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- EMDB-54379: Cryo-EM structure of Posidonia oceanica PSI-LHCI supercomplex - C... -

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Basic information

Entry
Database: EMDB / ID: EMD-54379
TitleCryo-EM structure of Posidonia oceanica PSI-LHCI supercomplex - Consensus map
Map dataSharpened map
Sample
  • Complex: Photosystem I (PSI-LHCI)
KeywordsPhotosystem I / PSI-LHCI / Posidonia oceanica / PHOTOSYNTHESIS
Biological speciesPosidonia oceanica (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsCapaldi S / Amelii A / Sanita G / Esposito M / Bassi R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101053983-GrInSunEuropean Union
CitationJournal: Nat Commun / Year: 2026
Title: Structural and spectral adaptation of the seagrass Posidonia oceanica photosystem I to seabed light.
Authors: Antonello Amelii / Stefano Capaldi / Mattia Russo / Zeno Guardini / Gennaro Sanità / Emanuela Esposito / Irene Olivé / Margherita Maiuri / Luca Dall'Osto / Giulio Cerullo / Gabriele ...Authors: Antonello Amelii / Stefano Capaldi / Mattia Russo / Zeno Guardini / Gennaro Sanità / Emanuela Esposito / Irene Olivé / Margherita Maiuri / Luca Dall'Osto / Giulio Cerullo / Gabriele Procaccini / Roberto Bassi /
Abstract: Seagrasses are marine angiosperms re-adapted to underwater life, forming productive ecosystems and long-term carbon sinks. Posidonia oceanica thrives up to 50 m depth, where light is scarce and ...Seagrasses are marine angiosperms re-adapted to underwater life, forming productive ecosystems and long-term carbon sinks. Posidonia oceanica thrives up to 50 m depth, where light is scarce and spectrally shifted; yet, the molecular basis of its photosynthetic adaptation remains unclear. Here, we report that P. oceanica genetically adapts for highly efficient photon use under dim light by enhancing photosystem antenna size and reducing exciton trapping time. We determine the structures of P. oceanica PSI supercomplexes by cryo-electron microscopy, revealing an expanded antenna system composed of PSI-LHCI, a trimeric phospho-LHCII, and an additional LHCI heterodimer. Low-energy chlorophyll forms associated with LHCI are lost. Ultrafast spectroscopy shows that this loss correlates with faster exciton trapping, which compensates for antenna expansion and enhances light-use efficiency under dim light. We identify key residues responsible for the loss of low-energy forms. Reversion to land-plant ortholog sequences restores red-shifted emission, providing strategies to enhance light-use efficiency in crops.
History
DepositionJul 15, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54379.png

Downloads & links

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Map

FileDownload / File: emd_54379.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.35720506 - 0.7436973
Average (Standard dev.)0.00047405716 (±0.017128464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54379_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_54379_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_54379_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_54379_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem I (PSI-LHCI)

EntireName: Photosystem I (PSI-LHCI)
Components
  • Complex: Photosystem I (PSI-LHCI)

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Supramolecule #1: Photosystem I (PSI-LHCI)

SupramoleculeName: Photosystem I (PSI-LHCI) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Posidonia oceanica (plant)

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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: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHepes
0.01 %C24H46O11n-DODECYL-beta-D-MALTOSIDE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 120603
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5zji


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.9)
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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