ATG9A and ATG2A form a heteromeric complex essential for autophagosome formation.

ATG9A and ATG2A are essential core members of the autophagy machinery. ATG9A is a lipid scramblase that allows equilibration of lipids across a membrane bilayer, while ATG2A facilitates lipid flow between tethered membranes. Although both have been functionally linked during the formation of autophagosomes, the molecular details and consequences of their interaction remain unclear. By combining data from peptide arrays, crosslinking and hydrogen deuterium exchange mass spectrometry, together with cryo-electron microscopy, we propose a molecular model of the ATG9A-2A complex. Using this integrative structure modelling approach, we identify several interfaces mediating ATG9A-2A interaction which would allow a direct transfer of lipids from ATG2A into the lipid-binding perpendicular branch of ATG9A. Mutational analyses combined with functional activity assays demonstrate their importance for autophagy, thereby shedding light on this protein complex at the heart of autophagy.ATG9A与ATG2A是自噬机制（autophagy machinery）中不可或缺的核心成员。ATG9A是一种脂质翻转酶（lipid scramblase），可实现脂质在膜双层双侧的平衡分布；而ATG2A则可促进锚定膜之间的脂质转运。尽管二者在自噬体（autophagosome）形成过程中存在功能关联，但二者相互作用的分子细节与功能效应仍不明确。本研究结合肽阵列（peptide array）、交联（crosslinking）、氢氘交换质谱（hydrogen deuterium exchange mass spectrometry）及冷冻电镜（cryo-electron microscopy）的数据，提出了ATG9A-ATG2A复合物的分子模型。借助该整合结构建模方法，本研究鉴定出多个介导ATG9A与ATG2A相互作用的互作界面，该界面可实现脂质从ATG2A直接转运至ATG9A的脂质结合垂直分支。结合突变分析与功能活性测定的实验结果证实，该互作界面对自噬过程至关重要，从而阐明了这一位于自噬核心的蛋白复合物的作用机制。