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- EMDB-55693: Murine RNF213 bound to maltoheptaose (Focused refinement of E3 shell) -

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Basic information

Entry
Database: EMDB / ID: EMD-55693
TitleMurine RNF213 bound to maltoheptaose (Focused refinement of E3 shell)
Map dataUnsharpened map
Sample
  • Complex: E3 ubiquitin-protein ligase RNF213
KeywordsE3 ubiquitin ligase / AAA+ ATPase / CBM20 / SUGAR BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYip MCJ / Naydenova K / Randow F
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
European Molecular Biology Organization (EMBO)European Union
UK Research and Innovation (UKRI) United Kingdom
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
DepositionNov 12, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55693.png

Downloads & links

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Map

FileDownload / File: emd_55693.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 300 pix.
= 373.2 Å		1.24 Å/pix.
x 300 pix.
= 373.2 Å		1.24 Å/pix.
x 300 pix.
= 373.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.244 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.017480139 - 0.03552726
Average (Standard dev.)0.000024605646 (±0.0007351724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 373.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2

Fileemd_55693_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_55693_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E3 ubiquitin-protein ligase RNF213

EntireName: E3 ubiquitin-protein ligase RNF213
Components
  • Complex: E3 ubiquitin-protein ligase RNF213

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Supramolecule #1: E3 ubiquitin-protein ligase RNF213

SupramoleculeName: E3 ubiquitin-protein ligase RNF213 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 31.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 557952
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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