Figure 6. Integrative structure of Pom152^FL based on NMR spectroscopy, negative-stain EM, and SAXS.

(A) (left) The localization probability density map computed from 364 superposed structures that satisfy the input spatial restraints shows the location of each of the 9 Ig-like domains (ranging from blue to red). The negative-stain EM density map is superposed in grey. A representative molecular model of Pom152^LD (ribbon plot) was obtained by adjusting the relative orientations of adjacent Ig-like domains to resemble those in known cadherin structures (PDB codes 1L3W, 1EPF, 1NCI, 4ZI9, and 5K8R) (Boggon et al., 2002; Kasper et al., 2000; Nicoludis et al., 2015; Nicoludis et al., 2016; Shapiro et al., 1995).

(right) Validation of the integrative structure of Pom152^LD by SAXS data for five Pom152 segments, spanning residues 718–820 (Ig-4), 718–920 (Ig-4,5), 603–820 (Ig-3,4), 919–1020 (Ig-6), and 718–1148 (Ig-4,5,6,7). The shapes of these segments in our integrative structure match the envelopes (ab initio shapes) computed from the corresponding SAXS profiles.

(B) Fit of 16 copies of Pom152^LD into the yeast NPC map (Alber et al., 2007b). A good fit positions two copies of the extended Pom152^LD molecule in an anti-parallel fashion on top of each other, forming a homodimer; we only show the potential arrangement of the antiparallel homodimer, which is implied by the C₂-symmetry of the NPC (Alber et al., 2007b; Kosinski et al., 2016; Lin et al., 2016).

See also Figures 5, S4–S7 and Table S1.