9OT6
Cryo-EM structure of the PI4KA complex bound to an EFR3 interfering nanobody (F3IN)
Summary for 9OT6
| Entry DOI | 10.2210/pdb9ot6/pdb |
| EMDB information | 70826 |
| Descriptor | Phosphatidylinositol 4-kinase alpha, EFR3 interfering Nanobody (F3IN), Tetratricopeptide repeat protein 7B, ... (4 entities in total) |
| Functional Keywords | pi4ka, ttc7b, fam126a, nanobody, complex, signaling protein |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 8 |
| Total formula weight | 768409.29 |
| Authors | Shaw, A.L.,Suresh, S.,Yip, C.K.,Burke, J.E. (deposition date: 2025-05-26, release date: 2025-12-03, Last modification date: 2025-12-24) |
| Primary citation | Suresh, S.,Shaw, A.L.,Akintola, D.K.,Lunke, M.,Doerr, S.,Rohilla, P.,Balla, T.,Yip, C.K.,Hansen, S.D.,Cobb, J.A.,Burke, J.E. Development of an inhibitory TTC7B selective nanobody that blocks EFR3 recruitment of PI4KA. J.Biol.Chem., 301:110886-110886, 2025 Cited by PubMed Abstract: Phosphatidylinositol 4 kinase IIIα (PI4KIIIα/PI4KA) is an essential lipid kinase that plays a critical role in regulating plasma membrane identity. PI4KA is primarily recruited to the plasma membrane 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 characterised 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-electron microscopy 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 PI4P. Collectively, these findings provide new insights into PI4KA regulation and provide a tool for manipulating PI4KA complexes, that may be valuable for therapeutic targeting. PubMed: 41197736DOI: 10.1016/j.jbc.2025.110886 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.54 Å) |
Structure validation
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