5D7G

Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mutation in ATG5 reduces autophagy and leads to ataxia with developmental delay.

Kim, M.Sandford, E.Gatica, D.Qiu, Y.Liu, X.Zheng, Y.Schulman, B.A.Xu, J.Semple, I.Ro, S.H.Kim, B.Mavioglu, R.N.Tolun, A.Jipa, A.Takats, S.Karpati, M.Li, J.Z.Yapici, Z.Juhasz, G.Lee, J.H.Klionsky, D.J.Burmeister, M.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.12245
  • Primary Citation of Related Structures:  
    5D7G

  • PubMed Abstract: 

    Autophagy is required for the homeostasis of cellular material and is proposed to be involved in many aspects of health. Defects in the autophagy pathway have been observed in neurodegenerative disorders; however, no genetically-inherited pathogenic mutations in any of the core autophagy-related (ATG) genes have been reported in human patients to date. We identified a homozygous missense mutation, changing a conserved amino acid, in ATG5 in two siblings with congenital ataxia, mental retardation, and developmental delay. The subjects' cells display a decrease in autophagy flux and defects in conjugation of ATG12 to ATG5. The homologous mutation in yeast demonstrates a 30-50% reduction of induced autophagy. Flies in which Atg5 is substituted with the mutant human ATG5 exhibit severe movement disorder, in contrast to flies expressing the wild-type human protein. Our results demonstrate the critical role of autophagy in preventing neurological diseases and maintaining neuronal health.


  • Organizational Affiliation

    Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy protein 5
A, C, E, G
280Homo sapiensMutation(s): 1 
Gene Names: ATG5APG5LASP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1Y0 (Homo sapiens)
Explore Q9H1Y0 
Go to UniProtKB:  Q9H1Y0
PHAROS:  Q9H1Y0
GTEx:  ENSG00000057663 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1Y0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy-related protein 16-1
B, D, F, H
71Homo sapiensMutation(s): 0 
Gene Names: ATG16L1APG16LUNQ9393/PRO34307
UniProt & NIH Common Fund Data Resources
Find proteins for Q676U5 (Homo sapiens)
Explore Q676U5 
Go to UniProtKB:  Q676U5
PHAROS:  Q676U5
GTEx:  ENSG00000085978 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ676U5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.114α = 90
b = 84.478β = 133.81
c = 151.849γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description