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TitleDevelopment of an inhibitory TTC7B selective nanobody that blocks EFR3 recruitment of PI4KA.
Journal, issue, pagesJ Biol Chem, Vol. 301, Issue 12, Page 110886, Year 2025
Publish dateNov 4, 2025
AuthorsSushant Suresh / Alexandria L Shaw / Damilola K Akintola / Martine Lunke / Sophia Doerr / Pooja Rohilla / Tamas Balla / Calvin K Yip / Scott D Hansen / Jennifer A Cobb / John E Burke /
PubMed AbstractPhosphatidylinositol 4 kinase IIIα (PI4KIIIα/PI4KA) is an essential lipid kinase that plays a critical role in regulating plasma membrane (PM) identity. PI4KA is primarily recruited to the PM ...Phosphatidylinositol 4 kinase IIIα (PI4KIIIα/PI4KA) is an essential lipid kinase that plays a critical role in regulating plasma membrane (PM) identity. PI4KA is primarily recruited to the PM through the targeted recruitment by the proteins, EFR3A and EFR3B, which bind to the PI4KA accessory proteins, TTC7 (TTC7A/B) and FAM126 (FAM126A/B). Here, we characterized how both EFR3 isoforms interact with all possible TTC7-FAM126 combinations and developed a nanobody that specifically blocked EFR3-mediated PI4KA recruitment in TTC7B-containing complexes. Most EFR3-TTC7-FAM126 combinations show similar binding affinities, with the exception of EFR3A-TTC7B-FAM126A, which binds with a ∼10-fold higher affinity. Moreover, we showed that EFR3B phosphorylation markedly decreased binding to TTC7-FAM126. Using a yeast display approach, we isolated a TTC7B selective nanobody that blocked EFR3 binding. Cryo-EM and hydrogen deuterium exchange mass spectrometry showed an extended interface with both PI4KA and TTC7B that sterically blocks EFR3 binding. The nanobody caused decreased membrane recruitment both on lipid bilayers and in cells, with decreased PM production of phosphatidylinositol 4-phosphate. Collectively, these findings provide new insights into PI4KA regulation and provide a tool for manipulating PI4KA complexes, which may be valuable for therapeutic targeting.
External linksJ Biol Chem / PubMed:41197736 / PubMed Central
MethodsEM (single particle)
Resolution3.54 - 3.77 Å
Structure data

EMDB-70822: Consensus Map of PI4KA/TTC7B/FAM126A/F3IN Nanobody
Method: EM (single particle) / Resolution: 3.54 Å

EMDB-70824: Local Refinement A of PI4KA/TTC7B/FAM126A/F3IN Nanobody
Method: EM (single particle) / Resolution: 3.61 Å

EMDB-70825: Local Refinement B of PI4KA/TTC7B/FAM126A/F3IN nanbody
Method: EM (single particle) / Resolution: 3.77 Å

70826

9ot6

EMDB-70826, PDB-9ot6:
Cryo-EM structure of the PI4KA complex bound to an EFR3 interfering nanobody (F3IN)
Method: EM (single particle) / Resolution: 3.54 Å

Source
  • homo sapiens (human)
  • lama glama (llama)
KeywordsSIGNALING PROTEIN / PI4KA / TTC7B / FAM126A / Nanobody / Complex

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