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- EMDB-54840: native cytoplasmic lattices from mouse oocytes, one asymmetric un... -

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Basic information

Entry
Database: EMDB / ID: EMD-54840
Titlenative cytoplasmic lattices from mouse oocytes, one asymmetric unit, local refinement of PADI6 region
Map datalocscale sharpened map
Sample
  • Complex: native cytoplasmic lattices from mouse oocytes
Keywordsoocyte / embryo / cytoskeleton / tubulin / ubiquitin / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKilic ZI / van Loenhout J / Chaillet M / Noteborn WEM / Leung MR
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Other government Netherlands
CitationJournal: Nature / Year: 2026
Title: Cytoplasmic lattices are megadalton storage complexes in mammalian oocytes.
Authors: Zeynep Ilgın Kılıç / Joyce van Loenhout / Marten Chaillet / Robert M van Es / Paula Sobrevals Alcaraz / Harmjan R Vos / Willem E M Noteborn / Miguel Ricardo Leung /
Abstract: Mammalian oocytes store proteins for embryonic development on abundant structures called cytoplasmic lattices (CPLs). However, the mechanisms by which they achieve this are unclear, largely because ...Mammalian oocytes store proteins for embryonic development on abundant structures called cytoplasmic lattices (CPLs). However, the mechanisms by which they achieve this are unclear, largely because the molecular composition of the lattices themselves is unknown. Here we use cryo-electron microscopy and artificial intelligence-based modelling to reveal the molecular architecture and protein composition of native CPLs from mouse oocytes. We find that CPLs are formed by at least 13 different proteins that assemble into a megadalton-scale complex, including multiple copies of maternal effect factors such as PADI6 and the subcortical maternal complex. We show that proteins that are essential for early embryonic development are structural components of the CPLs, including the cytoskeletal proteins α-tubulin and β-tubulin, which are incorporated into CPLs as unpolymerized dimers, and an array of ubiquitination factors such as the epigenetic regulator and E3 ligase UHRF1, ubiquitin-conjugating E2 enzymes, and ubiquitin ligase substrate adapters. This represents an elegant molecular mechanism by which oocytes stockpile vital proteins through direct incorporation into highly stable supramolecular assemblies. Our findings provide a structural framework for understanding how disrupting stored maternal factors leads to infertility and developmental defects.
History
DepositionAug 20, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54840.png

Downloads & links

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Map

FileDownload / File: emd_54840.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocscale sharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.01930214 - 0.5128399
Average (Standard dev.)0.000678729 (±0.009447326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54840_msk_1.map
Projections & Slices
AxesZYX

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Additional map: unsharpened map

Fileemd_54840_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Half map: half-map 1

Fileemd_54840_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_54840_half_map_2.map
Annotationhalf-map 2
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Sample components

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Entire : native cytoplasmic lattices from mouse oocytes

EntireName: native cytoplasmic lattices from mouse oocytes
Components
  • Complex: native cytoplasmic lattices from mouse oocytes

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Supramolecule #1: native cytoplasmic lattices from mouse oocytes

SupramoleculeName: native cytoplasmic lattices from mouse oocytes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Mus musculus (house mouse)

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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: 7.2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

16458

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 255865
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final 3D classificationSoftware - Name: RELION (ver. 5)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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