Fig. 2. Cross-linking mass spectrometry confirms intraand inter-subcomplex interactions of the IR architecture.

(A) Primary schematic of the IR proteins, showing the cross-links obtained by mass spectrometry. Inter-protein cross-links are shown in black, intra-protein links in light purple, and homodimeric cross-links (linking the same residues of a protein) in red. For clarity, Nup53 is not drawn to scale. Colored areas within the primary structures mark domains and motifs as individually labeled (residues are indicated below). A larger version is shown in fig. S6, and table S1 provides details on the cross-link data sets. The cross-links [blue lines in (B) to (D)] confirm specific features suggested by the composite structure, such as (B) head-to-tail arrangement of the inner and outer copy of Nup93, (C) interaction between Nup93 and Nup205, and (D) positioning of the Nup54 ferredoxin-like domain within the Nup62 complex.