5DFZ
Structure of Vps34 complex II from S. cerevisiae.
Summary for 5DFZ
| Entry DOI | 10.2210/pdb5dfz/pdb |
| Descriptor | Vacuolar protein sorting-associated protein 38, Phosphatidylinositol 3-kinase VPS34, Serine/threonine-protein kinase VPS15, ... (6 entities in total) |
| Functional Keywords | vps34, vps15, vps30, vps38, autophagy, vacuolar protein sorting, yeast, complex ii, pi3p, kinase, lipid, wd40, bara, c2, coiled-coil, heat, nanobody, transferase |
| Biological source | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) More |
| Cellular location | Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein: Q05919 P22543 Golgi apparatus, trans-Golgi network membrane; Lipid-anchor: P22219 Endosome membrane; Peripheral membrane protein: Q02948 |
| Total number of polymer chains | 6 |
| Total formula weight | 400489.65 |
| Authors | Rostislavleva, K.,Soler, N.,Ohashi, Y.,Zhang, L.,Williams, R.L. (deposition date: 2015-08-27, release date: 2015-10-07, Last modification date: 2024-05-08) |
| Primary citation | Rostislavleva, K.,Soler, N.,Ohashi, Y.,Zhang, L.,Pardon, E.,Burke, J.E.,Masson, G.R.,Johnson, C.,Steyaert, J.,Ktistakis, N.T.,Williams, R.L. Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science, 350:aac7365-aac7365, 2015 Cited by PubMed Abstract: Phosphatidylinositol 3-kinase Vps34 complexes regulate intracellular membrane trafficking in endocytic sorting, cytokinesis, and autophagy. We present the 4.4 angstrom crystal structure of the 385-kilodalton endosomal complex II (PIK3C3-CII), consisting of Vps34, Vps15 (p150), Vps30/Atg6 (Beclin 1), and Vps38 (UVRAG). The subunits form a Y-shaped complex, centered on the Vps34 C2 domain. Vps34 and Vps15 intertwine in one arm, where the Vps15 kinase domain engages the Vps34 activation loop to regulate its activity. Vps30 and Vps38 form the other arm that brackets the Vps15/Vps34 heterodimer, suggesting a path for complex assembly. We used hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal conformational changes accompanying membrane binding and identify a Vps30 loop that is critical for the ability of complex II to phosphorylate giant liposomes on which complex I is inactive. PubMed: 26450213DOI: 10.1126/science.aac7365 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (4.4 Å) |
Structure validation
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