9UDF

Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-G141A mutant from Vibrio cholerae reduced by NADH, with bound korormicin A, shifted state

Summary for 9UDF

• Entry DOI: 10.2210/pdb9udf/pdb
• EMDB information: 64068
• Descriptor: Na(+)-translocating NADH-quinone reductase subunit A, DODECYL-BETA-D-MALTOSIDE, Korormicin, ... (15 entities in total)
• Functional Keywords: na+-nqr, na+ pump, oxidoreductase, inhibitor, membrane protein
• Biological source: Vibrio cholerae O395; More
• Total number of polymer chains: 6
• Total formula weight: 217424.37

Authors

Ishikawa-Fukuda, M.,Kishikawa, J.,Kato, T.,Murai, M. (deposition date: 2025-04-06, release date: 2025-06-25)

Primary citation

Ishikawa-Fukuda, M.,Seki, T.,Kishikawa, J.I.,Takahiro, M.,Okazaki, K.I.,Kato, T.,Barquera, B.,Miyoshi, H.,Murai, M.
The Na + -pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from Vibrio cholerae relies on dynamic conformational changes.
Biorxiv, 2025

PubMed Abstract: The Na -pumping NADH-quinone oxidoreductase (Na -NQR) is a key respiratory enzyme in many marine and pathogenic bacteria that couples electron transfer to Na -pumping across the membrane. Earlier X-ray and cryo-EM structures of Na -NQR from suggested that the subunits harboring redox cofactors undergo conformational changes during catalytic turnover. However, these proposed rearrangements have not yet been confirmed. Here, we have identified at least five distinct conformational states of Na -NQR using: mutants that lack specific cofactors, specific inhibitors or low-sodium conditions. Molecular dynamics simulations based on these structural insights indicate that 2Fe-2S reduction in NqrD/E plays a crucial role in triggering Na translocation by driving structural rearrangements in the NqrD/E subunits, which subsequently influence NqrC and NqrF positioning. This study provides the first structural insights into the mechanism of Na translocation coupled to electron transfer in Na⁺-NQR.

PubMed: 40501732
DOI: 10.1101/2025.06.01.656757

Experimental method

ELECTRON MICROSCOPY (2.93 Å)