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- EMDB-66974: In situ C2S2M2L4-type PSII-LHCII supercomplex, two loosely bound ... -

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Entry
Database: EMDB / ID: EMD-66974
TitleIn situ C2S2M2L4-type PSII-LHCII supercomplex, two loosely bound (L-) LHCII trimers at one side, protomer 2
Map data
Sample
  • Complex: In situ C2S2M2L4-type PSII-LHCII supercomplex, two loosely bound (L-) LHCII trimers at one side, protomer 2
    • Other: Chlorophyll a-b binding protein 1, chloroplastic
    • Other: Chlorophyll a-b binding protein, chloroplastic
KeywordsPhotosystem II / C2S2M2L4-type / L-LHCII / in situ / Oryza sativa / chloroplast / photosynthesis
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.04 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 6, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66974.png

Downloads & links

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Map

FileDownload / File: emd_66974.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.)
1.28 Å/pix.
x 512 pix.
= 656. Å		1.28 Å/pix.
x 512 pix.
= 656. Å		1.28 Å/pix.
x 512 pix.
= 656. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.28125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-1.2264234 - 1.0872489
Average (Standard dev.)0.000016058437 (±0.0044351756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 656.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66974_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66974_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, two loosely bound ...

EntireName: In situ C2S2M2L4-type PSII-LHCII supercomplex, two loosely bound (L-) LHCII trimers at one side, protomer 2
Components
  • Complex: In situ C2S2M2L4-type PSII-LHCII supercomplex, two loosely bound (L-) LHCII trimers at one side, protomer 2
    • Other: Chlorophyll a-b binding protein 1, chloroplastic
    • Other: Chlorophyll a-b binding protein, chloroplastic

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Supramolecule #1: In situ C2S2M2L4-type PSII-LHCII supercomplex, two loosely bound ...

SupramoleculeName: In situ C2S2M2L4-type PSII-LHCII supercomplex, two loosely bound (L-) LHCII trimers at one side, protomer 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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

MacromoleculeName: Chlorophyll a-b binding protein 1, chloroplastic / type: other / ID: 1 / Classification: other
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
SequenceString: SPWYGADRVL YLGPLSGEPP SYLTGEFPGD YGWDTAGLSA DPETFAKNRE LEVIHSRWAM LGALGCVFPE LLARNGVKFG EAVWFKAGSQ IFSEGGLDYL GNPSLIHAQS ILAIWAVQVV LMGAVEGYRI AGGPLGEVVD PLYPGGAFDP LGLADDPEAF AELKVKEIKN ...String:
SPWYGADRVL YLGPLSGEPP SYLTGEFPGD YGWDTAGLSA DPETFAKNRE LEVIHSRWAM LGALGCVFPE LLARNGVKFG EAVWFKAGSQ IFSEGGLDYL GNPSLIHAQS ILAIWAVQVV LMGAVEGYRI AGGPLGEVVD PLYPGGAFDP LGLADDPEAF AELKVKEIKN GRLAMFSMFG FFVQAIVTGK GPLENLADHL ADPVNNNAWA YATNFVPGK

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: other / ID: 2 / Classification: other
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
SequenceString: APQSIWYGPD RPKYLGPFSE QTPSYLTGEF PGDYGWDTAG LSADPETFAR NRELEVIHSR WAMLGALGCV FPEILSKNGV KFGEAVWFKA GAQIFSEGGL DYLGNPNLVH AQSILAIWAV QVVLMGFVEG YRVGGGPLGE GLDKVYPGGA FDPLGLADDP DTFAELKVKE ...String:
APQSIWYGPD RPKYLGPFSE QTPSYLTGEF PGDYGWDTAG LSADPETFAR NRELEVIHSR WAMLGALGCV FPEILSKNGV KFGEAVWFKA GAQIFSEGGL DYLGNPNLVH AQSILAIWAV QVVLMGFVEG YRVGGGPLGE GLDKVYPGGA FDPLGLADDP DTFAELKVKE LKNGRLAMFS MFGFFVQAIV TGKGPIENLF DHVADPVANN AWAYATNFVP GK

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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: 5.04 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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