Assembly and dynamics of the autophagy-initiating Atg1 complex

Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12793-8. doi: 10.1073/pnas.1407214111. Epub 2014 Aug 19.


The autophagy-related 1 (Atg1) complex of Saccharomyces cerevisiae has a central role in the initiation of autophagy following starvation and TORC1 inactivation. The complex consists of the protein kinase Atg1, the TORC1 substrate Atg13, and the trimeric Atg17-Atg31-Atg29 scaffolding subcomplex. Autophagy is triggered when Atg1 and Atg13 assemble with the trimeric scaffold. Here we show by hydrogen-deuterium exchange coupled to mass spectrometry that the mutually interacting Atg1 early autophagy targeting/tethering domain and the Atg13 central domain are highly dynamic in isolation but together form a stable complex with ∼ 100-nM affinity. The Atg1-Atg13 complex in turn binds as a unit to the Atg17-Atg31-Atg29 scaffold with ∼ 10-μM affinity via Atg13. The resulting complex consists primarily of a dimer of pentamers in solution. These results lead to a model for autophagy initiation in which Atg1 and Atg13 are tightly associated with one another and assemble transiently into the pentameric Atg1 complex during starvation.

Keywords: analytical ultracentrifugation; intrinsically disordered proteins; isothermal titration calorimetry; membrane tethering; protein structure.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / chemistry
  • Adaptor Proteins, Signal Transducing / genetics
  • Adaptor Proteins, Signal Transducing / metabolism*
  • Amino Acid Sequence
  • Autophagy / physiology*
  • Autophagy-Related Proteins
  • Calorimetry
  • Carrier Proteins / chemistry
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism
  • Crystallography, X-Ray
  • Gene Deletion
  • Molecular Sequence Data
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / metabolism*
  • Protein Binding
  • Protein Kinases / chemistry
  • Protein Kinases / genetics
  • Protein Kinases / metabolism*
  • Protein Structure, Quaternary
  • Saccharomyces cerevisiae / cytology
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*


  • ATG13 protein, S cerevisiae
  • ATG29 protein, S cerevisiae
  • Adaptor Proteins, Signal Transducing
  • Atg17 protein, S cerevisiae
  • Atg31 protein, S cerevisiae
  • Autophagy-Related Proteins
  • Carrier Proteins
  • Multiprotein Complexes
  • Saccharomyces cerevisiae Proteins
  • Protein Kinases
  • ATG1 protein, S cerevisiae