[English] 日本語
![](img/lk-miru.gif)
- PDB-8a1u: Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8a1u | ||||||
---|---|---|---|---|---|---|---|
Title | Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2 | ||||||
![]() | (Na(+)-translocating NADH-quinone reductase subunit ...) x 6 | ||||||
![]() | MEMBRANE PROTEIN / NADH / quinone | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||
![]() | Hau, J.-L. / Kaltwasser, S. / Vonck, J. / Fritz, G. / Steuber, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 731.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 601.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 15089MC ![]() 8a1tC ![]() 8a1vC ![]() 8a1wC ![]() 8a1xC ![]() 8a1yC ![]() 8acwC ![]() 8acyC ![]() 8ad3C ![]() 8ad4C ![]() 8ad5C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Na(+)-translocating NADH-quinone reductase subunit ... , 6 types, 6 molecules ABCDEF
#1: Protein | Mass: 51125.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Subunit NqrA and N-terminal His6-tag and cleavage site for HRV-3C protease Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9KPS1, NADH:ubiquinone reductase (Na+-transporting) |
---|---|
#2: Protein | Mass: 45390.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal residues in model not resolved. / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9KPS2, 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.) ![]() ![]() ![]() ![]() References: UniProt: P0C6E0, NADH:ubiquinone reductase (Na+-transporting) |
#4: Protein | Mass: 22853.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues at the N-terminus and at the C-terminus were not resolved in the density and are not part of the model. Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9X4Q6, 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.) ![]() ![]() ![]() ![]() References: UniProt: Q9X4Q7, NADH:ubiquinone reductase (Na+-transporting) |
#6: Protein | Mass: 45113.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal and C-terminal residues were not resolved in the density and are not part of the model. Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9X4Q8, NADH:ubiquinone reductase (Na+-transporting) |
-Sugars , 1 types, 3 molecules ![](data/chem/img/LMT.gif)
#9: Sugar |
---|
-Non-polymers , 9 types, 201 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/RBF.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/UQ2.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/RBF.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/UQ2.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Chemical | ChemComp-RBF / | #10: Chemical | ChemComp-3PE / #11: Chemical | ChemComp-UQ2 / | #12: Chemical | #13: Chemical | #14: Chemical | ChemComp-FAD / | #15: Chemical | ChemComp-NAI / | #16: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: NQR complex with substrates NADH and Q2 / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
---|---|
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 |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 215000 X / Calibrated magnification: 244328 X / Nominal defocus max: 2100 nm / Nominal defocus min: 800 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: 4 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9592 |
EM imaging optics | Energyfilter name: TFS Selectris X / Energyfilter slit width: 7 eV |
-
Processing
EM software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 549586 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 435715 / 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 |