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TitleCharacterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex.
Journal, issue, pagesAutophagy, Vol. 12, Issue 11, Page 2129-2144, Year 2016
Publish dateSep 14, 2016
AuthorsYohei Ohashi / Nicolas Soler / Miguel García Ortegón / Lufei Zhang / Marie L Kirsten / Olga Perisic / Glenn R Masson / John E Burke / Arjen J Jakobi / Apostolos A Apostolakis / Christopher M Johnson / Maki Ohashi / Nicholas T Ktistakis / Carsten Sachse / Roger L Williams /
PubMed AbstractThe phosphatidylinositol 3-kinase Vps34 is part of several protein complexes. The structural organization of heterotetrameric complexes is starting to emerge, but little is known about organization ...The phosphatidylinositol 3-kinase Vps34 is part of several protein complexes. The structural organization of heterotetrameric complexes is starting to emerge, but little is known about organization of additional accessory subunits that interact with these assemblies. Combining hydrogen-deuterium exchange mass spectrometry (HDX-MS), X-ray crystallography and electron microscopy (EM), we have characterized Atg38 and its human ortholog NRBF2, accessory components of complex I consisting of Vps15-Vps34-Vps30/Atg6-Atg14 (yeast) and PIK3R4/VPS15-PIK3C3/VPS34-BECN1/Beclin 1-ATG14 (human). HDX-MS shows that Atg38 binds the Vps30-Atg14 subcomplex of complex I, using mainly its N-terminal MIT domain and bridges the coiled-coil I regions of Atg14 and Vps30 in the base of complex I. The Atg38 C-terminal domain is important for localization to the phagophore assembly site (PAS) and homodimerization. Our 2.2 Å resolution crystal structure of the Atg38 C-terminal homodimerization domain shows 2 segments of α-helices assembling into a mushroom-like asymmetric homodimer with a 4-helix cap and a parallel coiled-coil stalk. One Atg38 homodimer engages a single complex I. This is in sharp contrast to human NRBF2, which also forms a homodimer, but this homodimer can bridge 2 complex I assemblies.
External linksAutophagy / PubMed:27630019 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.2 - 28.0 Å
Structure data

8235

5kc2

EMDB-8235, PDB-5kc2:
Negative stain structure of Vps15/Vps34 complex
Method: EM (single particle) / Resolution: 28.0 Å

PDB-5kc1:
Structure of the C-terminal dimerization domain of Atg38
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-NO3:
NITRATE ION / Nitrate

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-CL:
Unknown entry / Chloride

ChemComp-NH4:
AMMONIUM ION / Ammonium

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-IOD:
IODIDE ION / Iodide

ChemComp-HOH:
WATER / Water

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsENDOCYTOSIS / Atg38 / coiled-coil / dimerization / NRBF2 / autophagy / phosphatidylinositol 3-kinase (PtdIns3K)

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