8ZEQ | pdb_00008zeq

Molecular Architecture of Human Glycogen Debranching Enzyme: Insights into Glycogen Storage Disease III Pathogenesis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular architecture and catalytic mechanism of human glycogen debranching enzyme.

Guan, H.Chen, H.Geng, H.Ma, R.Liu, Z.Wang, Y.Chen, Y.Yan, K.

(2025) Nat Commun 16: 5962-5962

  • DOI: https://doi.org/10.1038/s41467-025-61077-6
  • Primary Citation of Related Structures:  
    8ZEQ

  • PubMed Abstract: 

    Glycogen, a key branched glucose polymer, acts as a vital energy reservoir in mammalian cells, particularly during intense activity or fasting. The glycogen debranching enzyme (GDE) plays a key role in glycogen degradation by removing branches, ensuring efficient glucose release. Dysfunction of GDE leads to the accumulation of limit dextrin and is implicated in the pathogenesis of Glycogen Storage Disease Type III (GSD III). We present the cryo-EM structure of human GDE (hsGDE) at 3.23 Å resolution, providing molecular insights into its substrate selectivity and catalytic mechanism. Our study further investigates the molecular consequences of disease-associated mutations by correlating structural data with enzymatic activities of representative GSD III-causing variants. We discover that these mutations induce GSD III through diverse mechanisms, including significant reductions in enzymatic activity, and disruptions to the glycogen-bound region and overall structural integrity. The elucidation of these pathways not only advances our understanding of hsGDE's role in substrate recognition and catalysis but also illuminates the molecular pathology of GSD III. Our findings pave the way for the development of targeted therapeutic strategies for this disease.


  • Organizational Affiliation
    • Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen debranching enzyme1,532Homo sapiensMutation(s): 0 
Gene Names: AGLGDE
EC: 2.4.1.25 (PDB Primary Data), 3.2.1.33 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P35573 (Homo sapiens)
Explore P35573 
Go to UniProtKB:  P35573
PHAROS:  P35573
GTEx:  ENSG00000162688 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35573
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentZDSYS20220402111000001
Other governmentJCYJ20220530115214033
Other governmentKQTD20210811090115021

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references