Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly

Mol Cell. 2020 Nov 5;80(3):501-511.e3. doi: 10.1016/j.molcel.2020.09.029. Epub 2020 Oct 15.


Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the Vo complex. We define ATP6AP1 as a structural hub for Vo complex assembly because it connects to multiple Vo subunits and phospholipids in the c-ring. The glycolipids and the glycosylated Vo subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids.

Publication types

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

MeSH terms

  • Cryoelectron Microscopy / methods
  • Cytoplasm / metabolism
  • Cytosol / metabolism
  • HEK293 Cells
  • Humans
  • Protein Subunits / metabolism
  • Structure-Activity Relationship
  • Vacuolar Proton-Translocating ATPases / metabolism*
  • Vacuolar Proton-Translocating ATPases / physiology*
  • Vacuolar Proton-Translocating ATPases / ultrastructure*


  • ATP6AP1 protein, human
  • Protein Subunits
  • Vacuolar Proton-Translocating ATPases