5KC2

Negative stain structure of Vps15/Vps34 complex

Summary for 5KC2

• Entry DOI: 10.2210/pdb5kc2/pdb
• EMDB information: 8235
• Descriptor: Phosphatidylinositol 3-kinase VPS34, Serine/threonine-protein kinase VPS15 (2 entities in total)
• Functional Keywords: autophagy, phosphatidylinositol 3-kinase (ptdins3k), endocytosis
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 2
• Total formula weight: 267597.18

Authors

Kirsten, M.L.,Zhang, L.,Ohashi, Y.,Perisic, O.,Williams, R.L.,Sachse, C. (deposition date: 2016-06-04, release date: 2016-10-05, Last modification date: 2024-05-15)

Primary citation

Ohashi, Y.,Soler, N.,Garcia Ortegon, M.,Zhang, L.,Kirsten, M.L.,Perisic, O.,Masson, G.R.,Burke, J.E.,Jakobi, A.J.,Apostolakis, A.A.,Johnson, C.M.,Ohashi, M.,Ktistakis, N.T.,Sachse, C.,Williams, R.L.
Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex.
Autophagy, 12:2129-2144, 2016

PubMed Abstract: 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.

PubMed: 27630019
DOI: 10.1080/15548627.2016.1226736

Experimental method

ELECTRON MICROSCOPY (28 Å)