Cryo-EM structures of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae

Abstract

The Na+-pumping NADH-ubiquinone oxidoreductase (Na+-NQR) couples electron transfer 3 from NADH to ubiquinone with Na+-pumping, generating an electrochemical Na+ gradient that 4 is essential for energy-consuming reactions in bacteria. Since Na+-NQR is exclusively found in 5 prokaryotes, it is a promising target for highly selective antibiotics. However, the molecular 6 mechanism of inhibition is not well-understood for lack of the atomic structural information 7 about an inhibitor-bound state. Here we present cryo-electron microscopy structures of Na+- 8 NQR from Vibrio cholerae with or without a bound inhibitor at 2.5- to 3.1-Å resolution. The 9 structures reveal the arrangement of all six redox cofactors including riboflavin, whose position 10 has been under debate, and a newly assigned 2Fe-2SNqrD/E cluster located between the 11 membrane embedded NqrD and NqrE subunits.