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- EMDB-56697: Cryo-ET of a plasmodesma in wild type Physcomitrium patens proton... -

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Basic information

Entry
Database: EMDB / ID: EMD-56697
TitleCryo-ET of a plasmodesma in wild type Physcomitrium patens protonema tissue
Map dataCryo-electron tomogram of a plasmodesma in a protonemal cell of Physcomitrium patens, reconstructed at bin4 and denoised using cryoCARE.
Sample
  • Tissue: Wild-type Physcomitrium patens protonemal tissue
Keywordsplasmodesmata / membrane contact site / endoplasmic reticulum / cell wall / PLANT PROTEIN
Biological speciesPhyscomitrium patens (plant)
Methodelectron tomography / cryo EM
AuthorsDickmanns M / Poege M / Xu P / Gombos S / Barr ZK / Miras M / Plitzko J / Simon R / Schulze W / Frommer WB / Baumeister W
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)951292European Union
CitationJournal: To Be Published
Title: In situ architecture of plasmodesmata in Physcomitrium patens resolved by cryo-electron tomography
Authors: Dickmanns M / Poege M / Xu P / Gombos S / Barr ZK / Miras M / Plitzko J / Simon R / Schulze W / Frommer WB / Baumeister W
History
DepositionFeb 11, 2026-
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_56697.png

Downloads & links

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Map

FileDownload / File: emd_56697.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram of a plasmodesma in a protonemal cell of Physcomitrium patens, reconstructed at bin4 and denoised using 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 464 pix.
= 6533.12 Å		14.08 Å/pix.
x 464 pix.
= 6533.12 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 14.08 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-37424.480000000003201 - 18662.00800000000163
Average (Standard dev.)181.090839999999986 (±570.451350000000048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions464464464
Spacing464464464
CellA=B=C: 6533.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Wild-type Physcomitrium patens protonemal tissue

EntireName: Wild-type Physcomitrium patens protonemal tissue
Components
  • Tissue: Wild-type Physcomitrium patens protonemal tissue

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Supramolecule #1: Wild-type Physcomitrium patens protonemal tissue

SupramoleculeName: Wild-type Physcomitrium patens protonemal tissue / type: tissue / ID: 1 / Parent: 0
Details: Lamellae prepared from high-pressure frozen tissue by cryo-FIB milling. Cryo-electron tomogram reconstructed at bin4 and denoised using cryoCARE.
Source (natural)Organism: Physcomitrium patens (plant) / Tissue: Protonema

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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: 5.8
VitrificationCryogen name: NITROGEN
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 HPM100', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', ...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 HPM100', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', 'BAL-TEC HPM 010', 'OTHER', 'LEICA EM PACT2'} 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: 3600 / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 25000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is 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) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.11.25) / Number images used: 41
CTF correctionType: NONE

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