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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
CitationJournal: To Be Published
Title: Cryo-electron tomogram of intact spinach chloroplast at 14.08A bin4 pixel size; denoised with cryoCARE to improve contrast.
Authors: Wietrzynski W / Lamm L / Wood WHJ / Loukeri MJ / Malone L / Peng T / Johnson MP / Engel BD
History
DepositionJan 14, 2025-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 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

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