9JOV | pdb_00009jov

Cryo-EM structure of the myxol-bound light-driven proton pumping rhodopsin, NM-R1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.27 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

  • 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteorhodopsin
A, B, C, D, E
254Nonlabens marinus S1-08Mutation(s): 0 
Gene Names: NMS_0162
UniProt
Find proteins for W8VZ92 (Nonlabens marinus S1-08)
Explore W8VZ92 
Go to UniProtKB:  W8VZ92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW8VZ92
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L4O
Query on A1L4O

Download Ideal Coordinates CCD File 
BA [auth C],
JA [auth D],
L [auth A],
RA [auth E],
T [auth B]
(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
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
F [auth A],
FA [auth D],
NA [auth E],
P [auth B],
X [auth C]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
R16 (Subject of Investigation/LOI)
Query on R16

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth D]
G [auth A]
GA [auth D]
H [auth A]
CA [auth C],
DA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
KA [auth D],
LA [auth E],
M [auth A],
N [auth A],
OA [auth E],
Q [auth B],
R [auth B],
SA [auth E],
U [auth B],
V [auth C],
Y [auth C],
Z [auth C]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
D12 (Subject of Investigation/LOI)
Query on D12

Download Ideal Coordinates CCD File 
AA [auth C]
EA [auth D]
IA [auth D]
J [auth A]
K [auth A]
AA [auth C],
EA [auth D],
IA [auth D],
J [auth A],
K [auth A],
MA [auth E],
O [auth A],
PA [auth E],
QA [auth E],
S [auth B],
W [auth C]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Data collection, Database references