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Structure paper

TitleQuality control of glycogen through direct ubiquitylation by RNF213.
Journal, issue, pagesNature, Year 2026
Publish dateSep 15, 2026
AuthorsMatthew 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 /
PubMed AbstractQuality 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.
External linksNature / PubMed:42744304
MethodsEM (single particle) / EM (tomography)
Resolution2.7 - 3.1 Å
Structure data

55686

9t8h

EMDB-55686, PDB-9t8h:
Murine RNF213 bound to maltoheptaose
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-55687: Murine RNF213 bound to maltoheptaose (Consensus refinement)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-55688: Murine RNF213 bound to maltoheptaose (Focused refinement of ATPase domain)
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-55689: Murine RNF213 bound to maltoheptaose (Focused refinement of stalk)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-55690: Murine RNF213 bound to maltoheptaose (Focused refinement of top of stalk)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-55691: Murine RNF213 bound to maltoheptaose (Focused refinement of CBM20 domain)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-55692: Murine RNF213 bound to maltoheptaose (Focused refinement of E3 module)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-55693: Murine RNF213 bound to maltoheptaose (Focused refinement of E3 shell)
Method: EM (single particle) / Resolution: 2.9 Å

55694

9t8i

EMDB-55694, PDB-9t8i:
Murine RNF213
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-55695: Murine RNF213 (Consensus refinement)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-55696: Murine RNF213 (Focused refinement of ATPase domain)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-55697: Murine RNF213 (Focused refinement of stalk)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-55698: Murine RNF213 (Focused refinement of top of stalk)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-55699: Murine RNF213 (Focused refinement of CBM20 domain)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-55700: Murine RNF213 (Focused refinement of E3 module)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-55701: Murine RNF213 (Focused refinement of E3 shell)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-59437: Murine RNF213 (Y434A) (Focused refinement of ATPase domain)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-59438: Murine RNF213 (Y434A) (focused refinement of stalk)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-59439: murine RNF213 (Y434A) (focused refinement of top of stalk)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-59440: murine RNF213 (Y434A) (focused refinement of CBM20 domain)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-59441: murine RNF213 (Y434A) (focused refinement of E3)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-59442: murine RNF213 (Y434A) (focused refinement of E3 shell)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-59443: murine RNF213 (Y434A) (consensus refinement)
Method: EM (single particle) / Resolution: 3.1 Å

59444

33hm

EMDB-59444, PDB-33hm:
Murine RNF213 (Y434A)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-59854: Cryo-electron tomogram of MEF cell containing polyglucosan
Method: EM (tomography)

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-ZN:
Unknown entry

Source
  • mus musculus (house mouse)
KeywordsSUGAR BINDING PROTEIN / E3 ubiquitin ligase / AAA+ ATPase / CBM20

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