Phosphatidylinositol 3,5-bisphosphate (PI(3,5)P₂) is an essential phosphoinositide required for endosome homeostasis and sorting for lysosomal degradation; however, the underlying mechanisms, especially in mammals, remain elusive or unexplored. Here we determined a structure of PI(3,5)P₂ bound to Sorting Nexin 11 (SNX11) with an opened PPII-C loop. We also obtained an SNX11 structure with its PPII-C in “closed” form that serves as a potential PI3P-binding model. In addition, our results reveal that SNX11 can interact with the V1D subunit of vacuolar H⁺-ATPase (V-ATPase), which provides a link between PI(3,5)P₂ and human V-ATPase and further evidence for their roles in the endosome homeostasis regulation. Lastly, a new apo-form structure of SNX11, combined with molecular dynamics (MD) studies, indicates that the α5 helix can unfold from the PX domain of SNX11 when targeting the membrane or interacting with its partner. Taken together, these findings identify a novel PI(3,5)P₂ effector, which will shed light on the PIs recognizing mechanism and the understanding of the downstream sorting events triggered by different PI binding.

磷脂酰肌醇3,5-二磷酸（PI（3,5）P ₂）是内体稳态和溶酶体降解所需的必需的磷酸肌醇。然而，潜在的机制，尤其是在哺乳动物中，仍然难以捉摸或尚未探索。在这里，我们确定了一个PI（3,5）P ₂的结构，该结构绑定到具有打开的PPII-C回路的分选Nexin 11（SNX11）。我们还获得了带有“封闭”形式的PPII-C的SNX11结构，可作为潜在的PI3P绑定模型。此外，我们的研究结果表明SNX11可以与液泡H ⁺ -ATPase（V-ATPase）的V1D亚基相互作用，从而提供PI（3,5）P ₂之间的联系和人类V-ATPase，以及它们在内体稳态调节中作用的进一步证据。最后，结合分子动力学（MD）研究，SNX11的新脱辅基形式结构表明，当靶向膜或与其伴侣相互作用时，α5螺旋可从SNX11的PX域中展开。综上所述，这些发现确定了一种新颖的PI（3,5）P ₂效应子，它将阐明PI的识别机制以及对不同PI结合触发的下游分类事件的理解。