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- EMDB-15394: Cell-cell contact between two PTK-1 cells -

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Basic information

Entry
Database: EMDB / ID: EMD-15394
TitleCell-cell contact between two PTK-1 cells
Map dataRaw tomographic reconstruction of a cryo-FIB lamella through a cell-cell contact of two PTK-1 cells. "Contour level" is a placeholder. Use "Auto" button in IMOD.
Sample
  • Cell: cell-cell contact
Biological speciesPotorous tridactylus (long-nosed potoroo)
Methodelectron tomography / cryo EM
AuthorsBezault A / Sauvanet C / Lemos M / Hanein D / Volkmann N
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat Commun / Year: 2022
Title: Morphological control enables nanometer-scale dissection of cell-cell signaling complexes.
Authors: Liam P Dow / Guido Gaietta / Yair Kaufman / Mark F Swift / Moara Lemos / Kerry Lane / Matthew Hopcroft / Armel Bezault / Cécile Sauvanet / Niels Volkmann / Beth L Pruitt / Dorit Hanein /
Abstract: Protein micropatterning enables robust control of cell positioning on electron-microscopy substrates for cryogenic electron tomography (cryo-ET). However, the combination of regulated cell boundaries ...Protein micropatterning enables robust control of cell positioning on electron-microscopy substrates for cryogenic electron tomography (cryo-ET). However, the combination of regulated cell boundaries and the underlying electron-microscopy substrate (EM-grids) provides a poorly understood microenvironment for cell biology. Because substrate stiffness and morphology affect cellular behavior, we devised protocols to characterize the nanometer-scale details of the protein micropatterns on EM-grids by combining cryo-ET, atomic force microscopy, and scanning electron microscopy. Measuring force displacement characteristics of holey carbon EM-grids, we found that their effective spring constant is similar to physiological values expected from skin tissues. Despite their apparent smoothness at light-microscopy resolution, spatial boundaries of the protein micropatterns are irregular at nanometer scale. Our protein micropatterning workflow provides the means to steer both positioning and morphology of cell doublets to determine nanometer details of punctate adherens junctions. Our workflow serves as the foundation for studying the fundamental structural changes governing cell-cell signaling.
History
DepositionJul 16, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15394.png

Downloads & links

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Map

FileDownload / File: emd_15394.map.gz / Format: CCP4 / Size: 928 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationRaw tomographic reconstruction of a cryo-FIB lamella through a cell-cell contact of two PTK-1 cells. "Contour level" is a placeholder. Use "Auto" button in IMOD.
Voxel sizeX=Y=Z: 8.114 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)6.7312713 (±15.179936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0089
Dimensions20482048232
Spacing20482048232
CellA: 16617.473 Å / B: 16617.473 Å / C: 1882.4481 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : cell-cell contact

EntireName: cell-cell contact
Components
  • Cell: cell-cell contact

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Supramolecule #1: cell-cell contact

SupramoleculeName: cell-cell contact / type: cell / ID: 1 / Parent: 0 / Details: cell-cell contact between two PTK-1 cells
Source (natural)Organism: Potorous tridactylus (long-nosed potoroo)

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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: 6.9
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 10.0 µm / Nominal defocus min: 10.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 3.0 e/Å2

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Image processing

Final reconstructionNumber images used: 35

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