Structure, dynamics and evolution of the Candida albicans multi-drug resistance ABC transporter CDR1

The pleiotropic drug resistance transporter Cdr1 from Candida albicans plays a crucial role in antifungal resistance. Here, we present high-resolution cryo-electron microscopy structures of C. albicans Cdr1 in multiple functional states: nucleotide-bound, substrate-bound, and apo forms. The 3.5 Å resolution structure of Cdr1 in complex with ATP and ADP reveals the molecular details of its asymmetric nucleotide-binding sites (NBS), with ATP bound to the deviant NBS1 and ADP to the canonical NBS2. Structures of Cdr1 bound to rhodamine 6G (3.4 Å) and Oregon Green 488 (3.5 Å) in complex with these nucleotides elucidate the pleiotropic substrate-binding pocket and highlight how nucleotide exchange drives conformational change required for transport. Additionally, we determined a 3.7 Å resolution structure of Cdr1 in the detergent LMNG without nucleotides, as well as a 3.5 Å resolution structure with nucleotides but no substrate, representing an apo state. We complemented these structural insights with molecular dynamics simulations to understand substrate binding dynamics, ancestral sequence reconstruction to trace the evolution of key functional motifs, and analysis of clinical isolates from sequence databases to identify potential resistance-associated variations. Comparison of these structures provides new insights into the conformational changes associated with the transport cycle of this asymmetric ABC transporter, revealing how ATP binding at the deviant NBS1 allosterically regulates the canonical NBS2, driving ATPase activity. This work significantly advances our understanding of the molecular mechanisms underlying multidrug resistance in pathogenic fungi and provides a structural and evolutionary framework for the rational design of Cdr1 inhibitors to combat antifungal resistance.