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- PDB-8acy: X-ray structure of Na+-NQR from Vibrio cholerae at 3.5 A resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 8acy | |||||||||
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Title | X-ray structure of Na+-NQR from Vibrio cholerae at 3.5 A resolution | |||||||||
![]() | (Na(+)-translocating NADH-quinone reductase subunit ...) x 6 | |||||||||
![]() | MEMBRANE PROTEIN / respiratory complex / NADH ubiquinone oxido reducatase / Na+ pump | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Fritz, G. | |||||||||
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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 695.1 KB | Display | ![]() |
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PDB format | ![]() | 568.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 69.5 KB | Display | |
Data in CIF | ![]() | 91.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a1tC ![]() 8a1uC ![]() 8a1vC ![]() 8a1wC ![]() 8a1xC ![]() 8a1yC ![]() 8acwC ![]() 8ad3C ![]() 8ad4C ![]() 8ad5C ![]() 4p6v C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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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 / Mutation: N-terminal His-tag Source method: isolated from a genetically manipulated source Details: N-terminal His-tag: MGSSHHHHHHSSGLEVLFQGPH / 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, 7 molecules ![](data/chem/img/FMN.gif)
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![](data/chem/img/NA.gif)
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#7: Chemical | #8: Chemical | ChemComp-RBF / | #10: Chemical | ChemComp-NA / | #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 40 mM KSCN, 21.0% PEG 2000MME, 100 mM Tris-acetic acid, 8% 1-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→48.73 Å / Num. obs: 32938 / % possible obs: 99.3 % / Redundancy: 6.844 % / Biso Wilson estimate: 165.33 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.082 / Χ2: 0.832 / Net I/σ(I): 12.6 / Num. measured all: 225415 / Scaling rejects: 53 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4P6V ![]() 4p6v Resolution: 3.5→48.73 Å / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 388.8 Å2 / Biso mean: 193.1007 Å2 / Biso min: 105.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→48.73 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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