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Yorodumi- PDB-7zc6: Na+ - translocating ferredoxin: NAD+ reductase (Rnf) of C. tetano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zc6 | |||||||||
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Title | Na+ - translocating ferredoxin: NAD+ reductase (Rnf) of C. tetanomorphum | |||||||||
Components |
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Keywords | FLAVOPROTEIN / Rnf / flavin / iron-sulfur cluster / sodium ion translocation / anaerobic energy metabolism / oxidoreductase / electron transport / redox-coupled sodium pump | |||||||||
Function / homology | : / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN / IRON/SULFUR CLUSTER Function and homology information | |||||||||
Biological species | Clostridium tetanomorphum (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.27 Å | |||||||||
Authors | Ermler, U. / Vitt, S. / Buckel, W. | |||||||||
Funding support | Germany, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zc6.cif.gz | 263.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zc6.ent.gz | 212.8 KB | Display | PDB format |
PDBx/mmJSON format | 7zc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zc6_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7zc6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7zc6_validation.xml.gz | 55.8 KB | Display | |
Data in CIF | 7zc6_validation.cif.gz | 84 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/7zc6 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zc6 | HTTPS FTP |
-Related structure data
Related structure data | 14622MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 6 types, 6 molecules ABCDEG
#1: Protein | Mass: 20594.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria) |
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#2: Protein | Mass: 28008.584 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria) |
#3: Protein | Mass: 47164.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria) |
#4: Protein | Mass: 32990.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria) |
#5: Protein | Mass: 21213.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria) |
#6: Protein | Mass: 19502.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria) |
-Non-polymers , 4 types, 12 molecules
#7: Chemical | ChemComp-FE / | ||||
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#8: Chemical | ChemComp-SF4 / #9: Chemical | #10: Chemical | ChemComp-RBF / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Na+ -translocating ferredoxin: NAD+ reductase (Rnf) / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL |
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Molecular weight | Value: 0.165 MDa / Experimental value: NO |
Source (natural) | Organism: Clostridium tetanomorphum (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88423 / Symmetry type: POINT |