Conformational selection in the recognition of the snurportin importin beta binding domain by importin beta

Abstract

The structural flexibility of beta-karyopherins is critical to mediate the interaction with transport substrates, nucleoporins, and the GTPase Ran. In this paper, we provide structural evidence that the molecular recognition of the transport adaptor snurportin by importin beta follows the population selection mechanism. We have captured two drastically different conformations of importin beta bound to the snurportin importin beta binding domain trapped in the same crystallographic asymmetric unit. We propose the population selection may be a general mechanism used by beta-karyopherins to recognize transport substrates.

Figure 1

Conformational plasticity of importin β bound to the sIBB domain. (A) Asymmetric unit content with two importin β • sIBB domain complexes in different conformations shown as coils. Importin β is colored red and blue and the sIBB domain yellow and orange. (B) Representative 2F_o − F_c electron density computed at 3.15 Å resolution and contoured 1.5σ above background. This figure was generated with Pymol (28).

Figure 2

Superimposed beads-on-string view of the two complexes in the asymmetric unit. The two importin β structures are colored blue and red, while the sIBB domains are colored yellow and orange. The maximum distance between importin β N-termini in complexes A and B is ~15Å.

Figure 3

Comparison of the new crystal form with previously determined structures of the importin β • sIBB domain (residues 25–65) complex: (A) 2.35Å structure (PDB entry 2P8Q) with one importin β • sIBB domain (residues 25–65) complex in the asymmetric unit, (B) 3.2 Å structure (PDB entry 2Q5D) with two importin β • sIBB domain (residues 25–65) complexes (indicated as mA-mB) in the same asymmetric unit, and (C) 3.15 Å structure presented in this paper (PDB entry 3LWW) with complexes A and B in the same asymmetric unit. All structures in panels A–C are aligned using importin β in complex A as a reference that is colored red.

Figure 4

Folding of sIBB domains in solution. Circular dichroism analysis of (A) the sIBB domain (residues 1–65 or 25–65) and (B) the αIBB domain (residues 11–54) at pH 7.4. The sIBB domain is partially helical in solution, while the αIBB domain adopts a completely random coil conformation. In both panels A and B, addition of trifluoroethanol (TFE) to a final concentration of 30 or 50% rapidly induced helix formation.

Figure 5

Population selection model proposed for recognition of the sIBB domain by importin β. (A) Putative conformers of importin β are shown as beads-on-string views to emphasize the different degrees of intramolecular opening. (B) Two importin β conformers with different structures are stabilized by the sIBB domain and hence trapped in the same crystal lattice.