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Yorodumi- EMDB-15089: Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15089 | |||||||||
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Title | Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2 | |||||||||
Map data | NQR with substrates NADH and Q2 | |||||||||
Sample |
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Keywords | NADH / quinone / MEMBRANE PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
Authors | Hau J-L / Kaltwasser S / Vonck J / Fritz G / Steuber J | |||||||||
Funding support | Germany, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15089.map.gz | 20.8 MB | EMDB map data format | |
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Header (meta data) | emd-15089-v30.xml emd-15089.xml | 28.7 KB 28.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15089_fsc.xml | 6.4 KB | Display | FSC data file |
Images | emd_15089.png | 246.2 KB | ||
Masks | emd_15089_msk_1.map | 22.2 MB | Mask map | |
Filedesc metadata | emd-15089.cif.gz | 8.4 KB | ||
Others | emd_15089_half_map_1.map.gz emd_15089_half_map_2.map.gz | 17.1 MB 17.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15089 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15089 | HTTPS FTP |
-Validation report
Summary document | emd_15089_validation.pdf.gz | 975.4 KB | Display | EMDB validaton report |
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Full document | emd_15089_full_validation.pdf.gz | 975 KB | Display | |
Data in XML | emd_15089_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_15089_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15089 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15089 | HTTPS FTP |
-Related structure data
Related structure data | 8a1uMC 8a1tC 8a1vC 8a1wC 8a1xC 8a1yC 8acwC 8acyC 8ad3C 8ad4C 8ad5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15089.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | NQR with substrates NADH and Q2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.273 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15089_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15089_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15089_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : NQR complex with substrates NADH and Q2
+Supramolecule #1: NQR complex with substrates NADH and 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: FLAVIN MONONUCLEOTIDE
+Macromolecule #8: RIBOFLAVIN
+Macromolecule #9: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #10: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #11: UBIQUINONE-2
+Macromolecule #12: SODIUM ION
+Macromolecule #13: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #14: FLAVIN-ADENINE DINUCLEOTIDE
+Macromolecule #15: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
+Macromolecule #16: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.6 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / 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 |
-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: 9592 / Average exposure time: 4.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 244328 / 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: 215000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |