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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: Nat Struct Mol Biol / Year: 2025
Title: The molecular basis of lamin-specific chromatin interactions.
Authors: Baihui Wang / Rafael Kronenberg-Tenga / Valentina Rosti / Emanuele Di Patrizio Soldateschi / Qiang Luo / Ugo Maria Iannacchero / Louise Pinet / Matthias Eibauer / Rajaa Boujemaa-Paterski / ...Authors: Baihui Wang / Rafael Kronenberg-Tenga / Valentina Rosti / Emanuele Di Patrizio Soldateschi / Qiang Luo / Ugo Maria Iannacchero / Louise Pinet / Matthias Eibauer / Rajaa Boujemaa-Paterski / Benjamin Schuler / Chiara Lanzuolo / Ohad Medalia /
Abstract: In the cell nucleus, chromatin is anchored to the nuclear lamina, a network of lamin filaments and binding proteins that underly the inner nuclear membrane. The nuclear lamina is involved in ...In the cell nucleus, chromatin is anchored to the nuclear lamina, a network of lamin filaments and binding proteins that underly the inner nuclear membrane. The nuclear lamina is involved in chromatin organization through the interaction of lamina-associated domains within the densely packed heterochromatin regions. Using cryo-focused ion beam milling in conjunction with cryo-electron tomography, we analyzed the distribution of nucleosomes at the lamin-chromatin interface at the nanometer scale. Depletion of lamins A and C reduced nucleosome concentration at the nuclear periphery, while B-type lamin depletion contributed to nucleosome density in proximity to the lamina but not further away. We then investigated whether specific lamins can mediate direct interactions with chromatin. Using cryo-electron microscopy, we identified a specific binding motif of the lamin A tail domain that interacts with nucleosomes, distinguishing it from the other lamin isoforms. Furthermore, we examined chromatin structure dynamics using a genome-wide analysis that revealed lamin-dependent macroscopic-scale alterations in gene expression and chromatin remodeling. Our findings provide detailed insights into the dynamic and structural interplay between lamin isoforms and chromatin, molecular interactions that shape chromatin architecture and epigenetic regulation.
History
DepositionMar 12, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 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
CTF correctionSoftware - Name: IMOD / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

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