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- EMDB-65924: Cryo-EM structure of psXR -

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Basic information

Entry
Database: EMDB / ID: EMD-65924
TitleCryo-EM structure of psXR
Map data
Sample
  • Complex: Cyanobacterial xanthorhodopsin reconstituted in MSP2N2 nanodiscs with soyPC
    • Protein or peptide: psXR
  • Ligand: RETINAL
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: water
Keywordsrhodopsin / inward proton pump / MEMBRANE PROTEIN
Biological speciesGloeobacter violaceus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsMurakoshi S / Marin MC / Tanaka T / Shihoya W / Beja O / Nureki O
Funding support Japan, 5 items
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, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65924.png

Downloads & links

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Map

FileDownload / File: emd_65924.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 216 pix.
= 239.76 Å		1.11 Å/pix.
x 216 pix.
= 239.76 Å		1.11 Å/pix.
x 216 pix.
= 239.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0456
Minimum - Maximum-1.2675344 - 1.6171293
Average (Standard dev.)-0.0000152293605 (±0.04264876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 239.76001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65924_msk_1.map
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Half map: #2

Fileemd_65924_half_map_1.map
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Half map: #1

Fileemd_65924_half_map_2.map
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Sample components

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Entire : Cyanobacterial xanthorhodopsin reconstituted in MSP2N2 nanodiscs ...

EntireName: Cyanobacterial xanthorhodopsin reconstituted in MSP2N2 nanodiscs with soyPC
Components
  • Complex: Cyanobacterial xanthorhodopsin reconstituted in MSP2N2 nanodiscs with soyPC
    • Protein or peptide: psXR
  • Ligand: RETINAL
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: water

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Supramolecule #1: Cyanobacterial xanthorhodopsin reconstituted in MSP2N2 nanodiscs ...

SupramoleculeName: Cyanobacterial xanthorhodopsin reconstituted in MSP2N2 nanodiscs with soyPC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gloeobacter violaceus (bacteria)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: psXR

MacromoleculeName: psXR / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus (bacteria)
Molecular weightTheoretical: 32.057432 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSISLITDFA LLAQSNLPET VSKVDFLSSG QYNLVYNAFS FAIATMLAAA LFFFNVRGQV GQKYQLALIV SALVVSIAGY HYYRIFGSW EAAYSLQNGN YVLTGAPFND AYRYVDWLLT VPLLLVETVA VLALPGMEAR PLLIKLVVAA ILMIATGYPG E ISTDLNTR ...String:
MSISLITDFA LLAQSNLPET VSKVDFLSSG QYNLVYNAFS FAIATMLAAA LFFFNVRGQV GQKYQLALIV SALVVSIAGY HYYRIFGSW EAAYSLQNGN YVLTGAPFND AYRYVDWLLT VPLLLVETVA VLALPGMEAR PLLIKLVVAA ILMIATGYPG E ISTDLNTR IVWGAVSTVP FIYILYILWI ELSKSLLRQP EGVQTLVKNM RLLLLFSWGV YPIAYLLPML GISGATADVG VQ IGYTIAD VLAKPIFGLL VFAIALEKTR VDAGEQPTKE SPMTMISSHH HHHH

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Macromolecule #2: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 2 / Number of copies: 1 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #3: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 3 / Number of copies: 1 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 25 / 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: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5949 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7937467
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 327293
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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