Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	The Na-pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from relies on dynamic conformational changes.
Journal, issue, pages	bioRxiv, Year 2025
Publish date	Jun 8, 2025
Authors	Moe Ishikawa-Fukuda / Takehito Seki / Jun-Ichi Kishikawa / Takahiro Masuya / Kei-Ichi Okazaki / Takayuki Kato / Blanca Barquera / Hideto Miyoshi / Masatoshi Murai /
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 ...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.
External links	bioRxiv / PubMed:40501732 / PubMed Central
Methods	EM (single particle)
Resolution	2.59 - 3.8 Å
Structure data	63872 9u5g EMDB-63872, PDB-9u5g: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrC-T225Y mutant from Vibrio cholerae Method: EM (single particle) / Resolution: 2.66 Å 64059 9ud2 EMDB-64059, PDB-9ud2: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrC-T225Y mutant from Vibrio cholerae reduced by NADH Method: EM (single particle) / Resolution: 2.59 Å 64060 9ud3 EMDB-64060, PDB-9ud3: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-T236Y mutant from Vibrio cholerae Method: EM (single particle) / Resolution: 3.8 Å 64061 9ud4 EMDB-64061, PDB-9ud4: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-T236Y mutant from Vibrio cholerae reduced by NADH Method: EM (single particle) / Resolution: 3.31 Å 64062 9ud5 EMDB-64062, PDB-9ud5: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, with bound korormicin A Method: EM (single particle) / Resolution: 2.9 Å 64063 9ud6 EMDB-64063, PDB-9ud6: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, upper state Method: EM (single particle) / Resolution: 2.65 Å 64064 9ud8 EMDB-64064, PDB-9ud8: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, middle state Method: EM (single particle) / Resolution: 3.75 Å 64065 9ud9 EMDB-64065, PDB-9ud9: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, down state Method: EM (single particle) / Resolution: 3.11 Å 64066 9uda EMDB-64066, PDB-9uda: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-G141A mutant from Vibrio cholerae reduced by NADH, with bound korormicin A, stable state Method: EM (single particle) / Resolution: 2.61 Å 64068 9udf EMDB-64068, PDB-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 Method: EM (single particle) / Resolution: 2.93 Å 64069 9udg EMDB-64069, PDB-9udg: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, with bound aurachin D-42 Method: EM (single particle) / Resolution: 3.18 Å 64518 9uuu EMDB-64518, PDB-9uuu: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH Method: EM (single particle) / Resolution: 3.17 Å
Chemicals	ChemComp-FMN: FLAVIN MONONUCLEOTIDE ChemComp-RBF: RIBOFLAVIN ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergentYM ChemComp-CA: Unknown entry ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-FAD: FLAVIN-ADENINE DINUCLEOTIDE / FADYM ChemComp-HOH: WATER ChemComp-IQT: Korormicin ChemComp-PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipidYM ChemComp-0NI: Aurachin D ChemComp-NAI*: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Source	vibrio cholerae o395 (bacteria)
Keywords	MEMBRANE PROTEIN / Na+-NQR / Na+ pump / oxidoreductase / inhibitor