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- EMDB-52633: MEF in-situ nucleosome canonical structure -

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Basic information

Entry
Database: EMDB / ID: EMD-52633
TitleMEF in-situ nucleosome canonical structure
Map dataMEF in-situ nucleosome canonical structure
Sample
  • Complex: Native nucleosome of mouse embryonic fibroblasts
KeywordsMEF / nucleosome / NUCLEAR PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 13.0 Å
AuthorsEibauer M / Medalia O
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_207453 Switzerland
Swiss National Science Foundation310030_197776 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
DepositionJan 28, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52633.png

Downloads & links

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Map

FileDownload / File: emd_52633.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMEF in-situ nucleosome canonical structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.21 Å/pix.
x 128 pix.
= 282.88 Å		2.21 Å/pix.
x 128 pix.
= 282.88 Å		2.21 Å/pix.
x 128 pix.
= 282.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-0.6959556 - 2.0937471
Average (Standard dev.)0.0005970867 (±0.14707631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 282.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half2 z flip

Fileemd_52633_half_map_1.map
Annotationhalf2_z_flip
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1 z flip

Fileemd_52633_half_map_2.map
Annotationhalf1_z_flip
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native nucleosome of mouse embryonic fibroblasts

EntireName: Native nucleosome of mouse embryonic fibroblasts
Components
  • Complex: Native nucleosome of mouse embryonic fibroblasts

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Supramolecule #1: Native nucleosome of mouse embryonic fibroblasts

SupramoleculeName: Native nucleosome of mouse embryonic fibroblasts / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Tissue: embryonic fibroblast / Organelle: nucleus / Location in cell: nucleus
Molecular weightTheoretical: 200 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
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 / 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

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Electron microscopy

MicroscopeTFS KRIOS
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 / Cs: 2.7 mm / 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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta3)
Details: Reference model EMD-33132, low-pass filtered to 40 A
Number subtomograms used: 13255
ExtractionNumber tomograms: 43 / Number images used: 130000 / Software - Name: crYOLO (ver. 1.3)
CTF correctionSoftware: (Name: IMOD, RELION (ver. 5.0-beta3)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 40 / Software - Name: RELION (ver. 5.0-beta3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta3)
FSC plot (resolution estimation)

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