NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1

How a variety of nuclear export signals (NESs) are recognized by their receptor CRM1 is now examined by crystallography, NMR spectroscopy, biochemistry and cellular approaches. The work reveals that the different NES peptides adopt different conformations to fit into five rigid hydrophobic binding pockets on CRM1, and redefines an NES consensus. Classic nuclear export signals (NESs) confer CRM1-dependent nuclear export. Here we present crystal structures of the RanGTP−CRM1 complex alone and bound to the prototypic PKI or HIV-1 Rev NESs. These NESs differ markedly in the spacing of their key hydrophobic (Φ) residues, yet CRM1 recognizes them with the same rigid set of five Φ pockets. The different Φ spacings are compensated for by different conformations of the bound NESs: in the case of PKI, an α-helical conformation, and in the case of Rev, an extended conformation with a critical proline docking into a Φ pocket. NMR analyses of CRM1-bound and CRM1-free PKI NES suggest that CRM1 selects NES conformers that pre-exist in solution. Our data lead to a new structure-based NES consensus, and explain why NESs differ in their affinities for CRM1 and why supraphysiological NESs bind the exportin so tightly.