Extended Data Figure 7: Validation of the NPC structure (part 1).
From: Integrative structure and functional anatomy of a nuclear pore complex
a–c, Satisfaction of the chemical cross-links. a, Identified chemical cross-links were mapped onto the integrative structure of the entire NPC, as shown in front (upper) and top (lower) views. Satisfied cross-links, with Cα–Cα distances that fall within the distance threshold of 35?Å in at least one good-scoring NPC structure, are shown in blue. Violated cross-links, with Cα–Cα distances that are larger than 35?Å, are shown in orange. The histogram on the right shows the distribution of the cross-linked Cα–Cα distances, validating the NPC structure. b, Mapping of the cross-links onto the cytoplasmic and nucleoplasmic connector Nups (Nup116, Nup100, Nup145N, Nup1 and Nup60). Front (right) and side (left) views show how the NPC outer rings are connected to the inner ring through a network of connector Nups across the length of the spoke. c, Mapping of the cross-links onto the inner (and membrane) and outer rings, in front (upper) and top (lower) views. d–g, Satisfaction of data and considerations that were not used to compute the structure. d, Our integrative structure of the NPC (left) was compared a previously published topological map3,8 (right). The two structures are consistent with each other, though our integrative structure is defined at an order of magnitude higher precision. e, Satisfaction of affinity purification and overlay assays data (composites); our current structure satisfies all 82 composites determined by affinity purification and overlay assays3,8, even though these data were not used in its determination. For example, Pom152, Pom34, Ndc1, Nup157 and Nup170 are connected with each other (left), consistent with the previously published composites determined using the affinity purification data3,8 (right). f, Satisfaction of SAXS data; the atomic structures of eight Nups are consistent with the corresponding SAXS profiles for their constructs9,12,23,83,84,85,86 (Supplementary Tables 2, 6 and Methods). For example, the SAXS profile calculated from the atomic structure of Pom152718–1148 (red curve) using FoXS111 is well-matched (χ?=?1.48) to the corresponding experimental SAXS profile23 (black dots; n?=?20 exposures). For visualization purposes, the Pom152718–1148 structure (represented as a ribbon) is shown along with the best fit of the ab initio shape (represented as a transparent envelope) computed from the experimental SAXS profile. g, Satisfaction of the negative-stain electron microscopy 2D class averages for the Nic96 complex; the structures of the Nic96 complex (composed of Nic96, Nsp1, Nup49 and Nup57) in the dominant cluster can be projected well on 2D class averages obtained for the natively isolated complex (n?=?5,458 particles; Methods). The experimental class averages were satisfied by the structure with cross-correlation coefficients of 0.85 and 0.80, respectively (Methods).
