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Yorodumi- PDB-8a1u: Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a1u | ||||||
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Title | Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2 | ||||||
Components | (Na(+)-translocating NADH-quinone reductase subunit ...) x 6 | ||||||
Keywords | MEMBRANE PROTEIN / NADH / quinone | ||||||
Function / homology | Function and homology information 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 | Vibrio cholerae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||
Authors | Hau, J.-L. / Kaltwasser, S. / Vonck, J. / Fritz, G. / Steuber, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a1u.cif.gz | 731.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a1u.ent.gz | 601.4 KB | Display | PDB format |
PDBx/mmJSON format | 8a1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/8a1u ftp://data.pdbj.org/pub/pdb/validation_reports/a1/8a1u | HTTPS FTP |
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-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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-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.) Vibrio cholerae (bacteria) / Gene: nqrA, VC_2295 / Production host: Vibrio cholerae (bacteria) References: UniProt: Q9KPS1, 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 Details: N-terminal residues in model not resolved. / Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: nqrB, VC_2294 / Production host: Vibrio cholerae (bacteria) 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.) Vibrio cholerae (bacteria) / Gene: nqrC, VC_2293 / Production host: Vibrio cholerae (bacteria) 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.) Vibrio cholerae (bacteria) / Gene: nqrD, VC_2292 / Production host: Vibrio cholerae (bacteria) 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.) Vibrio cholerae (bacteria) / Gene: nqrE, VC_2291 / Production host: Vibrio cholerae (bacteria) 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.) Vibrio cholerae (bacteria) / Gene: nqrF, VC_2290 / Production host: Vibrio cholerae (bacteria) References: UniProt: Q9X4Q8, NADH:ubiquinone reductase (Na+-transporting) |
-Sugars , 1 types, 3 molecules
#9: Sugar |
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-Non-polymers , 9 types, 201 molecules
#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 / | |
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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 |
-Sample preparation
Component | Name: NQR complex with substrates NADH and Q2 / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Molecular weight | Value: 0.22 MDa / Experimental value: YES |
Source (natural) | Organism: Vibrio cholerae (bacteria) |
Source (recombinant) | Organism: Vibrio cholerae (bacteria) |
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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 |
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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 |