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- EMDB-19829: Tomogram of nuclear envlope of LBDKO mouse embryonic fibroblast -

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Basic information

Entry
Database: EMDB / ID: EMD-19829
TitleTomogram of nuclear envlope of LBDKO mouse embryonic fibroblast
Map dataTomogram of nuclear envelope in FIB-milled lamella of LBDKO mouse embryonic fibroblast
Sample
  • Cell: Nuclear envelope of FIB-milled lamellae of mouse embryonic fibroblasts
KeywordsNucleosome / FIB-SEM / cryo-ET / Subtomogram-averaging / DNA / histones / DNA BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsKronenberg-Tenga R / Medalia O
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Lamins modulate chromatin organization from the nano- to macroscale
Authors: Kronenberg-Tenga R / Rosti V / Di Patrizio Soldateschi E / Eibauer M / Lanzuolo C / Medalia O
History
DepositionMar 12, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19829.png

Downloads & links

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Map

FileDownload / File: emd_19829.map.gz / Format: CCP4 / Size: 849.6 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationTomogram of nuclear envelope in FIB-milled lamella of LBDKO mouse embryonic fibroblast
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.42 Å/pix.
x 500 pix.
= 2210. Å		4.42 Å/pix.
x 928 pix.
= 4101.76 Å		4.42 Å/pix.
x 960 pix.
= 4243.2 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: 4.42 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-148.0 - 56.0
Average (Standard dev.)3.287436 (±6.9836726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-500-3331
Dimensions928960500
Spacing960928500
CellA: 4243.2 Å / B: 4101.7603 Å / C: 2210.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Nuclear envelope of FIB-milled lamellae of mouse embryonic fibroblasts

EntireName: Nuclear envelope of FIB-milled lamellae of mouse embryonic fibroblasts
Components
  • Cell: Nuclear envelope of FIB-milled lamellae of mouse embryonic fibroblasts

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Supramolecule #1: Nuclear envelope of FIB-milled lamellae of mouse embryonic fibroblasts

SupramoleculeName: Nuclear envelope of FIB-milled lamellae of mouse embryonic fibroblasts
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Tissue: embryonic fibroblast

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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 / Component - Concentration: 1.0 x / Component - Name: PBS
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.02 / Focused ion beam - Duration: 360 / Focused ion beam - Temperature: 118 K / Focused ion beam - Initial thickness: 5000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Zeiss Auriga 40 CrossBeam. 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

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 2.2 sec. / Average electron dose: 4.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 35

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