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Open data
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Basic information
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Title | Sodium pumping NADH-quinone oxidoreductase with substrate Q2 | |||||||||
![]() | NQR with substrate Q2 | |||||||||
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![]() | quinone / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / flavin adenine dinucleotide binding / electron transfer activity ...NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / flavin adenine dinucleotide binding / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.73 Å | |||||||||
![]() | Hau J-L / Kaltwasser S / Vonck J / Fritz G / Steuber J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational coupling of redox-driven Na-translocation in Vibrio cholerae NADH:quinone oxidoreductase. 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 / ...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 / ![]() ![]() 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. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 117.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.8 KB 27.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.3 KB | Display | ![]() |
Images | ![]() | 218.3 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 8.4 KB | ||
Others | ![]() ![]() | 98.7 MB 98.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a1vMC ![]() 8a1tC ![]() 8a1uC ![]() 8a1wC ![]() 8a1xC ![]() 8a1yC ![]() 8acwC ![]() 8acyC ![]() 8ad3C ![]() 8ad4C ![]() 8ad5C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | NQR with substrate Q2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.9125 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #1
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Sample components
+Entire : NQR complex with substrate Q2
+Supramolecule #1: NQR complex with substrate Q2
+Macromolecule #1: Na(+)-translocating NADH-quinone reductase subunit A
+Macromolecule #2: Na(+)-translocating NADH-quinone reductase subunit B
+Macromolecule #3: Na(+)-translocating NADH-quinone reductase subunit C
+Macromolecule #4: Na(+)-translocating NADH-quinone reductase subunit D
+Macromolecule #5: Na(+)-translocating NADH-quinone reductase subunit E
+Macromolecule #6: Na(+)-translocating NADH-quinone reductase subunit F
+Macromolecule #7: RIBOFLAVIN
+Macromolecule #8: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #9: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #10: UBIQUINONE-2
+Macromolecule #11: FLAVIN MONONUCLEOTIDE
+Macromolecule #12: SODIUM ION
+Macromolecule #13: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #14: FLAVIN-ADENINE DINUCLEOTIDE
+Macromolecule #15: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.6 |
Grid | Model: C-flat-1.2/1.3 / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 276 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 7 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 7647 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 191781 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |