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- PDB-9jow: Cryo-EM structure of the myxol-bound light-driven chloride ion-pu... -

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Basic information

Entry
Database: PDB / ID: 9jow
TitleCryo-EM structure of the myxol-bound light-driven chloride ion-pumping rhodopsin, NM-R3
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / chloride ion-pumping rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin
Function / homology
Function and homology information


photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
Octadecane / : / TETRADECANE / DECANE / DODECANE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DIUNDECYL PHOSPHATIDYL CHOLINE / HEXADECANE / RETINAL / Chloride pumping rhodopsin
Similarity search - Component
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsHosaka, T. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Microbiol / Year: 2025
Title: Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota.
Authors: Takayoshi Fujiwara / Toshiaki Hosaka / Masumi Hasegawa-Takano / Yosuke Nishimura / Kento Tominaga / Kaho Mori / Satoshi Nishino / Yuno Takahashi / Tomomi Uchikubo-Kamo / Kazuharu Hanada / ...Authors: Takayoshi Fujiwara / Toshiaki Hosaka / Masumi Hasegawa-Takano / Yosuke Nishimura / Kento Tominaga / Kaho Mori / Satoshi Nishino / Yuno Takahashi / Tomomi Uchikubo-Kamo / Kazuharu Hanada / Takashi Maoka / Shinichi Takaichi / Keiichi Inoue / Mikako Shirouzu / Susumu Yoshizawa /
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 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.
History
DepositionSep 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloride pumping rhodopsin
B: Chloride pumping rhodopsin
C: Chloride pumping rhodopsin
D: Chloride pumping rhodopsin
E: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,41959
Polymers153,5555
Non-polymers16,86454
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Chloride pumping rhodopsin


Mass: 30710.936 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Gene: ClR, NMS_1267 / Production host: Escherichia coli (E. coli) / References: UniProt: W8VZW3

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Non-polymers , 11 types, 241 molecules

#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-A1L4O / (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


Mass: 584.871 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#6: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H65NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#7: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C16H34 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H30 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NM-R3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60.425 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 791219 / Symmetry type: POINT
RefinementResolution: 2.48→2.48 Å / Cor.coef. Fo:Fc: 0.833 / SU B: 4.051 / SU ML: 0.08 / ESU R: 0.205
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.28332 --
obs0.28332 165207 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 101.513 Å2
Refinement stepCycle: 1 / Total: 11677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0130.01211711
ELECTRON MICROSCOPYr_bond_other_d00.01612118
ELECTRON MICROSCOPYr_angle_refined_deg2.1311.79815727
ELECTRON MICROSCOPYr_angle_other_deg0.8421.69427773
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.79951315
ELECTRON MICROSCOPYr_dihedral_angle_2_deg16.314585
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.098101700
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1090.21740
ELECTRON MICROSCOPYr_gen_planes_refined0.0120.0212760
ELECTRON MICROSCOPYr_gen_planes_other0.0080.022750
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it10.8118.5675275
ELECTRON MICROSCOPYr_mcbond_other10.7738.5655274
ELECTRON MICROSCOPYr_mcangle_it12.12215.4546585
ELECTRON MICROSCOPYr_mcangle_other12.12115.4556586
ELECTRON MICROSCOPYr_scbond_it15.85910.8426436
ELECTRON MICROSCOPYr_scbond_other15.85810.8436437
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other21.84919.269143
ELECTRON MICROSCOPYr_long_range_B_refined23.68586.5113143
ELECTRON MICROSCOPYr_long_range_B_other23.68486.5113144
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.609 12317 -
obs--100 %

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