7ZC6

Na+ - translocating ferredoxin: NAD+ reductase (Rnf) of C. tetanomorphum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Purification and structural characterization of the Na + -translocating ferredoxin: NAD + reductase (Rnf) complex of Clostridium tetanomorphum.

Vitt, S.Prinz, S.Eisinger, M.Ermler, U.Buckel, W.

(2022) Nat Commun 13: 6315-6315

  • DOI: https://doi.org/10.1038/s41467-022-34007-z
  • Primary Citation of Related Structures:  
    7ZC6

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, Frankfurt am Main, Germany. Stella.vitt@mpibp-frankfurt.mpg.de.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RnfA191Clostridium tetanomorphumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A923J0P9 (Clostridium tetanomorphum)
Explore A0A923J0P9 
Go to UniProtKB:  A0A923J0P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A923J0P9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RnfB274Clostridium tetanomorphumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A923E755 (Clostridium tetanomorphum)
Explore A0A923E755 
Go to UniProtKB:  A0A923E755
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A923E755
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RnfC435Clostridium tetanomorphumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A923IZ11 (Clostridium tetanomorphum)
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Entity Groups  
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UniProt GroupA0A923IZ11
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RnfD310Clostridium tetanomorphumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A923IYK2 (Clostridium tetanomorphum)
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UniProt GroupA0A923IYK2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RnfE201Clostridium tetanomorphumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A923IZB8 (Clostridium tetanomorphum)
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UniProt GroupA0A923IZB8
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RnfGF [auth G]189Clostridium tetanomorphumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A923J084 (Clostridium tetanomorphum)
Explore A0A923J084 
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UniProt GroupA0A923J084
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
O [auth C],
P [auth D],
R [auth G]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
RBF (Subject of Investigation/LOI)
Query on RBF

Download Ideal Coordinates CCD File 
Q [auth D]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
H [auth B]
I [auth B]
J [auth B]
K [auth B]
L [auth B]
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
G [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyVI 778/2-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 2.0: 2022-11-23
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Atomic model, Data collection, Database references, Derived calculations