Descriptor: Chloride pumping rhodopsin, RETINAL, CHLORIDE ION, ... (10 entities in total)
• Functional Keywords: chloride ion-pumping rhodopsin retinal cell-free synthesis bacterial type rhodopsin, membrane protein
• Biological source: Nonlabens marinus S1-08
• Total number of polymer chains: 5
• Total formula weight: 165001.37

Authors

Hosaka, T.,Shirouzu, M. (deposition date: 2024-09-25, release date: 2025-07-30, Last modification date: 2026-02-18)

Primary citation

Fujiwara, T.,Hosaka, T.,Hasegawa-Takano, M.,Nishimura, Y.,Tominaga, K.,Mori, K.,Nishino, S.,Takahashi, Y.,Uchikubo-Kamo, T.,Hanada, K.,Maoka, T.,Takaichi, S.,Inoue, K.,Shirouzu, M.,Yoshizawa, S.
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota.
Nat Microbiol, 10:2603-2615, 2025

PubMed Abstract: Microbial rhodopsins are photoreceptor proteins widely distributed in marine microorganisms that harness light energy and support marine ecosystems. While retinal is typically the sole chromophore in microbial rhodopsins, some proteorhodopsins, which are proton-pumping rhodopsins abundant in the ocean, use carotenoid antennae to transfer light energy to retinal. However, the mechanism by which carotenoids enhance rhodopsin functions remains unclear. Here, using the marine Bacteroidota isolate Nonlabens marinus S1-08, we reconstituted complexes of rhodopsins with the carotenoid myxol and detected energy transfer to retinal in both proteorhodopsin and chloride ion-pumping rhodopsin. Carotenoid binding facilitated light harvesting and accelerated the photocycle, thereby improving the light utilization efficiency of proteorhodopsin. Cryogenic electron microscopy structural analysis further revealed the molecular architecture of the carotenoid-rhodopsin complexes. The ability to bind carotenoids is conserved in rhodopsins of the marine-dominant phylum Bacteroidota, which are widely transcribed in the photic zone. These findings reveal how carotenoids enhance rhodopsin functions in marine Bacteroidota.

PubMed: 40908369
DOI: 10.1038/s41564-025-02109-1

Experimental method

ELECTRON MICROSCOPY (2.5 Å)