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Yorodumi- EMDB-14622: Na+ - translocating ferredoxin: NAD+ reductase (Rnf) of C. tetano... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14622 | |||||||||
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Title | Na+ - translocating ferredoxin: NAD+ reductase (Rnf) of C. tetanomorphum | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Clostridium tetanomorphum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.27 Å | |||||||||
Authors | Ermler U / Vitt S / Buckel W | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Purification and structural characterization of the Na-translocating ferredoxin: NAD reductase (Rnf) complex of Clostridium tetanomorphum. Authors: Stella Vitt / Simone Prinz / Martin Eisinger / Ulrich Ermler / Wolfgang Buckel / Abstract: Various microbial metabolisms use H/Na-translocating ferredoxin:NAD reductase (Rnf) either to exergonically oxidize reduced ferredoxin by NAD for generating a transmembrane electrochemical potential ...Various microbial metabolisms use H/Na-translocating ferredoxin:NAD reductase (Rnf) either to exergonically oxidize reduced ferredoxin by NAD for generating a transmembrane electrochemical potential or reversely to exploit the latter for producing reduced ferredoxin. For cryo-EM structural analysis, we elaborated a quick four-step purification protocol for the Rnf complex from Clostridium tetanomorphum and integrated the homogeneous and active enzyme into a nanodisc. The obtained 4.27 Å density map largely allows chain tracing and redox cofactor identification complemented by biochemical data from entire Rnf and single subunits RnfB, RnfC and RnfG. On this basis, we postulated an electron transfer route between ferredoxin and NAD via eight [4Fe-4S] clusters, one Fe ion and four flavins crossing the cell membrane twice related to the pathway of NADH:ubiquinone reductase. Redox-coupled Na translocation is provided by orchestrating Na uptake/release, electrostatic effects of the assumed membrane-integrated FMN semiquinone anion and accompanied polypeptide rearrangements mediated by different redox steps. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14622.map.gz | 48.2 MB | EMDB map data format | |
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Header (meta data) | emd-14622-v30.xml emd-14622.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14622_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_14622.png | 45.6 KB | ||
Masks | emd_14622_msk_1.map | 52.7 MB | Mask map | |
Others | emd_14622_half_map_1.map.gz emd_14622_half_map_2.map.gz | 40.7 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14622 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14622 | HTTPS FTP |
-Validation report
Summary document | emd_14622_validation.pdf.gz | 795 KB | Display | EMDB validaton report |
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Full document | emd_14622_full_validation.pdf.gz | 794.5 KB | Display | |
Data in XML | emd_14622_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_14622_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14622 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14622 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14622.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14622_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14622_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14622_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Na+ -translocating ferredoxin: NAD+ reductase (Rnf)
+Supramolecule #1: Na+ -translocating ferredoxin: NAD+ reductase (Rnf)
+Macromolecule #1: RnfA
+Macromolecule #2: RnfB
+Macromolecule #3: RnfC
+Macromolecule #4: RnfD
+Macromolecule #5: RnfE
+Macromolecule #6: RnfG
+Macromolecule #7: FE (III) ION
+Macromolecule #8: IRON/SULFUR CLUSTER
+Macromolecule #9: FLAVIN MONONUCLEOTIDE
+Macromolecule #10: RIBOFLAVIN
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |