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- PDB-9wfa: Cryo-EM structure of psXR -

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Basic information

Entry
Database: PDB / ID: 9wfa
TitleCryo-EM structure of psXR
ComponentspsXR
KeywordsMEMBRANE PROTEIN / rhodopsin / inward proton pump
Function / homologyChem-LUT / RETINAL
Function and homology information
Biological speciesGloeobacter violaceus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsMurakoshi, S. / Marin, M.C. / Tanaka, T. / Shihoya, W. / Beja, O. / Nureki, O.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP24KJ0909 Japan
Japan Science and TechnologyJPMJCR20E2 Japan
Japan Society for the Promotion of Science (JSPS)JP24K23232 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121012 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121002 Japan
CitationJournal: Commun Biol / Year: 2025
Title: Light-harvesting by antenna-containing xanthorhodopsin from an Antarctic Pseudanabaenaceae cyanobacterium.
Authors: María Del Carmen Marín / Shunya Murakoshi / Andrey Rozenberg / Tatsuki Tanaka / Masae Konno / Wataru Shihoya / Osamu Nureki / Oded Béjà / Keiichi Inoue /
Abstract: Microbial rhodopsins are light-sensitive proteins vital to various phototrophic and sensory processes in microorganisms. Xanthorhodopsins, with their dual chromophore system involving retinal and ...Microbial rhodopsins are light-sensitive proteins vital to various phototrophic and sensory processes in microorganisms. Xanthorhodopsins, with their dual chromophore system involving retinal and carotenoids, have been predominantly studied in the extreme halophilic bacterium Salinibacter ruber and in the early-branching thylakoid-less cyanobacterium Gloeobacter violaceus, where they facilitate light-driven outward proton pumping. However, their distribution, binding specificity, and ecological significance in cyanobacteria remain poorly understood. Here we report the incidence of xanthorhodopsin genes in cyanobacterial genomes and characterize psXR, a xanthorhodopsin from an uncultured Antarctic cyanobacterium from the filamentous family of Pseudanabaenaceae that binds a hydroxylated carotenoid antenna. Through bioinformatic, spectroscopic, functional and structural analyses, we determine the properties of psXR and potential physiological roles of cyanobacterial xanthorhodopsins. Our findings suggest xanthorhodopsins' role in modulating light-harvesting efficiency in cyanobacteria, particularly in extreme environments. The antenna binding and associated structural changes likely provide selective advantages for adapting to polar light conditions such as prolonged low light intensities and spectral shifts, contributing to cyanobacterial survival in harsh habitats.
History
DepositionAug 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: psXR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9113
Polymers32,0571
Non-polymers8532
Water45025
1
A: psXR
hetero molecules
x 5


Theoretical massNumber of molelcules
Total (without water)164,55415
Polymers160,2875
Non-polymers4,26710
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1_555x,y,z2
point symmetry operation2

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Components

#1: Protein psXR


Mass: 32057.432 Da / Num. of mol.: 1 / Mutation: N-terminal His6-tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: Cyanobacterial xanthorhodopsin reconstituted in MSP2N2 nanodiscs with soyPC
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.32 MDa / Experimental value: NO
Source (natural)Organism: Gloeobacter violaceus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5949
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19_4092model refinement
3EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7937467
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 327293 / Symmetry type: POINT
RefinementHighest resolution: 2.64 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0022019
ELECTRON MICROSCOPYf_angle_d0.5312763
ELECTRON MICROSCOPYf_dihedral_angle_d6.475313
ELECTRON MICROSCOPYf_chiral_restr0.037324
ELECTRON MICROSCOPYf_plane_restr0.004335

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