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Structure paper

TitleA GABARAP-PtdIns3K-C1 positive feedback loop at the heart of the phagophore nucleation.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateJul 30, 2026
AuthorsAntoine N Dessus / Yohei Ohashi / Maxime Bourguet / Tomos E Morgan / Anastasia Nunez / Maria Manifava / Nicholas T Ktistakis / Roger L Williams /
PubMed AbstractIn mammalian cells, autophagosomes can reach diameters of over 1000 nm within 30 min after triggering starvation, but how such substantial amounts of membranes can be synthesized remains elusive. ...In mammalian cells, autophagosomes can reach diameters of over 1000 nm within 30 min after triggering starvation, but how such substantial amounts of membranes can be synthesized remains elusive. The phagophore initiation needs the lipid kinase PIK3C3-Complex 1 (PtdIns3K-C1), which produces phosphatidylinositol-3-phosphate (PtdIns3P). PtdIns3P recruits WIPI2 that facilitates lipidation of mammalian ATG8 (mATG8) family proteins on phagophores. Here we show that recombinant membrane-coupled GABARAP binds to and potently activates PtdIns3K-C1. By a combination of cryo-electron microscopy, structural mass spectrometry, activity assays and mutagenesis, we show that GABARAP activates PtdIns3K-C1 through two binding sites. We propose that once GABARAP is indirectly recruited by PtdIns3P generated by basal activity of PtdIns3K-C1, a positive feedback loop is formed where PtdIns3K-C1 interacts with GABARAP and becomes activated to produce more PtdIns3P, thereby further stimulating GABARAP lipidation. This mechanism would be central for autophagosome biogenesis, where enlarged membranes need to be rapidly synthesized.
External linksNat Commun / PubMed:42693081 / PubMed Central
MethodsEM (single particle)
Resolution3.28 - 4.01 Å
Structure data

EMDB-56343: Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation, local refinement on BECLIN1 and ATG14L C-terminal domains.
Method: EM (single particle) / Resolution: 4.01 Å

EMDB-56345: Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation, consensus map
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-56346: Cryo-EM structure of human VPS34-CI in complex with GABARAP, consensus map
Method: EM (single particle) / Resolution: 3.58 Å

EMDB-56347: Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on VPS34 and VPS15 kinase domains.
Method: EM (single particle) / Resolution: 3.38 Å

EMDB-56348: Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on the core of VPS34-CI.
Method: EM (single particle) / Resolution: 3.48 Å

EMDB-56350: Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on VPS15 helical solenoid, and BECLIN1 and ATG14L N-terminal domains.
Method: EM (single particle) / Resolution: 3.28 Å

EMDB-56351: Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on GABARAP.
Method: EM (single particle) / Resolution: 3.46 Å

EMDB-56353: Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on BECLIN1 and ATG14L C-terminal domains.
Method: EM (single particle) / Resolution: 3.82 Å

56357

9tw2

EMDB-56357: Cryo-EM structure of human VPS34-CI in complex with GABARAP, composite map
PDB-9tw2: Cryo-EM structure of human VPS34-CI in complex with GABARAP
Method: EM (single particle) / Resolution: 3.58 Å

56358

9tw3

EMDB-56358: Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation, composite map
PDB-9tw3: Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-56454: Cryo-EM structure of human VPS34-CI with ADP:MgF3 - consensus map
Method: EM (single particle) / Resolution: 3.66 Å

EMDB-56455: Cryo-EM structure of human VPS34-CI with ADP:MgF3 - local refinement on the complex base
Method: EM (single particle) / Resolution: 3.51 Å

EMDB-56456: Cryo-EM structure of human VPS34-CI with ADP:MgF3 - local refinement on VPS34 and VPS15 kinases
Method: EM (single particle) / Resolution: 3.33 Å

EMDB-56457: Cryo-EM structure of human VPS34-CI with ADP:MgF3 - local refinement on ATG14L and BECLIN1 C-termini
Method: EM (single particle) / Resolution: 3.95 Å

56458

9tz3

EMDB-56458: Cryo-EM structure of human VPS34-CI with ADP:MgF3 - composite map
PDB-9tz3: Cryo-EM structure of human VPS34-CI with ADP:MgF3
Method: EM (single particle) / Resolution: 3.66 Å

Chemicals

ChemComp-MYR:
MYRISTIC ACID

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • homo sapiens (human)
KeywordsLIPID BINDING PROTEIN / Lipid kinase / Complex / Autophagy

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