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- PDB-9s1l: Cryo-EM structure of Posidonia oceanica PSI-LHCI supercomplex -

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Basic information

Entry
Database: PDB / ID: 9s1l
TitleCryo-EM structure of Posidonia oceanica PSI-LHCI supercomplex
Components
  • (Chlorophyll a-b binding protein ...) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I chlorophyll a/b-binding protein ...) x 2
  • (Photosystem I reaction center subunit ...) x 9
  • Photosystem I iron-sulfur center (PsaC)
KeywordsPHOTOSYNTHESIS / Photosystem I / PSI-LHCI / Posidonia oceanica
Function / homology
Function and homology information


BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT
Similarity search - Component
Biological speciesPosidonia oceanica (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsCapaldi, S. / Amelii, A. / Sanita, G. / Esposito, M. / Bassi, R.
Funding supportEuropean Union, 1items
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 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 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

Downloads & links

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein 6, chloroplastic (Lhca1)
2: Photosystem I chlorophyll a/b-binding protein 2 (Lhca2)
3: Photosystem I chlorophyll a/b-binding protein 3-1 (Lhca3)
4: Chlorophyll a-b binding protein 4 (Lhca4)
A: Photosystem I P700 chlorophyll a apoprotein A1 (PsaA)
B: Photosystem I P700 chlorophyll a apoprotein A2 (PsaB)
C: Photosystem I iron-sulfur center (PsaC)
D: Photosystem I reaction center subunit II-1 (PsaD)
E: Photosystem I reaction center subunit IV A (PsaE1)
F: Photosystem I reaction center subunit III (PsaF)
G: Photosystem I reaction center subunit V (PsaG)
H: Photosystem I reaction center subunit VI-1 (PsaH1)
I: Photosystem I reaction center subunit VIII (PsaI)
J: Photosystem I reaction center subunit IX (PsaJ)
K: Photosystem I reaction center subunit psaK (PsaK)
L: Photosystem I reaction center subunit XI (PsaL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,968231
Polymers369,23316
Non-polymers173,735215
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Chlorophyll a-b binding protein ... , 2 types, 2 molecules 14

#1: Protein Chlorophyll a-b binding protein 6, chloroplastic (Lhca1)


Mass: 21878.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#4: Protein Chlorophyll a-b binding protein 4 (Lhca4)


Mass: 22158.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)

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Photosystem I chlorophyll a/b-binding protein ... , 2 types, 2 molecules 23

#2: Protein Photosystem I chlorophyll a/b-binding protein 2 (Lhca2)


Mass: 23094.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#3: Protein Photosystem I chlorophyll a/b-binding protein 3-1 (Lhca3)


Mass: 25149.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#5: Protein Photosystem I P700 chlorophyll a apoprotein A1 (PsaA)


Mass: 83217.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 (PsaB)


Mass: 82521.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)

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Protein , 1 types, 1 molecules C

#7: Protein Photosystem I iron-sulfur center (PsaC)


Mass: 9040.499 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)

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Photosystem I reaction center subunit ... , 9 types, 9 molecules DEFGHIJKL

#8: Protein Photosystem I reaction center subunit II-1 (PsaD)


Mass: 17169.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#9: Protein Photosystem I reaction center subunit IV A (PsaE1)


Mass: 10392.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#10: Protein Photosystem I reaction center subunit III (PsaF)


Mass: 17759.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#11: Protein Photosystem I reaction center subunit V (PsaG)


Mass: 11023.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#12: Protein Photosystem I reaction center subunit VI-1 (PsaH1)


Mass: 10508.876 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#13: Protein/peptide Photosystem I reaction center subunit VIII (PsaI)


Mass: 3940.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#14: Protein/peptide Photosystem I reaction center subunit IX (PsaJ)


Mass: 4777.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#15: Protein Photosystem I reaction center subunit psaK (PsaK)


Mass: 8471.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#16: Protein Photosystem I reaction center subunit XI (PsaL)


Mass: 18128.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)

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Sugars , 2 types, 5 molecules

#24: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#27: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 9 types, 210 molecules

#17: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 143 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#19: 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.: 5 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#23: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

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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: Photosystem I (PSI-LHCI) / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Posidonia oceanica (plant)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHepesC8H18N2O4S1
20.01 %n-DODECYL-beta-D-MALTOSIDEC24H46O111
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
7UCSF ChimeraX1.9model fitting
9PHENIX1.21.2_5419model refinement
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120603 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5ZJI

5zji


Accession code: 5ZJI / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 66.87 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003337562
ELECTRON MICROSCOPYf_angle_d0.627453493
ELECTRON MICROSCOPYf_chiral_restr0.07444664
ELECTRON MICROSCOPYf_plane_restr0.00755811
ELECTRON MICROSCOPYf_dihedral_angle_d19.03268731

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