9UD3
Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-T236Y mutant from Vibrio cholerae
Summary for 9UD3
| Entry DOI | 10.2210/pdb9ud3/pdb |
| EMDB information | 64060 |
| Descriptor | Na(+)-translocating NADH-quinone reductase subunit A, CALCIUM ION, FE2/S2 (INORGANIC) CLUSTER, ... (12 entities in total) |
| Functional Keywords | membrane protein, na+-nqr, na+ pump, oxidoreductase |
| Biological source | Vibrio cholerae O395 More |
| Total number of polymer chains | 6 |
| Total formula weight | 214583.80 |
| 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 Cited by 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: 40501732DOI: 10.1101/2025.06.01.656757 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.8 Å) |
Structure validation
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