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- EMDB-59854: Cryo-electron tomogram of MEF cell containing polyglucosan -

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Basic information

Entry
Database: EMDB / ID: EMD-59854
TitleCryo-electron tomogram of MEF cell containing polyglucosan
Map dataCryo-electron tomogram of MEF cell containing polyglucosan, binned
Sample
  • Cell: Mouse embryonic fibroblast (MEF) cells expressing polyglucosan and doxycycline-inducible GFP-RNF213
KeywordsGlycogenin / Polyglucosan / Glycogen / SUGAR BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsYip MCJ / Naydenova K / Otten EG / Heatley A / Moe A / Anton L / de los Reyes-Ramirez L / Jolin HE / Langevin F / Wiacek M ...Yip MCJ / Naydenova K / Otten EG / Heatley A / Moe A / Anton L / de los Reyes-Ramirez L / Jolin HE / Langevin F / Wiacek M / Franco C / Bertolotti A / Kukulski W / McKenzie ANJ / Randow F
Funding support Switzerland, United Kingdom, Germany, Sweden, European Union, 6 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Medical Research Council (MRC, United Kingdom) United Kingdom
Wellcome Trust United Kingdom
Max Planck Society Germany
Other private Sweden
European Molecular Biology Organization (EMBO)European Union
CitationJournal: Nature / Year: 2026
Title: Quality control of glycogen through direct ubiquitylation by RNF213.
Authors: Matthew C J Yip / Katerina Naydenova / Elsje G Otten / Alexander Heatley / Agnes Moe / Leonie Anton / Lucía de Los Reyes-Ramírez / Helen E Jolin / Frederic Langevin / Michal Wiacek / ...Authors: Matthew C J Yip / Katerina Naydenova / Elsje G Otten / Alexander Heatley / Agnes Moe / Leonie Anton / Lucía de Los Reyes-Ramírez / Helen E Jolin / Frederic Langevin / Michal Wiacek / Catarina Franco / Anne Bertolotti / Wanda Kukulski / Andrew N J McKenzie / Felix Randow /
Abstract: Quality control of biomolecules is vital for organismal health. While DNA repair and protein quality control are well understood, how cells monitor other important biomolecules such as glycogen ...Quality control of biomolecules is vital for organismal health. While DNA repair and protein quality control are well understood, how cells monitor other important biomolecules such as glycogen remains ill-defined. The accumulation of aberrant, poorly branched glycogen into insoluble polyglucosan bodies causes severe disease. Here, we discover autophagy of ubiquitylated aberrant glycogen as a previously unrecognized quality control mechanism safeguarding the brain from polyglucosan buildup. This mechanism depends on the E3 ubiquitin ligase RNF213. Mice lacking ligase activity in RNF213 accumulate polyglucosan in cerebellum, pons, and hippocampus. Using cells engineered to produce polyglucosan, we show that RNF213 selectively ubiquitylates abnormal glycogen. Cryo-EM analysis of RNF213 bound to glycogen-derived maltoheptaose revealed its CBM20 domain binds linear oligosaccharides. Disrupting carbohydrate binding results in gain of E3 ligase activity towards physiological glycogen, indicating the CBM20 domain limits RNF213 activity towards physiological glycogen. Epistasis analysis places RNF213 upstream of LUBAC, suggesting a hierarchical network of multiple E3 ligases surveying glycogen quality. Ubiquitylated polyglucosan recruits the autophagy receptors SQSTM1, TAX1BP1, and optineurin, thereby triggering uptake into autophagosomes. These findings identify RNF213 as a quality control factor preventing polyglucosan accumulation in astrocytes through direct ubiquitylation of polyglucosan, revealing an essential role for non-protein ubiquitylation in glycogen quality control.
History
DepositionSep 14, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59854.png

Downloads & links

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Map

FileDownload / File: emd_59854.map.gz / Format: CCP4 / Size: 400 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-electron tomogram of MEF cell containing polyglucosan, binned
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
15.21 Å/pix.
x 400 pix.
= 6084. Å		15.21 Å/pix.
x 1024 pix.
= 15575.04 Å		15.21 Å/pix.
x 1024 pix.
= 15575.04 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: 15.21 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)0.92868423 (±20.28312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-188
Dimensions10241024400
Spacing10241024400
CellA: 15575.04 Å / B: 15575.04 Å / C: 6084.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mouse embryonic fibroblast (MEF) cells expressing polyglucosan an...

EntireName: Mouse embryonic fibroblast (MEF) cells expressing polyglucosan and doxycycline-inducible GFP-RNF213
Components
  • Cell: Mouse embryonic fibroblast (MEF) cells expressing polyglucosan and doxycycline-inducible GFP-RNF213

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Supramolecule #1: Mouse embryonic fibroblast (MEF) cells expressing polyglucosan an...

SupramoleculeName: Mouse embryonic fibroblast (MEF) cells expressing polyglucosan and doxycycline-inducible GFP-RNF213
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: 7.4
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 1 / Focused ion beam - Duration: 2000 / Focused ion beam - Temperature: 80 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 300
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is TFS Aquilos2. 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: TFS FALCON 4i (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 36
CTF correctionType: NONE

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