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- EMDB-56367: Cryo-electron tomogram acquired on a cryo-FIB lamella of two adja... -

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Basic information

Entry
Database: EMDB / ID: EMD-56367
TitleCryo-electron tomogram acquired on a cryo-FIB lamella of two adjacent NIH 3T3 cells.
Map data
Sample
  • Cell: Cell surface of two adjacent round NIH 3T3 cells
Keywordsactomyosin cortex / plasma membrane / cell surface / membrane-to-cortex attachment / PROTEIN BINDING
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsGerard SF / Cheng DCW / Toro-Nahuelpan M / Mahamid J / Diz-Munoz A
Funding supportEuropean Union, Germany, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)101124221European Union
German Research Foundation (DFG)DI 2205/3-1 Germany
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND Germany
European Molecular Biology Organization (EMBO)European Union
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Nat Methods / Year: 2020
Title: Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies.
Authors: Mauricio Toro-Nahuelpan / Ievgeniia Zagoriy / Fabrice Senger / Laurent Blanchoin / Manuel Théry / Julia Mahamid /
Abstract: Spatially controlled cell adhesion on electron microscopy supports remains a bottleneck in specimen preparation for cellular cryo-electron tomography. Here, we describe contactless and mask-free ...Spatially controlled cell adhesion on electron microscopy supports remains a bottleneck in specimen preparation for cellular cryo-electron tomography. Here, we describe contactless and mask-free photo-micropatterning of electron microscopy grids for site-specific deposition of extracellular matrix-related proteins. We attained refined cell positioning for micromachining by cryo-focused ion beam milling. Complex micropatterns generated predictable intracellular organization, allowing direct correlation between cell architecture and in-cell three-dimensional structural characterization of the underlying molecular machinery.
History
DepositionJan 14, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56367.png

Downloads & links

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Map

FileDownload / File: emd_56367.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.48 Å/pix.
x 500 pix.
= 6740. Å		13.48 Å/pix.
x 928 pix.
= 12509.439 Å		13.48 Å/pix.
x 928 pix.
= 12509.439 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: 13.48 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-287.0 - 230.0
Average (Standard dev.)1.9134254 (±9.836024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928928500
Spacing928928500
CellA: 12509.439 Å / B: 12509.439 Å / C: 6740.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cell surface of two adjacent round NIH 3T3 cells

EntireName: Cell surface of two adjacent round NIH 3T3 cells
Components
  • Cell: Cell surface of two adjacent round NIH 3T3 cells

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Supramolecule #1: Cell surface of two adjacent round NIH 3T3 cells

SupramoleculeName: Cell surface of two adjacent round NIH 3T3 cells / type: cell / ID: 1 / Parent: 0
Details: The cell surface includes the actomyosin cortex and the plasma membrane.
Source (natural)Organism: Mus musculus (house mouse) / Strain: NIH 3T3 cell line

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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: 7.4
GridModel: Quantifoil / Material: GOLD / Support film - Material: SILICON DIOXIDE / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE
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: 120 / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Thermo Fisher 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 opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 58
CTF correctionType: NONE

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