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Open data
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Basic information
Entry | Database: PDB / ID: 8a1x | ||||||
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Title | Sodium pumping NADH-quinone oxidoreductase with inhibitor DQA | ||||||
![]() | (Na(+)-translocating NADH-quinone reductase subunit ...) x 6 | ||||||
![]() | MEMBRANE PROTEIN / quinone / NADH / sodium pump / inhibitor | ||||||
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 / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 713.3 KB | Display | ![]() |
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PDB format | ![]() | 588.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 15092MC ![]() 8a1tC ![]() 8a1uC ![]() 8a1vC ![]() 8a1wC ![]() 8a1yC ![]() 8acwC ![]() 8acyC ![]() 8ad3C ![]() 8ad4C ![]() 8ad5C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Na(+)-translocating NADH-quinone reductase subunit ... , 6 types, 6 molecules ABCDEF
#1: Protein | Mass: 48680.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nqrA, ERS013165_00619, ERS013186_02081, ERS013199_02394, ERS013202_01882, ERS013206_02986, ERS013207_01957 Production host: ![]() ![]() References: UniProt: A0A655PZA5, NADH:ubiquinone reductase (Na+-transporting) |
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#2: Protein | Mass: 45390.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nqrB, D6U24_04465, ERS013186_02082, ERS013198_02508, ERS013199_02395, ERS013200_04117, ERS013202_01883, ERS013206_02987, ERS013207_01958, EYB64_17950, F0H40_10090, FLM02_04820, FLM12_12920, FXE67_12105, HPY07_02915 Production host: ![]() ![]() References: UniProt: A0A085SSI3, NADH:ubiquinone reductase (Na+-transporting) |
#3: Protein | Mass: 27652.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nqrC, BC353_01370, D6U24_04470, ERS013165_00616, ERS013186_02083, ERS013198_02507, ERS013199_02396, ERS013200_04118, ERS013201_01110, ERS013202_01884, ERS013206_02988, ERS013207_01959, F0H40_ ...Gene: nqrC, BC353_01370, D6U24_04470, ERS013165_00616, ERS013186_02083, ERS013198_02507, ERS013199_02396, ERS013200_04118, ERS013201_01110, ERS013202_01884, ERS013206_02988, ERS013207_01959, F0H40_10095, FLM02_04815, FLM12_12915 Production host: ![]() ![]() References: UniProt: A0A085R7S2, NADH:ubiquinone reductase (Na+-transporting) |
#4: Protein | Mass: 22853.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nqrD, BC353_01365, D6U24_04475, ERS013165_00615, ERS013186_02084, ERS013198_02506, ERS013199_02397, ERS013200_04119, ERS013201_01111, ERS013202_01885, ERS013206_02989, ERS013207_01960, EYB64_ ...Gene: nqrD, BC353_01365, D6U24_04475, ERS013165_00615, ERS013186_02084, ERS013198_02506, ERS013199_02397, ERS013200_04119, ERS013201_01111, ERS013202_01885, ERS013206_02989, ERS013207_01960, EYB64_17940, F0315_08345, F0H40_10100, F0M16_14020, FLM02_04810, FLM12_12910, HPY07_02925 Production host: ![]() ![]() References: UniProt: A0A085RHY8, NADH:ubiquinone reductase (Na+-transporting) |
#5: Protein | Mass: 21481.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nqrE, BC353_01360, D6U24_04480, ERS013165_00614, ERS013186_02085, ERS013198_02505, ERS013199_02398, ERS013200_04120, ERS013201_01112, ERS013202_01886, ERS013206_02990, ERS013207_01961, EYB64_ ...Gene: nqrE, BC353_01360, D6U24_04480, ERS013165_00614, ERS013186_02085, ERS013198_02505, ERS013199_02398, ERS013200_04120, ERS013201_01112, ERS013202_01886, ERS013206_02990, ERS013207_01961, EYB64_17935, F0315_08350, F0H40_10105, F0M16_14025, FLM02_04805, FLM12_12905, HPY07_02930 Production host: ![]() ![]() References: UniProt: A0A085QWM0, NADH:ubiquinone reductase (Na+-transporting) |
#6: Protein | Mass: 45113.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nqrF, D6U24_04485, ERS013198_02504, ERS013199_02399, ERS013201_01113, ERS013202_01887, ERS013206_02991, EYB64_17930, FLM12_12900 Production host: ![]() ![]() References: UniProt: A0A085ST13, NADH:ubiquinone reductase (Na+-transporting) |
-Sugars , 1 types, 3 molecules ![](data/chem/img/LMT.gif)
#9: Sugar |
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-Non-polymers , 5 types, 8 molecules ![](data/chem/img/FMN.gif)
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#7: Chemical | #8: Chemical | ChemComp-RBF / | #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-FAD / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: NQR complex with inhibitor DQA / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Molecular weight | Value: 0.22 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 276 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 60168 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.2 sec. / Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7168 |
EM imaging optics | Energyfilter name: GIF Bioquantum |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 302557 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 273218 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4P6V![]() 4p6v Accession code: 4P6V / Source name: PDB / Type: experimental model |