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- EMDB-53142: Cryo-electron tomograms of Physcomitrium patens phyllids. -

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Basic information

Entry
Database: EMDB / ID: EMD-53142
TitleCryo-electron tomograms of Physcomitrium patens phyllids.
Map dataThis is the tomogram shown in the original publication.
Sample
  • Tissue: Physcomitrium patens phyllids
KeywordsPhyscomitrium patens / Moss / PLANT PROTEIN
Biological speciesPhyscomitrium patens (plant)
Methodelectron tomography / cryo EM
AuthorsPoege M / Dickmanns M / Xu P / Li M / Schioetz OH / Kaiser COJ / Ma J / Bieber A / Capitanio C / Brenner JA ...Poege M / Dickmanns M / Xu P / Li M / Schioetz OH / Kaiser COJ / Ma J / Bieber A / Capitanio C / Brenner JA / Riggi M / Miras M / Kazemein Jasemi NS / Schulze SX / Simon R / Frommer WB / Plitzko JM / Baumeister W
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)951292European Union
CitationJournal: To Be Published
Title: Making plant tissue accessible for cryo-electron tomography
Authors: Poege M / Dickmanns M / Xu P / Li M / Schioetz OH / Kaiser COJ / Ma J / Bieber A / Capitanio C / Brenner JA / Riggi M / Miras M / Kazemein Jasemi NS / Schulze SX / Simon R / Frommer WB / ...Authors: Poege M / Dickmanns M / Xu P / Li M / Schioetz OH / Kaiser COJ / Ma J / Bieber A / Capitanio C / Brenner JA / Riggi M / Miras M / Kazemein Jasemi NS / Schulze SX / Simon R / Frommer WB / Plitzko JM / Baumeister W
History
DepositionMar 14, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53142.png

Downloads & links

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Map

FileDownload / File: emd_53142.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the tomogram shown in the original publication.
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-62971.805000000000291 - 48928.504000000000815
Average (Standard dev.)354.069369999999992 (±688.703740000000039)
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: This is another tomogram example.

Fileemd_53142_additional_1.map
AnnotationThis is another tomogram example.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: This is another tomogram example.

Fileemd_53142_additional_2.map
AnnotationThis is another tomogram example.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Physcomitrium patens phyllids

EntireName: Physcomitrium patens phyllids
Components
  • Tissue: Physcomitrium patens phyllids

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Supramolecule #1: Physcomitrium patens phyllids

SupramoleculeName: Physcomitrium patens phyllids / type: tissue / ID: 1 / Parent: 0
Source (natural)Organism: Physcomitrium patens (plant) / Tissue: Phyllid

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statetissue

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Sample preparation

BufferpH: 5.7
VitrificationCryogen name: NITROGEN
Details: Tissue was high-pressure frozen as described in the publication and the corresponding protocol..
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is Leica EM ICE. This is not in a list of allowed values {'LEICA EM PACT2', 'EMS-002 RAPID IMMERSION FREEZER', 'BAL-TEC HPM 010', ...Details: The value given for _em_high_pressure_freezing.instrument is Leica EM ICE. This is not in a list of allowed values {'LEICA EM PACT2', 'EMS-002 RAPID IMMERSION FREEZER', 'BAL-TEC HPM 010', 'OTHER', 'LEICA EM PACT', 'LEICA EM HPM100'} so OTHER is written into the XML file.
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 10 / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 800 / Focused ion beam - Final thickness: 300
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is TFS Scios/Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.5 µm / Nominal defocus min: 5.5 µm / Nominal magnification: 42000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 51
CTF correctionType: NONE

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