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- EMDB-16472: In situ cryo-electron tomogram of cytoplasmic lattice filaments f... -

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Entry
Database: EMDB / ID: EMD-16472
TitleIn situ cryo-electron tomogram of cytoplasmic lattice filaments from a mouse oocyte
Map dataIn situ cryo-electron tomogram of cytoplasmic lattice filaments from a mouse oocyte (unprocessed tomogram)
Sample
  • Cell: mouse oocyte
Keywordsmammalian oocytes / cytoplasmic lattices / protein storage / filaments / CYTOSOLIC PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsBauerlein FJB / Jentoft IMA / Petrovic A / Fernandez-Busnadiego R / Schuh M
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 18, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16472.png

Downloads & links

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Map

FileDownload / File: emd_16472.map.gz / Format: CCP4 / Size: 450 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationIn situ cryo-electron tomogram of cytoplasmic lattice filaments from a mouse oocyte (unprocessed tomogram)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.61 Å/pix.
x 225 pix.
= 3287.25 Å		14.61 Å/pix.
x 1024 pix.
= 14960.64 Å		14.61 Å/pix.
x 1024 pix.
= 14960.64 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: 14.61 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-197.0 - 165.0
Average (Standard dev.)5.7269006 (±21.846765999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0-512-113
Dimensions10241024225
Spacing10241024225
CellA: 14960.64 Å / B: 14960.64 Å / C: 3287.25 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: In situ cryo-electron tomogram of cytoplasmic lattice filaments...

Fileemd_16472_additional_1.map
AnnotationIn situ cryo-electron tomogram of cytoplasmic lattice filaments from a mouse oocyte (deconvoluted tomogram)
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
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
DetailsFIB milled lamella of mouse oocytes
Cryo protectant7.5%/7.5% DMSO/EG
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 3600 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 80000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: We develop a 'deep-FIBing' approach, by which the cells were first milled perpendicular to the EM grid to reveal a clean surface from which lamellae were subsequently ...Focused ion beam - Details: We develop a 'deep-FIBing' approach, by which the cells were first milled perpendicular to the EM grid to reveal a clean surface from which lamellae were subsequently prepared (see publication).. The value given for _em_focused_ion_beam.instrument is Aquilos II. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 33000
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 (ver. 4.11.13) / Number images used: 30

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