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- EMDB-61687: Cryo-EM structure of the myxol-bound light-driven chloride ion-pu... -

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Basic information

Entry
Database: EMDB / ID: EMD-61687
TitleCryo-EM structure of the myxol-bound light-driven chloride ion-pumping rhodopsin, NM-R3
Map data
Sample
  • Complex: NM-R3
    • Protein or peptide: x 1 types
  • Ligand: x 11 types
Keywordschloride ion-pumping rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin / MEMBRANE PROTEIN
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / photoreceptor activity / phototransduction / membrane / Chloride pumping rhodopsin
Function and homology information
Biological speciesNonlabens marinus S1-08 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsHosaka T / Shirouzu M
Funding support Japan, 1 items
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, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61687.png

Downloads & links

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Map

FileDownload / File: emd_61687.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 220 pix.
= 182.27 Å		0.83 Å/pix.
x 220 pix.
= 182.27 Å		0.83 Å/pix.
x 220 pix.
= 182.27 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.042
Minimum - Maximum-0.05022373 - 0.12722413
Average (Standard dev.)0.0011104569 (±0.0079644285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 182.26999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61687_msk_1.map
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Half map: #2

Fileemd_61687_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_61687_half_map_2.map
Projections & Slices
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Sample components

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Entire : NM-R3

EntireName: NM-R3
Components
  • Complex: NM-R3
    • Protein or peptide: Chloride pumping rhodopsin
  • Ligand: RETINAL
  • Ligand: (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
  • Ligand: CHLORIDE ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: HEXADECANE
  • Ligand: Octadecane
  • Ligand: DODECANE
  • Ligand: TETRADECANE
  • Ligand: DECANE
  • Ligand: water

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Supramolecule #1: NM-R3

SupramoleculeName: NM-R3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)

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Macromolecule #1: Chloride pumping rhodopsin

MacromoleculeName: Chloride pumping rhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)
Molecular weightTheoretical: 30.710936 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSSGSSGMKN IESLFDYSAG QFEFIDHLLT MGVGVHFAAL IFFLVVSQFV APKYRIATAL SCIVMVSAGL ILNSQAVMWT DAYAYVDGS YQLQDLTFSN GYRYVNWMAT IPCLLLQLLI VLNLKGKELF STATWLILAA WGMIITGYVG QLYEVDDIAQ L MIWGAVST ...String:
GSSGSSGMKN IESLFDYSAG QFEFIDHLLT MGVGVHFAAL IFFLVVSQFV APKYRIATAL SCIVMVSAGL ILNSQAVMWT DAYAYVDGS YQLQDLTFSN GYRYVNWMAT IPCLLLQLLI VLNLKGKELF STATWLILAA WGMIITGYVG QLYEVDDIAQ L MIWGAVST AFFVVMNWIV GTKIFKNRAT MLGGTDSTIT KVFWLMMFAW TLYPIAYLVP AFMNNADGVV LRQLLFTIAD IS SKVIYGL MITYIAIQQS AAAGYVPAQQ ALGRIGMDSK AA

UniProtKB: Chloride pumping rhodopsin

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Macromolecule #2: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 2 / Number of copies: 5 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #3: (3~{S},4~{Z},6~{E},8~{Z},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E...

MacromoleculeName: (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- ...Name: (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
type: ligand / ID: 3 / Number of copies: 5 / Formula: A1L4O
Molecular weightTheoretical: 584.871 Da

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Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 10 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #5: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 5 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #6: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 6 / Number of copies: 5 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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Macromolecule #7: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 7 / Number of copies: 11 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #8: Octadecane

MacromoleculeName: Octadecane / type: ligand / ID: 8 / Number of copies: 3 / Formula: 8K6
Molecular weightTheoretical: 254.494 Da
Chemical component information

ChemComp-8K6:
Octadecane

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Macromolecule #9: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 9 / Number of copies: 3 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #10: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 10 / Number of copies: 6 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #11: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 11 / Number of copies: 1 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 187 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.425 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5b2n

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 791219
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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