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- EMDB-50291: The molecular basis and modulation of lamin-specific chromatin in... -

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Basic information

Entry
Database: EMDB / ID: EMD-50291
TitleThe molecular basis and modulation of lamin-specific chromatin interactions
Map data
Sample
  • Complex: Complex of laminA C-tail domain with nucleosome
Keywordsnucleosome / laminA C tail / complex / NUCLEAR PROTEIN
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang B / Luo Q
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationSNSF 391 310030_207453 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
DepositionMay 13, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50291.png

Downloads & links

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Map

FileDownload / File: emd_50291.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
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Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-0.14880264 - 0.25657058
Average (Standard dev.)-0.000062002044 (±0.0050267447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50291_msk_1.map
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Half map: #1

Fileemd_50291_half_map_1.map
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Half map: #2

Fileemd_50291_half_map_2.map
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Sample components

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Entire : Complex of laminA C-tail domain with nucleosome

EntireName: Complex of laminA C-tail domain with nucleosome
Components
  • Complex: Complex of laminA C-tail domain with nucleosome

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Supramolecule #1: Complex of laminA C-tail domain with nucleosome

SupramoleculeName: Complex of laminA C-tail domain with nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19495
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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