Autophagy: Solution Structure of the Atg17-Atg29-Atg31-Atg1-Atg13 Complex

Abstract

Autophagy is a complex bulk clearance mechanism that collects cellular material intended for degradation. In yeast, this highly conserved machinery comprises about 40 autophagy-related (Atg) proteins, most of which form multiprotein complexes. We elucidated the structure of the Atg17-Atg29-Atg31-Atg1-Atg13 complex in solution using small-angle X-ray scattering experiments (SAXS), coarse-grained simulations, and the ensemble refinement of SAXS (EROS) method. Our model consists of rigid domains based on the crystal structures of the Atg17-Atg29-Atg31 complex and of the Atg1-Atg13 complex. The modeling and simulation of disordered regions, which have not been resolved in the crystal structures, is crucial for the determination of the solution structures. Specifically, the Atg17 binding site on Atg13 has not been resolved and is located on such a disordered part of the protein. We therefore modeled disordered regions as flexible chains and link the Atg17 proteins and Atg13 proteins accordingly. We performed coarse-grained simulations for various multiprotein complex topologies and refined the resulting ensembles of structures using EROS. The resulting structural models account consistently for the SAXS measurements of the Atg17-Atg29-Atg31-Atg1-Atg13 supercomplex and several of its subcomplexes.