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: 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 ...

    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

    Philipps-Universität Marburg, Faculty of Biology, Karl-von-Frisch Straße 8, Marburg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RnfAA191Clostridium tetanomorphumMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RnfBB274Clostridium tetanomorphumMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RnfCC435Clostridium tetanomorphumMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RnfDD310Clostridium tetanomorphumMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RnfEE201Clostridium tetanomorphumMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RnfGF [auth G]189Clostridium tetanomorphumMutation(s): 0 
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

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

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Q [auth D]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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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-VKOJMFJBAC
 Ligand Interaction
FE
Query on FE

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G [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
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