The 3.5-Å CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase Vo Proton Channel

Mol Cell. 2018 Mar 15;69(6):993-1004.e3. doi: 10.1016/j.molcel.2018.02.006. Epub 2018 Mar 8.


The molecular mechanism of transmembrane proton translocation in rotary motor ATPases is not fully understood. Here, we report the 3.5-Å resolution cryoEM structure of the lipid nanodisc-reconstituted Vo proton channel of the yeast vacuolar H+-ATPase, captured in a physiologically relevant, autoinhibited state. The resulting atomic model provides structural detail for the amino acids that constitute the proton pathway at the interface of the proteolipid ring and subunit a. Based on the structure and previous mutagenesis studies, we propose the chemical basis of transmembrane proton transport. Moreover, we discovered that the C terminus of the assembly factor Voa1 is an integral component of mature Vo. Voa1's C-terminal transmembrane α helix is bound inside the proteolipid ring, where it contributes to the stability of the complex. Our structure rationalizes possible mechanisms by which mutations in human Vo can result in disease phenotypes and may thus provide new avenues for therapeutic interventions.

Keywords: V(o) proton channel; V-ATPase assembly; Voa1; cryoEM; lipid nanodisc; membrane protein structure; proton pumping; reversible disassembly; vacuolar H(+)-ATPase.

Publication types

  • Research Support, N.I.H., Extramural
  • Video-Audio Media

MeSH terms

  • Cryoelectron Microscopy*
  • Genotype
  • Humans
  • Membrane Lipids / chemistry
  • Models, Molecular
  • Mutation
  • Nanoparticles*
  • Phenotype
  • Protein Conformation, alpha-Helical
  • Protein Interaction Domains and Motifs
  • Protein Multimerization
  • Protein Subunits
  • Protons
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Saccharomyces cerevisiae Proteins / ultrastructure*
  • Structure-Activity Relationship
  • Vacuolar Proton-Translocating ATPases / genetics
  • Vacuolar Proton-Translocating ATPases / metabolism
  • Vacuolar Proton-Translocating ATPases / ultrastructure*


  • Membrane Lipids
  • Protein Subunits
  • Protons
  • Saccharomyces cerevisiae Proteins
  • ATP6V0A1 protein, human
  • VOA1 protein, S cerevisiae
  • Vacuolar Proton-Translocating ATPases