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- EMDB-16458: Electron cryo-tomography and subtomogram averaging of cytoplasmic... -

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Basic information

Entry
Database: EMDB / ID: EMD-16458
TitleElectron cryo-tomography and subtomogram averaging of cytoplasmic lattice filaments from mammalian oocytes
Map datasubtomogram average of the central filament
Sample
  • Cell: mouse oocyte
Keywordsmammalian oocytes / cytoplasmic lattices / protein storage / filaments / CYTOSOLIC PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsPetrovic A / Bauerlein FJB / Jentoft IMA / Schuh M / Fernandez-Busnadiego R
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1286 (SFB1286 - 317475864) Germany
German Research Foundation (DFG)MBExC (EXC 2067/1- 390729940) Germany
German Research Foundation (DFG)SCHU 3047/1-1 Germany
CitationJournal: Cell / Year: 2023
Title: Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices.
Authors: Ida M A Jentoft / Felix J B Bäuerlein / Luisa M Welp / Benjamin H Cooper / Arsen Petrovic / Chun So / Sarah Mae Penir / Antonio Z Politi / Yehor Horokhovskyi / Iina Takala / Heike Eckel / ...Authors: Ida M A Jentoft / Felix J B Bäuerlein / Luisa M Welp / Benjamin H Cooper / Arsen Petrovic / Chun So / Sarah Mae Penir / Antonio Z Politi / Yehor Horokhovskyi / Iina Takala / Heike Eckel / Rüdiger Moltrecht / Peter Lénárt / Tommaso Cavazza / Juliane Liepe / Nils Brose / Henning Urlaub / Rubén Fernández-Busnadiego / Melina Schuh /
Abstract: Mammalian oocytes are filled with poorly understood structures called cytoplasmic lattices. First discovered in the 1960s and speculated to correspond to mammalian yolk, ribosomal arrays, or ...Mammalian oocytes are filled with poorly understood structures called cytoplasmic lattices. First discovered in the 1960s and speculated to correspond to mammalian yolk, ribosomal arrays, or intermediate filaments, their function has remained enigmatic to date. Here, we show that cytoplasmic lattices are sites where oocytes store essential proteins for early embryonic development. Using super-resolution light microscopy and cryoelectron tomography, we show that cytoplasmic lattices are composed of filaments with a high surface area, which contain PADI6 and subcortical maternal complex proteins. The lattices associate with many proteins critical for embryonic development, including proteins that control epigenetic reprogramming of the preimplantation embryo. Loss of cytoplasmic lattices by knocking out PADI6 or the subcortical maternal complex prevents the accumulation of these proteins and results in early embryonic arrest. Our work suggests that cytoplasmic lattices enrich maternally provided proteins to prevent their premature degradation and cellular activity, thereby enabling early mammalian development.
History
DepositionJan 15, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16458.png

Downloads & links

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Map

FileDownload / File: emd_16458.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of the central filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.31 Å/pix.
x 192 pix.
= 1402.56 Å		7.31 Å/pix.
x 192 pix.
= 1402.56 Å		7.31 Å/pix.
x 192 pix.
= 1402.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.305 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.4216316 - 1.2805398
Average (Standard dev.)-0.00034150374 (±0.1152628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 1402.5599 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: subtomogram average of the filament bundle

Fileemd_16458_additional_1.map
Annotationsubtomogram average of the filament bundle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map (odd)

Fileemd_16458_half_map_1.map
Annotationhalf-map (odd)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map (even)

Fileemd_16458_half_map_2.map
Annotationhalf-map (even)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse oocyte

EntireName: mouse oocyte
Components
  • Cell: mouse oocyte

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Supramolecule #1: mouse oocyte

SupramoleculeName: mouse oocyte / type: cell / 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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil / Material: MOLYBDENUM / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
DetailsFIB milled lamella of mouse oocytes

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 3.34 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo (ver. 1.1.532) / Number subtomograms used: 1246
ExtractionNumber tomograms: 5 / Number images used: 1246 / Software - Name: Dynamo (ver. 1.1.532)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Dynamo (ver. 1.1.532)
FSC plot (resolution estimation)

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