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- EMDB-52548: Cryo-electron tomogram #01 of thylakoids in spinach chloroplast. ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52548
TitleCryo-electron tomogram #01 of thylakoids in spinach chloroplast. Denoised with cryoCARE
Map dataCryo-electron tomogram #01 of thylakoids in spinach chloroplast. Denoised with cryoCARE.
Sample
  • Organelle or cellular component: Chloroplast
Keywordschloroplast / spinach / thylakoids / plastoglobules / PHOTOSYNTHESIS
Biological speciesSpinacia oleracea (spinach)
Methodelectron tomography / cryo EM
AuthorsWietrzynski W / Lamm L / Engel BD
Funding support France, 1 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0005/2021 France
Citation
Journal: Elife / Year: 2025
Title: Molecular architecture of thylakoid membranes within intact spinach chloroplasts.
Authors: Wojciech Wietrzynski / Lorenz Lamm / William H J Wood / Matina-Jasemi Loukeri / Lorna Malone / Tingying Peng / Matthew P Johnson / Benjamin D Engel /
Abstract: Thylakoid membranes coordinate the light reactions of photosynthesis across multiple scales, coupling the architecture of an elaborate membrane network to the spatial organization of individual ...Thylakoid membranes coordinate the light reactions of photosynthesis across multiple scales, coupling the architecture of an elaborate membrane network to the spatial organization of individual protein complexes embedded within this network. Previously, we used in situ cryo-electron tomography (cryo-ET) to reveal the native thylakoid architecture of the green alga (Engel et al., 2015) and then map the molecular organization of these thylakoids with single-molecule precision (Wietrzynski et al., 2020). However, it remains to be shown how generalizable this green algal blueprint is to the thylakoids of vascular plants, which possess distinct membrane architecture subdivided into grana stacks interconnected by non-stacked stromal lamellae. Here, we continue our cryo-ET investigation to reveal the molecular architecture of thylakoids within intact chloroplasts isolated from spinach (). We visualize the fine ultrastructural details of grana membranes, as well as interactions between thylakoids and plastoglobules. We apply AI-based computational approaches (Lamm et al., 2024) to quantify the organization of photosynthetic complexes within the plane of the thylakoid membrane and across adjacent stacked membranes. Our analysis reveals that the molecular organization of thylakoid membranes in vascular plants and green algae is strikingly similar. We find that PSII organization is non-crystalline and has uniform concentration both within the membrane plane and across stacked grana membranes. Similar to , we observe strict lateral heterogeneity of PSII and PSI at the boundary between appressed and non-appressed thylakoid domains, with no evidence for a distinct grana margin region where these complexes have been proposed to intermix. Based on these measurements, we support a simple two-domain model for the molecular organization of thylakoid membranes in both green algae and plants.
#1: Journal: Elife / Year: 2025
Title: Molecular architecture of thylakoid membranes within intact spinach chloroplasts
Authors: Wietrzynski W / Lamm L / Wood WH / Loukeri MJ / Malone L / Peng T / Johnson MP / Engel BD
History
DepositionJan 14, 2025-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52548.png

Downloads & links

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Map

FileDownload / File: emd_52548.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram #01 of thylakoids in spinach chloroplast. Denoised with cryoCARE.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.08 Å/pix.
x 464 pix.
= 6533.12 Å		14.08 Å/pix.
x 928 pix.
= 13066.24 Å		14.08 Å/pix.
x 928 pix.
= 13066.24 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 14.08 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-30.497237999999999 - 20.270793999999999
Average (Standard dev.)-0.012276958 (±1.1550685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928928464
Spacing928928464
CellA: 13066.24 Å / B: 13066.24 Å / C: 6533.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Segmentation of membranes from the tomogram #01 containing...

Fileemd_52548_additional_1.map
AnnotationSegmentation of membranes from the tomogram #01 containing thylakoids in spinach chloroplast
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chloroplast

EntireName: Chloroplast
Components
  • Organelle or cellular component: Chloroplast

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Supramolecule #1: Chloroplast

SupramoleculeName: Chloroplast / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: Isolated chloroplast of Spinach (Spinacia oleracea) visualised by cryo-ET
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf / Organelle: chloroplast

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.2
Details: 0.45 M Sorbitol, 20 mM Tricine-KOH, 10 mM EDTA, 10 mM NaHCO3, 5 mM MgCl2, 0.1% BSA, 0.2% D-Ascorbate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 75 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Cryo protectantno cryoprotectant
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.1 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 77 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 120
Focused ion beam - Details: Clumps of chloroplast were milled in a step-wise manner according to the routine protocols.. The value given for _em_focused_ion_beam.instrument is TFS Aquilos. This is ...Focused ion beam - Details: Clumps of chloroplast were milled in a step-wise manner according to the routine protocols.. The value given for _em_focused_ion_beam.instrument is TFS Aquilos. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 60 / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 60
CTF correctionType: NONE

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