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- EMDB-82304: In situ structure of the trans-lumenal/trans-stromal PSII-LHCII t... -

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Basic information

Entry
Database: EMDB / ID: EMD-82304
TitleIn situ structure of the trans-lumenal/trans-stromal PSII-LHCII trimer (focused on copy 1)
Map data
Sample
  • Complex: Chloroplast
KeywordsPhotosystem II / Trans-lumenal/trans-stromal PSII-LHCII trimer / in situ / Oryza sativa / Chloroplast / Photosynthesis
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.07 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
DepositionJul 17, 2026-
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_82304.png

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Map

FileDownload / File: emd_82304.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 384 pix.
= 574. Å		1.49 Å/pix.
x 384 pix.
= 574. Å		1.49 Å/pix.
x 384 pix.
= 574. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.49479 Å
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Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.25954744 - 0.51489735
Average (Standard dev.)0.00022823538 (±0.008691202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 574.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_82304_msk_1.map
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Half map: #2

Fileemd_82304_half_map_1.map
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Half map: #1

Fileemd_82304_half_map_2.map
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Sample components

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Entire : Chloroplast

EntireName: Chloroplast
Components
  • Complex: Chloroplast

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Supramolecule #1: Chloroplast

SupramoleculeName: Chloroplast / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#51
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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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:

21wv

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 37107
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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