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- EMDB-57168: Cryo-ET of a plasmodesma in wild type Physcomitrium patens proton... -

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Basic information

Entry
Database: EMDB / ID: EMD-57168
TitleCryo-ET of a plasmodesma in wild type Physcomitrium patens protonema tissue treated with abscisic acid
Map data
Sample
  • Tissue: Wild-type Physcomitrium patens protonemal tissue treated with abscisic acid
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: Nat Plants / Year: 2026
Title: In situ architecture of plasmodesmata in Physcomitrium patens resolved by cryo-electron tomography.
Authors: Marcel Dickmanns / Matthias Pöge / Peng Xu / Sven Gombos / Zoe K Barr / Manuel Miras / Jürgen M Plitzko / Rüdiger Simon / Waltraud X Schulze / Wolf B Frommer / Wolfgang Baumeister /
Abstract: Plasmodesmata are nanoscopic channels that traverse plant cell walls, enabling direct intercellular exchange through membrane and cytosolic continuity. Although numerous plasmodesmal components have ...Plasmodesmata are nanoscopic channels that traverse plant cell walls, enabling direct intercellular exchange through membrane and cytosolic continuity. Although numerous plasmodesmal components have been identified, their molecular organization remains poorly defined. Here we used cryo-electron tomography to resolve the in situ architecture of plasmodesmata in Physcomitrium patens across tissues and physiological states. We show how callose-related cell wall remodelling shapes pore architecture to modulate permeability, including a previously undescribed fully sealed state, and resolve helical protein assemblies scaffolding the central, endoplasmic-reticulum-derived desmotubule. Candidate screening via proteomics and structure prediction indicates Multiple C2 Domain and Transmembrane Proteins (MCTPs) as key constituents of these assemblies. In this model, MCTPs tether the desmotubule to the plasma membrane, while their disordered linker regions with polyampholyte charge patterning may populate the cytosolic sleeve. These findings define core architectural features of plasmodesmata and provide a structural framework for understanding how membrane, protein and cell wall components coordinate intercellular connectivity in plants.
History
DepositionMar 11, 2026-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57168.png

Downloads & links

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Map

FileDownload / File: emd_57168.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 464 pix.
= 876.96 Å		1.89 Å/pix.
x 464 pix.
= 876.96 Å		1.89 Å/pix.
x 464 pix.
= 876.96 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-1493.676799999999957 - 1359.900300000000016
Average (Standard dev.)30.161552 (±84.568245000000005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions464464464
Spacing464464464
CellA=B=C: 876.96 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 treated with abs...

EntireName: Wild-type Physcomitrium patens protonemal tissue treated with abscisic acid
Components
  • Tissue: Wild-type Physcomitrium patens protonemal tissue treated with abscisic acid

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Supramolecule #1: Wild-type Physcomitrium patens protonemal tissue treated with abs...

SupramoleculeName: Wild-type Physcomitrium patens protonemal tissue treated with abscisic acid
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 {'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM PACT', 'LEICA EM ...Details: The value given for _em_high_pressure_freezing.instrument is Leica EM ICE. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM PACT', 'LEICA EM PACT2', 'BAL-TEC HPM 010', '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: 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 {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (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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