Structure and mechanics of the human nuclear pore complex basket using correlative AFM-fluorescence superresolution microscopy

Nuclear pore complexes (NPCs) are the only gateways between the nucleus and cytoplasm in eukaryotic cells. They restrict free diffusion to molecules below 5 nm while facilitating the active transport of selected cargoes, sometimes as large as the pore itself. This versatility implies an important pore plasticity. Recently, cryo-EM and AI-based protein modeling of human NPC revealed with acute precision how most constituents are arranged. But the basket, a fish trap-like structure capping the nucleoplasmic side of the pore, remains poorly resolved. Here by atomic force microscopy (AFM) coupled to single molecule localization microscopy (SMLM) we revealed that the basket is very soft and explores a large conformational landscape: apart from its canonical basket shape, it dives into the central pore channel or opens, with filaments reaching to the pore sides. Our observations highlight how this structure can adapt and let morphologically diverse cargoes shuttle through NPCs.

Automated summary

Nuclear pore complexes (NPCs) are the gateways that control molecular transport between the nucleus and cytoplasm in eukaryotic cells. Recent studies have revealed the arrangement of most constituents in human NPCs using cryo-EM and AI-based protein modeling. However, the structure of the basket, which caps the nucleoplasmic side of the pore, remains poorly resolved. Using atomic force microscopy (AFM) and single molecule localization microscopy (SMLM), researchers discovered that the basket is highly flexible and can adopt different conformations, allowing diverse cargoes to pass through NPCs.