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- EMDB-66952: In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (... -

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Basic information

Entry
Database: EMDB / ID: EMD-66952
TitleIn situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 2
Map data
Sample
  • Complex: In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 2
    • Protein or peptide: Chlorophyll a-b binding protein 2, chloroplastic
    • Protein or peptide: Chlorophyll a/b-binding protein
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL B
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (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
KeywordsPhotosystem II / C2S2M2L4-type / M-LHCII / in situ / Oryza sativa / chloroplast / Photosynthesis
Function / homology
Function and homology information


photosynthesis, light harvesting / chloroplast thylakoid membrane / photosynthesis / mRNA binding
Similarity search - Function
Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein
Similarity search - Domain/homology
Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein 2, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsLi J / Elias E / Zhang K / Croce R / Zhu J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201038 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 5, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66952.png

Downloads & links

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Map

FileDownload / File: emd_66952.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.41953412 - 0.6712755
Average (Standard dev.)0.000020525142 (±0.0056959507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66952_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66952_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66952_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (...

EntireName: In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 2
Components
  • Complex: In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 2
    • Protein or peptide: Chlorophyll a-b binding protein 2, chloroplastic
    • Protein or peptide: Chlorophyll a/b-binding protein
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL B
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (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

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Supramolecule #1: In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (...

SupramoleculeName: In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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Macromolecule #1: Chlorophyll a-b binding protein 2, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 2, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 23.441461 KDa
SequenceString: GSPWYGADRV LYLGPLSGEP PSYLTGEFPG DYGWDTAGLS ADPETFAKNR ELEVIHSRWA MLGALGCVFP ELLARNGVKF GEAVWFKAG SQIFSEGGLD YLGNPSLIHA QSILAIWAVQ VVLMGAVEGY RIAGGPLGEV VDPLYPGGSF DPLGLADDPE A FAELKVKE ...String:
GSPWYGADRV LYLGPLSGEP PSYLTGEFPG DYGWDTAGLS ADPETFAKNR ELEVIHSRWA MLGALGCVFP ELLARNGVKF GEAVWFKAG SQIFSEGGLD YLGNPSLIHA QSILAIWAVQ VVLMGAVEGY RIAGGPLGEV VDPLYPGGSF DPLGLADDPE A FAELKVKE IKNGRLAMFS MFGFFVQAIV TGKGPLENLA DHLADPVNNN AWAYATNFVP G

UniProtKB: Chlorophyll a-b binding protein 2, chloroplastic

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Macromolecule #2: Chlorophyll a/b-binding protein

MacromoleculeName: Chlorophyll a/b-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 24.065338 KDa
SequenceString: ELWYGPDRVK YLGPFSAQTP SYLRGEFPGD YGWDTAGLSA DPEAFARNRA LEVIHGRWAM LGALGCITPE VLEKWVRVDF KEPVWFKAG AQIFSDGGLD YLGNPNLVHA QSILAVLGFQ VVLMGLVEGY RINGLPGVGD GNDLYPGGQY FDPLGLADDP V TFAELKVK ...String:
ELWYGPDRVK YLGPFSAQTP SYLRGEFPGD YGWDTAGLSA DPEAFARNRA LEVIHGRWAM LGALGCITPE VLEKWVRVDF KEPVWFKAG AQIFSDGGLD YLGNPNLVHA QSILAVLGFQ VVLMGLVEGY RINGLPGVGD GNDLYPGGQY FDPLGLADDP V TFAELKVK EIKNGRLAMF SMFGFFVQAI VTGKGPLENL LDHLADPVAN NAWVYATKFT PG

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 22.55058 KDa
SequenceString: AKKSWIPAFK SDAEFINPPW LDGSLPGDFG FDPLGLGKDP AFLKWYREAE LIHGRWAMAA VLGIFVGQAW SGVPWFEAGA QPEAIAPFS FGSLLGTQLL LMGWVESKRW VDFFNPDSQA VEWATPWSRT AENFSNATGE QGYPGGKFFD PLGLGGETRD G VYIPDTDK ...String:
AKKSWIPAFK SDAEFINPPW LDGSLPGDFG FDPLGLGKDP AFLKWYREAE LIHGRWAMAA VLGIFVGQAW SGVPWFEAGA QPEAIAPFS FGSLLGTQLL LMGWVESKRW VDFFNPDSQA VEWATPWSRT AENFSNATGE QGYPGGKFFD PLGLGGETRD G VYIPDTDK LDRLKLAEIK HARLAMLAML IFYFEAGQGK TPLGALG

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #4: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 25.938283 KDa
SequenceString: RPLWFPGAVA PDYLDGSLVG DYGFDPFGLG KPAEYLQFEL DSLDQNLAKN NAGEIIGTRF ETGEVKSTPF QPYTEVFGLQ RFRECELIH GRWAMLATLG ALSVEWLTGV TWQDAGKVEL VDGSSYLGQP LPFSISTLIW IEVLVIGYIE FQRNAELDPE K RLYPGGSY ...String:
RPLWFPGAVA PDYLDGSLVG DYGFDPFGLG KPAEYLQFEL DSLDQNLAKN NAGEIIGTRF ETGEVKSTPF QPYTEVFGLQ RFRECELIH GRWAMLATLG ALSVEWLTGV TWQDAGKVEL VDGSSYLGQP LPFSISTLIW IEVLVIGYIE FQRNAELDPE K RLYPGGSY FDPLGLASDP EKKERLQLAE IKHARLAMVA FLGFAVQAAA TGKGPLNNWA THLSDPLHTT IFDTFS

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #5: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 5 / Number of copies: 37 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #6: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 6 / Number of copies: 25 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #7: (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: 7 / Number of copies: 3 / 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 #8: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 8 / Number of copies: 2 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #9: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (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
type: ligand / ID: 9 / Number of copies: 1 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

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

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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: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.375 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xnl

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 172752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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