9JOX | pdb_00009jox

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

PDB DOI: https://doi.org/10.2210/pdb9JOX/pdb
EM Map EMD-61688: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Nonlabens marinus S1-08
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-25 Released: 2025-07-30
Deposition Author(s): Hosaka, T., Shirouzu, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota.

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.

(2025) Nat Microbiol 10: 2603-2615

PubMed: 40908369 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41564-025-02109-1
Primary Citation of Related Structures:
9JOU, 9JOV, 9JOW, 9JOX

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 ^T, 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.

Organizational Affiliation

Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

Macromolecule Content

Total Structure Weight: 165 kDa
Atom Count: 11,229
Modeled Residue Count: 1,315
Deposited Residue Count: 1,395
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloride pumping rhodopsin	A, B, C, D, E	279	Nonlabens marinus S1-08	Mutation(s): 0 Gene Names: ClR, NMS_1267
UniProt
Find proteins for W8VZW3 (Nonlabens marinus S1-08) Explore W8VZW3 Go to UniProtKB: W8VZW3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W8VZW3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 (Subject of Investigation/LOI) Query on PC1 Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain I [auth A] SDF format, chain NA [auth E] SDF format, chain R [auth B] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C]	FA [auth D], I [auth A], NA [auth E], R [auth B], Y [auth C]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain FA [auth D] Focus chain I [auth A] Focus chain NA [auth E] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain I [auth A] Focus chain NA [auth E] Focus chain R [auth B] Focus chain Y [auth C]
PLC (Subject of Investigation/LOI) Query on PLC Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain Z [auth C] SDF format, chain GA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain GA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain GA [auth D]	GA [auth D], J [auth A], L [auth A], S [auth B], Z [auth C]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain GA [auth D] Focus chain J [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain J [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain Z [auth C]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain F [auth A] SDF format, chain KA [auth E] SDF format, chain O [auth B] SDF format, chain V [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C]	CA [auth D], F [auth A], KA [auth E], O [auth B], V [auth C]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain CA [auth D] Focus chain F [auth A] Focus chain KA [auth E] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain F [auth A] Focus chain KA [auth E] Focus chain O [auth B] Focus chain V [auth C]
8K6 (Subject of Investigation/LOI) Query on 8K6 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain N [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain N [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain N [auth B]	AA [auth C], N [auth B]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain N [auth B] Interactions & Density Focus chain AA [auth C] Focus chain N [auth B]
R16 (Subject of Investigation/LOI) Query on R16 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain HA [auth D] SDF format, chain JA [auth E] SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain OA [auth E] MOL2 format, chain BA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain OA [auth E] mmCIF format, chain BA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B] mmCIF format, chain OA [auth E]	BA [auth D] HA [auth D] JA [auth E] M [auth A] OA [auth E] BA [auth D], HA [auth D], JA [auth E], M [auth A], OA [auth E], T [auth B]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain M [auth A] Focus chain OA [auth E] Focus chain T [auth B] Interactions & Density Focus chain BA [auth D] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain M [auth A] Focus chain OA [auth E] Focus chain T [auth B]
C14 (Subject of Investigation/LOI) Query on C14 Download Ideal Coordinates CCD File SDF format, chain PA [auth E] SDF format, chain U [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain U [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain U [auth B]	PA [auth E], U [auth B]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain PA [auth E] Focus chain U [auth B] Interactions & Density Focus chain PA [auth E] Focus chain U [auth B]
D12 (Subject of Investigation/LOI) Query on D12 Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain K [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain K [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain K [auth A]	IA [auth D], K [auth A]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain IA [auth D] Focus chain K [auth A] Interactions & Density Focus chain IA [auth D] Focus chain K [auth A]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain LA [auth E] SDF format, chain MA [auth E] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain P [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain P [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain P [auth B]	DA [auth D] EA [auth D] G [auth A] H [auth A] LA [auth E] DA [auth D], EA [auth D], G [auth A], H [auth A], LA [auth E], MA [auth E], P [auth B], Q [auth B], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C]