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TitleMonoclonal nanobodies alter the activity and assembly of the yeast vacuolar H-ATPase.
Journal, issue, pagesbioRxiv, Year 2025
Publish dateJan 11, 2025
AuthorsKassidy Knight / Jun Bae Park / Rebecca A Oot / Md Murad Khan / Soung-Hun Roh / Stephan Wilkens /
PubMed AbstractThe vacuolar ATPase (V-ATPase; VV) is a multi-subunit rotary nanomotor proton pump that acidifies organelles in virtually all eukaryotic cells, and extracellular spaces in some specialized tissues of ...The vacuolar ATPase (V-ATPase; VV) is a multi-subunit rotary nanomotor proton pump that acidifies organelles in virtually all eukaryotic cells, and extracellular spaces in some specialized tissues of higher organisms. Evidence suggests that metastatic breast cancers mislocalize V-ATPase to the plasma membrane to promote cell survival and facilitate metastasis, making the V-ATPase a potential drug target. We have generated a library of camelid single-domain antibodies (Nanobodies; Nbs) against lipid-nanodisc reconstituted yeast V-ATPase V proton channel subcomplex. Here, we present an in-depth characterization of three anti-V Nbs using biochemical and biophysical experiments. We find that the Nbs bind V with high affinity, with one Nb inhibiting holoenzyme activity and another one preventing enzyme assembly. Using cryoEM, we find that two of the Nbs bind the subunit ring of the V on the lumen side of the complex. Additionally, we show that one of the Nbs raised against yeast V can pull down human V-ATPase (VV). Our research demonstrates Nb versatility to target and modulate the activity of the V-ATPase, and highlights the potential for future therapeutic Nb development.
External linksbioRxiv / PubMed:39829782 / PubMed Central
MethodsEM (single particle)
Resolution3.33 - 4.5 Å
Structure data

47659

9e76

EMDB-47659, PDB-9e76:
Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25
Method: EM (single particle) / Resolution: 3.4 Å

47679

9e7l

EMDB-47679, PDB-9e7l:
Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7
Method: EM (single particle) / Resolution: 3.33 Å

48311

9mj4

EMDB-48311, PDB-9mj4:
Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-48592: Yeast V-ATPase bound to Nanobody 2WVA7, state 3-18
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-48593: Yeast V-ATPase bound to Nanobody 2WVA7, state 1
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-48594: Yeast V-ATPase bound to Nanobody 2WVA7, state 3+18
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-48595: Yeast Vo bound to Nanobody 2WVA7, state 1
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-48596: Yeast Vo bound to Nanobody 2WVA7, state 3-18
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-48597: Yeast Vo bound to Nanobody 2WVA7, state 3+18
Method: EM (single particle) / Resolution: 3.62 Å

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • lama glama (llama)
KeywordsPROTON TRANSPORT / Vacuolar ATPase / Vo proton channel / lipid nanodisc / nanobody

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