Structure of Human ATG9A, the Only Transmembrane Protein of the Core Autophagy Machinery

Cell Rep. 2020 Jun 30;31(13):107837. doi: 10.1016/j.celrep.2020.107837.


Autophagy is a catabolic process involving capture of cytoplasmic materials into double-membraned autophagosomes that subsequently fuse with lysosomes for degradation of the materials by lysosomal hydrolases. One of the least understood components of the autophagy machinery is the transmembrane protein ATG9. Here, we report a cryoelectron microscopy structure of the human ATG9A isoform at 2.9-Å resolution. The structure reveals a fold with a homotrimeric domain-swapped architecture, multiple membrane spans, and a network of branched cavities, consistent with ATG9A being a membrane transporter. Mutational analyses support a role for the cavities in the function of ATG9A. In addition, structure-guided molecular simulations predict that ATG9A causes membrane bending, explaining the localization of this protein to small vesicles and highly curved edges of growing autophagosomes.

Keywords: ATG9A; autophagosome; autophagy; cryo-EM; membrane curvature; membrane morphology; membrane protein structure; membrane transport; molecular dynamics; transmembrane protein.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Amino Acid Sequence
  • Autophagy*
  • Autophagy-Related Proteins / chemistry*
  • Autophagy-Related Proteins / metabolism*
  • Autophagy-Related Proteins / ultrastructure
  • Cryoelectron Microscopy
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Lipid Bilayers / chemistry
  • Membrane Proteins / chemistry*
  • Membrane Proteins / metabolism*
  • Membrane Proteins / ultrastructure
  • Molecular Dynamics Simulation
  • Mutagenesis / genetics
  • Phosphatidylcholines / chemistry
  • Protein Domains
  • Protein Multimerization
  • Protein Structure, Secondary
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • Vesicular Transport Proteins / chemistry*
  • Vesicular Transport Proteins / metabolism*
  • Vesicular Transport Proteins / ultrastructure


  • ATG2A protein, human
  • Atg9a protein, human
  • Autophagy-Related Proteins
  • Lipid Bilayers
  • Membrane Proteins
  • Phosphatidylcholines
  • Protein Subunits
  • Vesicular Transport Proteins
  • 1-palmitoyl-2-oleoylphosphatidylcholine