9JOW | pdb_00009jow

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

PDB DOI: https://doi.org/10.2210/pdb9JOW/pdb
EM Map EMD-61687: 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: 2.48 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: 170.42 kDa
Atom Count: 11,677
Modeled Residue Count: 1,320
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 10 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 W [auth B] SDF format, chain SA [auth D] SDF format, chain J [auth A] SDF format, chain HA [auth C] SDF format, chain CB [auth E] MOL2 format, chain W [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain CB [auth E] mmCIF format, chain W [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain CB [auth E]	CB [auth E], HA [auth C], J [auth A], SA [auth D], W [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain CB [auth E] Focus chain HA [auth C] Focus chain J [auth A] Focus chain SA [auth D] Focus chain W [auth B] Interactions & Density Focus chain CB [auth E] Focus chain HA [auth C] Focus chain J [auth A] Focus chain SA [auth D] Focus chain W [auth B]
PLC (Subject of Investigation/LOI) Query on PLC Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain TA [auth D] SDF format, chain P [auth A] SDF format, chain K [auth A] SDF format, chain IA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth C]	IA [auth C], K [auth A], P [auth A], TA [auth D], X [auth B]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain IA [auth C] Focus chain K [auth A] Focus chain P [auth A] Focus chain TA [auth D] Focus chain X [auth B] Interactions & Density Focus chain IA [auth C] Focus chain K [auth A] Focus chain P [auth A] Focus chain TA [auth D] Focus chain X [auth B]
A1L4O Query on A1L4O Download Ideal Coordinates CCD File SDF format, chain ZA [auth E] SDF format, chain T [auth B] SDF format, chain PA [auth D] SDF format, chain G [auth A] SDF format, chain EA [auth C] MOL2 format, chain ZA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth C] mmCIF format, chain ZA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth C]	EA [auth C], G [auth A], PA [auth D], T [auth B], ZA [auth E]	(3~{S},4~{Z},6~{E},8~{Z},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-25-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]pentacosa-4,6,8,10,12,14,16,18,20,22,24-undecaene-2,3-diol C₄₀ H₅₆ O₃ JJPMVSRTRMLHST-CNFSYYPWSA-N		Interactions Focus chain EA [auth C] Focus chain G [auth A] Focus chain PA [auth D] Focus chain T [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain EA [auth C] Focus chain G [auth A] Focus chain PA [auth D] Focus chain T [auth B] Focus chain ZA [auth E]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain YA [auth E] SDF format, chain S [auth B] SDF format, chain OA [auth D] SDF format, chain F [auth A] SDF format, chain DA [auth C] MOL2 format, chain YA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain DA [auth C] mmCIF format, chain YA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain DA [auth C]	DA [auth C], F [auth A], OA [auth D], S [auth B], YA [auth E]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain DA [auth C] Focus chain F [auth A] Focus chain OA [auth D] Focus chain S [auth B] Focus chain YA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain F [auth A] Focus chain OA [auth D] Focus chain S [auth B] Focus chain YA [auth E]
8K6 (Subject of Investigation/LOI) Query on 8K6 Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth C]	MA [auth C], N [auth A], R [auth B]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain MA [auth C] Focus chain N [auth A] Focus chain R [auth B] Interactions & Density Focus chain MA [auth C] Focus chain N [auth A] Focus chain R [auth B]
R16 (Subject of Investigation/LOI) Query on R16 Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain XA [auth E] SDF format, chain VA [auth D] SDF format, chain UA [auth D] SDF format, chain Q [auth A] SDF format, chain NA [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain FB [auth E] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain VA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain FB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain VA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain FB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] FB [auth E] L [auth A] M [auth A] AA [auth B], BA [auth B], FB [auth E], L [auth A], M [auth A], NA [auth D], Q [auth A], UA [auth D], VA [auth D], XA [auth E], Z [auth B]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain FB [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain Q [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain XA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain FB [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain Q [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain XA [auth E] Focus chain Z [auth B]
C14 (Subject of Investigation/LOI) Query on C14 Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain GB [auth E] SDF format, chain EB [auth E] SDF format, chain CA [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain GB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain CA [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain GB [auth E] mmCIF format, chain EB [auth E] mmCIF format, chain CA [auth B]	CA [auth B] EB [auth E] GB [auth E] JA [auth C] KA [auth C] CA [auth B], EB [auth E], GB [auth E], JA [auth C], KA [auth C], Y [auth B]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain EB [auth E] Focus chain GB [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain Y [auth B] Interactions & Density Focus chain CA [auth B] Focus chain EB [auth E] Focus chain GB [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain Y [auth B]
D12 (Subject of Investigation/LOI) Query on D12 Download Ideal Coordinates CCD File SDF format, chain WA [auth D] SDF format, chain O [auth A] SDF format, chain DB [auth E] MOL2 format, chain WA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain DB [auth E] mmCIF format, chain WA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain DB [auth E]	DB [auth E], O [auth A], WA [auth D]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain DB [auth E] Focus chain O [auth A] Focus chain WA [auth D] Interactions & Density Focus chain DB [auth E] Focus chain O [auth A] Focus chain WA [auth D]
D10 (Subject of Investigation/LOI) Query on D10 Download Ideal Coordinates CCD File SDF format, chain LA [auth C] MOL2 format, chain LA [auth C] mmCIF format, chain LA [auth C]	LA [auth C]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain LA [auth C] Interactions & Density Focus chain LA [auth C]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain BB [auth E] SDF format, chain AB [auth E] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain BB [auth E] MOL2 format, chain AB [auth E] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain BB [auth E] mmCIF format, chain AB [auth E]	AB [auth E] BB [auth E] FA [auth C] GA [auth C] H [auth A] AB [auth E], BB [auth E], FA [auth C], GA [auth C], H [auth A], I [auth A], QA [auth D], RA [auth D], U [auth B], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B]