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- EMDB-60801: The structure of C4S4M2 type PSII-LHCII megacomplex from Spinach -

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Basic information

Entry
Database: EMDB / ID: EMD-60801
TitleThe structure of C4S4M2 type PSII-LHCII megacomplex from Spinach
Map data
Sample
  • Complex: Photosystem II-light harvesting complex II megacomplex
KeywordsPSII / megacomplex / PSII array / PHOTOSYNTHESIS
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsShan J / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Sci Adv / Year: 2024
Title: Architecture and functional regulation of a plant PSII-LHCII megacomplex.
Authors: Jianyu Shan / Dariusz M Niedzwiedzki / Rupal S Tomar / Zhenfeng Liu / Haijun Liu /
Abstract: Photosystem II (PSII) splits water in oxygenic photosynthesis on Earth. The structure and function of the CSM-type PSII-LHCII (light-harvesting complex II) megacomplexes from the wild-type and PsbR- ...Photosystem II (PSII) splits water in oxygenic photosynthesis on Earth. The structure and function of the CSM-type PSII-LHCII (light-harvesting complex II) megacomplexes from the wild-type and PsbR-deletion mutant plants are studied through electron microscopy (EM), structural mass spectrometry, and ultrafast fluorescence spectroscopy [time-resolved fluorescence (TRF)]. The cryo-EM structure of a type I CSM megacomplex demonstrates that the three domains of PsbR bind to the stromal side of D1, D2, and CP43; associate with the single transmembrane helix of the redox active Cyt ; and stabilize the luminal extrinsic PsbP, respectively. This megacomplex, with PsbR and PsbY centered around the narrow interface between two dimeric PSII cores, provides the supramolecular structural basis that regulates the plastoquinone occupancy in Q site, excitation energy transfer, and oxygen evolution. PSII-LHCII megacomplexes (types I and II) and LHC aggregation levels in mutant were also interrogated and compared to wild-type plants through EM and picosecond TRF.
History
DepositionJul 15, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60801.png

Downloads & links

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Map

FileDownload / File: emd_60801.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 480 pix.
= 648. Å		1.35 Å/pix.
x 480 pix.
= 648. Å		1.35 Å/pix.
x 480 pix.
= 648. Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.7268565 - 4.745766
Average (Standard dev.)-0.00046424457 (±0.13944805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 648.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60801_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_60801_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Photosystem II-light harvesting complex II megacomplex

EntireName: Photosystem II-light harvesting complex II megacomplex
Components
  • Complex: Photosystem II-light harvesting complex II megacomplex

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Supramolecule #1: Photosystem II-light harvesting complex II megacomplex

SupramoleculeName: Photosystem II-light harvesting complex II megacomplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Spinacia oleracea (spinach) / Tissue: leave / Organelle: chloroplast / Location in cell: thylakoid

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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

Concentration6 mg/mL
BufferpH: 6.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 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:

3jcu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93684
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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