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- EMDB-19915: Cryo-EM structure of sodium pumping Rnf complex from Acetobacteri... -
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Basic information
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Title | Cryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii bound to NADH | |||||||||
![]() | Cryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii bound to NADH | |||||||||
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![]() | Bioenergetics / anaerobic cryoEM / membrane protein / electron transport / redox-driven sodium pumping | |||||||||
Function / homology | ![]() ferredoxin-NAD+ oxidoreductase (Na+-transporting) / electron transport chain / transmembrane transport / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Kumar A / Schuller JM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery. Authors: Anuj Kumar / Jennifer Roth / Hyunho Kim / Patricia Saura / Stefan Bohn / Tristan Reif-Trauttmansdorff / Anja Schubert / Ville R I Kaila / Jan M Schuller / Volker Müller / ![]() ![]() Abstract: The Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD and pumps ions (Na or H) across a membrane, powering ATP synthesis. ...The Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD and pumps ions (Na or H) across a membrane, powering ATP synthesis. Rnf is widespread in primordial organisms and the evolutionary predecessor of the Na-pumping NADH-quinone oxidoreductase (Nqr). By running in reverse, Rnf uses the electrochemical ion gradient to drive ferredoxin reduction with NADH, providing low potential electrons for nitrogenases and CO reductases. Yet, the molecular principles that couple the long-range electron transfer to Na translocation remain elusive. Here, we resolve key functional states along the electron transfer pathway in the Na-pumping Rnf complex from Acetobacterium woodii using redox-controlled cryo-electron microscopy that, in combination with biochemical functional assays and atomistic molecular simulations, provide key insight into the redox-driven Na pumping mechanism. We show that the reduction of the unique membrane-embedded [2Fe2S] cluster electrostatically attracts Na, and in turn, triggers an inward/outward transition with alternating membrane access driving the Na pump and the reduction of NAD. Our study unveils an ancient mechanism for redox-driven ion pumping, and provides key understanding of the fundamental principles governing energy conversion in biological systems. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.9 KB 23.9 KB | Display Display | ![]() |
Images | ![]() | 116.2 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9eriMC ![]() 9erjC ![]() 9erkC ![]() 9erlC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii bound to NADH | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B
File | emd_19915_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_19915_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
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Sample components
+Entire : rhodobacter nitrogen fixation complex from Acetobacterium woodii
+Supramolecule #1: rhodobacter nitrogen fixation complex from Acetobacterium woodii
+Macromolecule #1: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A
+Macromolecule #2: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit B
+Macromolecule #3: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit C
+Macromolecule #4: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit D
+Macromolecule #5: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit E
+Macromolecule #6: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit G
+Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #8: IRON/SULFUR CLUSTER
+Macromolecule #9: FLAVIN MONONUCLEOTIDE
+Macromolecule #10: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #11: RIBOFLAVIN
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 645102 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |