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	Conformational coupling of redox-driven Na-translocation in Vibrio cholerae NADH:quinone oxidoreductase.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 30, Issue 11, Page 1686-1694, Year 2023
Publish date	Sep 14, 2023
Authors	Jann-Louis Hau / Susann Kaltwasser / Valentin Muras / Marco S Casutt / Georg Vohl / Björn Claußen / Wojtek Steffen / Alexander Leitner / Eckhard Bill / George E Cutsail / Serena DeBeer / Janet Vonck / Julia Steuber / Günter Fritz /
PubMed Abstract	In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH: ...In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH:quinone oxidoreductase (Na-NQR) generates a sodium gradient by a so far unknown mechanism. Here we show that ion pumping in Na-NQR is driven by large conformational changes coupling electron transfer to ion translocation. We have determined a series of cryo-EM and X-ray structures of the Na-NQR that represent snapshots of the catalytic cycle. The six subunits NqrA, B, C, D, E, and F of Na-NQR harbor a unique set of cofactors that shuttle the electrons from NADH twice across the membrane to quinone. The redox state of a unique intramembranous [2Fe-2S] cluster orchestrates the movements of subunit NqrC, which acts as an electron transfer switch. We propose that this switching movement controls the release of Na from a binding site localized in subunit NqrB.
External links	Nat Struct Mol Biol / PubMed:37710014 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.5 - 3.5 Å
Structure data	15088 8a1t EMDB-15088, PDB-8a1t: Sodium pumping NADH-quinone oxidoreductase Method: EM (single particle) / Resolution: 3.37 Å 15089 8a1u EMDB-15089, PDB-8a1u: Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2 Method: EM (single particle) / Resolution: 2.86 Å 15090 8a1v EMDB-15090, PDB-8a1v: Sodium pumping NADH-quinone oxidoreductase with substrate Q2 Method: EM (single particle) / Resolution: 2.73 Å 15091 8a1w EMDB-15091, PDB-8a1w: Sodium pumping NADH-quinone oxidoreductase with substrate Q1 Method: EM (single particle) / Resolution: 2.56 Å 15092 8a1x EMDB-15092, PDB-8a1x: Sodium pumping NADH-quinone oxidoreductase with inhibitor DQA Method: EM (single particle) / Resolution: 3.2 Å 15093 8a1y EMDB-15093, PDB-8a1y: Sodium pumping NADH-quinone oxidoreductase with inhibitor HQNO Method: EM (single particle) / Resolution: 3.3 Å PDB-8acw: X-ray structure of Na+-NQR from Vibrio cholerae at 3.4 A resolution Method: X-RAY DIFFRACTION / Resolution: 3.4 Å PDB-8acy: X-ray structure of Na+-NQR from Vibrio cholerae at 3.5 A resolution Method: X-RAY DIFFRACTION / Resolution: 3.5 Å PDB-8ad3: X-ray structure of NqrF(129-408)of Vibrio cholerae variant F406A Method: X-RAY DIFFRACTION / Resolution: 1.55 Å PDB-8ad4: X-ray structure of NqrF(129-408)of Vibrio cholerae in complex with NADH Method: X-RAY DIFFRACTION / Resolution: 1.5 Å PDB-8ad5: X-ray structure of NqrF(129-408)of Vibrio cholerae variant F406A Method: X-RAY DIFFRACTION / Resolution: 1.65 Å
Chemicals	ChemComp-FMN: FLAVIN MONONUCLEOTIDE / Flavin mononucleotide ChemComp-RBF: RIBOFLAVIN / Riboflavin ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergentYM ChemComp-3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipidYM / Phosphatidylethanolamine ChemComp-NA: Unknown entry ChemComp-K: Unknown entry ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster ChemComp-FAD: FLAVIN-ADENINE DINUCLEOTIDE / FADYM / Flavin adenine dinucleotide ChemComp-UQ2: UBIQUINONE-2 ChemComp-NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide ChemComp-HOH: WATER / Water ChemComp-UQ1: UBIQUINONE-1 ChemComp-HQO: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE ChemComp-LYS: LYSINE / Lysine ChemComp-MG: Unknown entry ChemComp-SO4*: SULFATE ION / Sulfate
Source	vibrio cholerae (bacteria)
Keywords	MEMBRANE PROTEIN / quinone / NADH / sodium pump / inhibitor / respiratory complex / NADH ubiquinone oxido reducatase / Na+ pump / FLAVOPROTEIN / FAD / Na+-NQR