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- EMDB-15452: Cryo-EM structure of the nitrogen-fixation associated NADH:ferred... -
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Open data
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Basic information
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Title | Cryo-EM structure of the nitrogen-fixation associated NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii | |||||||||||||||
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![]() | metalloprotein / flavoprotein / electron transfer and Na+/H+ translocation / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() Translocases / 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: 3.11 Å | |||||||||||||||
![]() | Zhang L / Einsle O | |||||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Architecture of the RNF1 complex that drives biological nitrogen fixation. Authors: Lin Zhang / Oliver Einsle / ![]() Abstract: Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living ...Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living soil diazotroph Azotobacter vinelandii transfers electrons from the key metabolite NADH to the low-potential ferredoxin FdxA that serves as a direct electron donor to the dinitrogenase reductases. This process is mediated by the RNF complex that exploits the proton motive force over the cytoplasmic membrane to lower the midpoint potential of the transferred electron. Here we report the cryogenic electron microscopy structure of the nitrogenase-associated RNF complex of A. vinelandii, a seven-subunit membrane protein assembly that contains four flavin cofactors and six iron-sulfur centers. Its function requires the strict coupling of electron and proton transfer but also involves major conformational changes within the assembly that can be traced with a combination of electron microscopy and modeling. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 75.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.9 KB 25.9 KB | Display Display | ![]() |
Images | ![]() | 151.9 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() ![]() | 78.1 MB 77.8 MB 77.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 936.4 KB | Display | ![]() |
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Full document | ![]() | 936 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ahxMC ![]() 8rb8C ![]() 8rb9C ![]() 8rbmC ![]() 8rbqC 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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: sharpened map
File | emd_15452_additional_1.map | ||||||||||||
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Annotation | sharpened map | ||||||||||||
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-Half map: halp map A
File | emd_15452_half_map_1.map | ||||||||||||
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Annotation | halp map A | ||||||||||||
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-Half map: halp map B
File | emd_15452_half_map_2.map | ||||||||||||
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Annotation | halp map B | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Heptameric complex of NADH:ferredoxin oxidoreductase RNF
+Supramolecule #1: Heptameric complex of NADH:ferredoxin oxidoreductase RNF
+Macromolecule #1: Ion-translocating oxidoreductase complex subunit A
+Macromolecule #2: Ion-translocating oxidoreductase complex subunit B
+Macromolecule #3: Ion-translocating oxidoreductase complex subunit C
+Macromolecule #4: Ion-translocating oxidoreductase complex subunit D
+Macromolecule #5: Ion-translocating oxidoreductase complex subunit E
+Macromolecule #6: Ion-translocating oxidoreductase complex subunit G
+Macromolecule #7: Protein RnfH
+Macromolecule #8: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #9: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #10: IRON/SULFUR CLUSTER
+Macromolecule #11: FLAVIN MONONUCLEOTIDE
+Macromolecule #12: RIBOFLAVIN
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94807 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |