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- PDB-9xj1: In situ structure of the PSI-LHCI supercomplex from Oryza sativa -

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Entry
Database: PDB / ID: 9xj1
TitleIn situ structure of the PSI-LHCI supercomplex from Oryza sativa
Components
  • (Chlorophyll a-b binding protein, ...) x 4
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 10
  • Os04g0414700 protein
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / PSI-LHCI / in situ / Oryza sativa / chloroplast
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding ...photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaO / PsaO transmembrane domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant ...Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaO / PsaO transmembrane domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / : / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-LUT / Chem-MGE / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-LUT / Chem-MGE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit IV / Chlorophyll a-b binding protein, chloroplastic / Os04g0414700 protein / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsLi, J. / Elias, E. / Zhang, K. / Croce, R. / Zhu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2026
Title: In situ structures of plant photosystem supercomplexes.
Authors: Jiao Li / Eduard Elias / Kai Zhang / Roberta Croce / Jiapeng Zhu /
Abstract: Photosynthesis sustains life on Earth by converting light to chemical energy through the coordinated action of photosystem I (PSI) and photosystem II (PSII) within thylakoid membranes. Although ...Photosynthesis sustains life on Earth by converting light to chemical energy through the coordinated action of photosystem I (PSI) and photosystem II (PSII) within thylakoid membranes. Although structures of isolated photosystems are available, their native organization in chloroplasts remains unknown. Here, using in situ cryo-electron microscopy, we directly imaged Oryza sativa (rice) chloroplasts and determined structures of photosystem supercomplexes in their native membrane environment. We resolved a CSML-type PSII-light harvesting complex II (LHCII) supercomplex, including four LHCII antenna trimers that were not retained in purified preparations. Excitation energy transfer calculations based on this architecture closely reproduce in vivo measurements, indicating its physiological relevance. We also resolved asymmetric PSII-LHCII dimers, including side-by-side, trans-lumenal and trans-stromal architectures, and higher-order assemblies of trimers and tetramers. On the basis of these observations, we propose that PSII forms a trans-lumenal and trans-stromal 'skeleton' that shapes thylakoid morphology and supports grana stacking. In addition, we obtained high-resolution structures of PSI-LHCI-LHCII and PSI-LHCI supercomplexes. Together, these structures reveal extensive networks of lipids, pigments and cofactors, providing the first molecular framework for understanding how the native architecture of plant photosystem supports the exceptional photon-to-electron efficiency of photosynthesis.
History
DepositionNov 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 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
1: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
4: Chlorophyll a-b binding protein, chloroplastic
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II, chloroplastic
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
G: Photosystem I reaction center subunit V, chloroplastic
H: Photosystem I reaction center subunit VI, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK, chloroplastic
L: Photosystem I reaction center subunit XI, chloroplastic
N: Photosystem I reaction center subunit N, chloroplastic
O: Os04g0414700 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)578,414262
Polymers381,89518
Non-polymers196,519244
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Chlorophyll a-b binding protein, ... , 4 types, 4 molecules 1234

#1: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22068.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q9ZSU0
#2: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22836.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q6ZL95
#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24450.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q6H748
#4: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22188.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q6YWJ7

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

#5: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 82463.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C353, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82638.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C356, photosystem I

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Protein , 2 types, 2 molecules CO

#7: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8909.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C359, photosystem I
#18: Protein Os04g0414700 protein


Mass: 10276.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q7XTG4

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Photosystem I reaction center subunit ... , 10 types, 10 molecules DEFGHIJKLN

#8: Protein Photosystem I reaction center subunit II, chloroplastic


Mass: 15983.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q84PB4
#9: Protein Photosystem I reaction center subunit IV


Mass: 7692.722 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q6Z3V7
#10: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17514.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q8S7H8
#11: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G


Mass: 10711.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q652C4
#12: Protein Photosystem I reaction center subunit VI, chloroplastic / PSI-H / Light-harvesting complex I 11 kDa protein / Protein GOS5


Mass: 10002.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q0DG05
#13: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3293.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C371
#14: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4981.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C373
#15: Protein Photosystem I reaction center subunit psaK, chloroplastic / PSI-K / Photosystem I subunit X


Mass: 8884.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q84PB5
#16: Protein Photosystem I reaction center subunit XI, chloroplastic / PSI subunit V


Mass: 17252.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q2QSR5
#17: Protein Photosystem I reaction center subunit N, chloroplastic


Mass: 9746.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q2QWN3

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Sugars , 1 types, 4 molecules

#29: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 10 types, 240 molecules

#19: Chemical
ChemComp-CHL / CHLOROPHYLL B


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


Mass: 893.489 Da / Num. of mol.: 152 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#21: 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
#22: 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
#23: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#25: Chemical
ChemComp-MGE / (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE / MONOGALACTOSYL-DIACYLGLYCEROL


Mass: 688.972 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H72O10 / Feature type: SUBJECT OF INVESTIGATION
#26: 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
#27: 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
#28: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / 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: In situ structure of the PSI-LHCI supercomplex from Oryza sativa
Type: COMPLEX / Entity ID: #8-#9 / Source: NATURAL
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 defocus max: 2200 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 1.375 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182666 / Symmetry type: POINT
RefinementHighest resolution: 2.38 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0141375
ELECTRON MICROSCOPYf_angle_d6.8958652
ELECTRON MICROSCOPYf_dihedral_angle_d23.23411025
ELECTRON MICROSCOPYf_chiral_restr0.2875210
ELECTRON MICROSCOPYf_plane_restr0.0166821

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