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- EMDB-13056: Tomogram of a nuclease treated shVim HO H222P MEF nuclear lamina -

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Basic information

Entry
Database: EMDB / ID: EMD-13056
TitleTomogram of a nuclease treated shVim HO H222P MEF nuclear lamina
Map dataA tomogram of nuclease treated shvim HO H222P MEF nucleus. The tomogram is dose-weighted, CTF-corrected and reconstructed in IMOD. Fudicial markers are replaced by noise.
Sample
  • Organelle or cellular component: Nuclear Lamina
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsTatli M / Medalia O
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179418 Switzerland
CitationJournal: J Cell Sci / Year: 2021
Title: A lamin A/C variant causing striated muscle disease provides insights into filament organization.
Authors: Rafael Kronenberg-Tenga / Meltem Tatli / Matthias Eibauer / Wei Wu / Ji-Yeon Shin / Gisèle Bonne / Howard J Worman / Ohad Medalia /
Abstract: The gene encodes the A-type lamins, which polymerize into ∼3.5-nm-thick filaments and, together with B-type lamins and associated proteins, form the nuclear lamina. Mutations in cause a wide ...The gene encodes the A-type lamins, which polymerize into ∼3.5-nm-thick filaments and, together with B-type lamins and associated proteins, form the nuclear lamina. Mutations in cause a wide variety of pathologies. In this study, we analyzed the nuclear lamina of embryonic fibroblasts from mice, which develop cardiomyopathy and muscular dystrophy. Although the organization of the lamina appeared unaltered, there were changes in chromatin and B-type lamin expression. An increase in nuclear size and consequently a relative reduction in heterochromatin near the lamina allowed for a higher resolution structural analysis of lamin filaments using cryo-electron tomography. This was most apparent when visualizing lamin filaments and using a nuclear extraction protocol. Averaging of individual segments of filaments in mouse fibroblasts resolved two polymers that constitute the mature filaments. Our findings provide better views of the organization of lamin filaments and the effect of a striated muscle disease-causing mutation on nuclear structure.
History
DepositionJun 9, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateAug 25, 2021-
Current statusAug 25, 2021Processing site: PDBe / Status: Released

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Structure visualization

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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
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Supplemental images

emd_13056.png

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Map

FileDownload / File: emd_13056.map.gz / Format: CCP4 / Size: 165.7 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationA tomogram of nuclease treated shvim HO H222P MEF nucleus. The tomogram is dose-weighted, CTF-corrected and reconstructed in IMOD. Fudicial markers are replaced by noise.
Voxel sizeX=Y=Z: 8.82603 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)22.722765 (±17.823496)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin16-16-98
Dimensions928960195
Spacing960928195
CellA: 8472.988 Å / B: 8190.5557 Å / C: 1721.0758 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z8.82602916666678.82603017241388.8260307692308
M x/y/z960928195
origin x/y/z0.0000.0000.000
length x/y/z8472.9888190.5561721.076
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ332332332
MAP C/R/S123
start NC/NR/NS-1616-98
NC/NR/NS960928195
D min/max/mean-128.000127.00022.723

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Supplemental data

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Sample components

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Entire : Nuclear Lamina

EntireName: Nuclear Lamina
Components
  • Organelle or cellular component: Nuclear Lamina

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Supramolecule #1: Nuclear Lamina

SupramoleculeName: Nuclear Lamina / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 140.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 61

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