Extended Data Fig. 5: Updated model for native IR.
From: The cellular environment shapes the nuclear pore complex architecture
a, Side-by-side comparison of the previous IR model (PDB: 5IJN) with our updated model to fit the DLD-1 NPC map. b, Superimposition of our updated IR model with the previous model shows the rearrangements required to fit our density map. Each pane highlights a different nucleoporin colored in our updated model as in (a), or colored dark grey from the previous model. c, Views of three updated IR-models in our map compared with the previous model and human NPC map. d, Same as (c) but with only models. e, Cross-section views of the NR in our map at both high and low threshold to show connectivity with the IR. f, Same as (e), though no density can be observed between the CR-IR, likely due to flexibility. Flexibility could explain why the ring-connecting densities, proposed to be Nup1559, remain conspicuously poorly resolved in our map compared to the previous human maps12,15,16. We hypothesize that this observation may be unique to the more “constricted” IR state observed previously, locking the ring-connecting proteins into a more rigid state. In the same vein, others have shown that NPCs from yeast, both semi-purified36 and in their native state18, can contain multiple flexible linkers between the outer rings and IR, suggesting this arrangement could provide resilience to the NPC structure.
