The nuclear pore complex (NPC) mediates nucleocytoplasmic transport. While its core architecture is well understood, peripheral regions vary between species. The nuclear basket, important for mRNA surveillance and chromatin organization, has been structurally elusive. Using cryo-electron tomography and subtomogram analysis, we studied NPC variations and the nuclear basket in yeast, mouse, and protozoa. Integrative structural modeling revealed that Nups in the nuclear ring bind to basket-forming Mlp/Tpr proteins: their coiled-coil domains form basket struts, and their unstructured termini form distal densities, potentially docking mRNA for preprocessing before transport. [BioRXiv]