[English] 日本語
Yorodumi
- PDB-9s1m: Cryo-EM structure of Posidonia oceanica L-PSI-LHCI-LHCII supercomplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9s1m
TitleCryo-EM structure of Posidonia oceanica L-PSI-LHCI-LHCII supercomplex
Components
  • (Chlorophyll a-b binding protein ...) x 4
  • (Photosystem I ...) x 15
KeywordsPHOTOSYNTHESIS / Photosystem I / large PSI-LHCI-LHCII / L-PSI-LHCI-LHCII / 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 / Chem-NEX / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT
Similarity search - Component
Biological speciesPosidonia oceanica (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Chlorophyll a-b binding protein 6 (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)
5: Chlorophyll a-b binding protein 6 (Lhca1)
6: 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, chloroplastic (PsaD1)
E: Photosystem I reaction center subunit IV B (PsaE2)
F: Photosystem I reaction center subunit III (PsaF)
G: Photosystem I reaction center subunit V (PsaG)
H: Photosystem I reaction center subunit VI-1 (PsaH)
I: Photosystem I reaction center subunit VIII (PsaI)
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK (PsaK)
L: Photosystem I reaction center subunit XI (PsaL)
O: Photosystem I subunit O (PsaO)
X: Chlorophyll a-b binding protein 1 (Lhcb1)
Y: Chlorophyll a-b binding protein 2 (Lhcb2)
Z: Chlorophyll a-b binding protein 1 (Lhcb1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)755,313340
Polymers497,05722
Non-polymers258,256318
Water00
1


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

-
Components

-
Chlorophyll a-b binding protein ... , 4 types, 7 molecules 1546XZY

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


Mass: 21878.111 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#18: Protein Chlorophyll a-b binding protein 1 (Lhcb1)


Mass: 24467.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)
#19: Protein Chlorophyll a-b binding protein 2 (Lhcb2)


Mass: 24816.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: T / Source: (natural) Posidonia oceanica (plant)

-
Photosystem I ... , 15 types, 15 molecules 23ABCDEFGHIJKLO

#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)
#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)
#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)
#8: Protein Photosystem I reaction center subunit II-1, chloroplastic (PsaD1)


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 B (PsaE2)


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 (PsaH)


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


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)
#17: Protein Photosystem I subunit O (PsaO)


Mass: 10036.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Posidonia oceanica (plant)

-
Sugars , 2 types, 6 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#30: 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

-
Non-polymers , 10 types, 312 molecules

#20: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 194 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#22: 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.: 14 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#23: 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.: 7 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#26: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#28: 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
#29: 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
#31: Chemical ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Large PSI-LHCI-LHCII supercomplex (L-PSI-LHCI-LHCII) / Type: COMPLEX
Details: PotosystemI-LHCII complex with an additional Lhca1-Lhca4 dimer
Entity ID: #1-#19 / 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

-
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

-
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: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37162 / 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: 97.96 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003852326
ELECTRON MICROSCOPYf_angle_d0.64574843
ELECTRON MICROSCOPYf_chiral_restr0.07516433
ELECTRON MICROSCOPYf_plane_restr0.00748053
ELECTRON MICROSCOPYf_dihedral_angle_d18.962512370

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more