8RB8

Cryo-EM structure of the NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii, purified with 2-ME/TCEP, NADH added


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Architecture of the RNF1 complex that drives biological nitrogen fixation.

Zhang, L.Einsle, O.

(2024) Nat Chem Biol 20: 1078-1085

  • DOI: https://doi.org/10.1038/s41589-024-01641-1
  • Primary Citation of Related Structures:  
    8AHX, 8RB8, 8RB9, 8RBM, 8RBQ

  • PubMed 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 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.


  • Organizational Affiliation

    Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion-translocating oxidoreductase complex subunit A190Azotobacter vinelandii DJMutation(s): 0 
Gene Names: rnfA1rnfAAvin_50980
EC: 7
Membrane Entity: Yes 
UniProt
Find proteins for C1DMA8 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore C1DMA8 
Go to UniProtKB:  C1DMA8
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1DMA8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ion-translocating oxidoreductase complex subunit CB [auth C]496Azotobacter vinelandii DJMutation(s): 0 
Gene Names: rnfC1rnfCAvin_50960
EC: 7
Membrane Entity: Yes 
UniProt
Find proteins for C1DMA6 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
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UniProt GroupC1DMA6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ion-translocating oxidoreductase complex subunit DC [auth D]366Azotobacter vinelandii DJMutation(s): 0 
Gene Names: rnfD1rnfDAvin_50950
EC: 7
Membrane Entity: Yes 
UniProt
Find proteins for C1DMA5 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
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UniProt GroupC1DMA5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ion-translocating oxidoreductase complex subunit ED [auth E]238Azotobacter vinelandii DJMutation(s): 0 
Gene Names: rnfEAvin_50930
EC: 7
Membrane Entity: Yes 
UniProt
Find proteins for Q9F5Y1 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
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UniProt GroupQ9F5Y1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ion-translocating oxidoreductase complex subunit GE [auth G]237Azotobacter vinelandii DJMutation(s): 0 
Gene Names: rnfG1rnfGAvin_50940
EC: 7
Membrane Entity: Yes 
UniProt
Find proteins for C1DMA4 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
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UniProt GroupC1DMA4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protein RnfHF [auth H]86Azotobacter vinelandii DJMutation(s): 0 
Gene Names: rnfHAvin_50920
UniProt
Find proteins for Q9F5Y0 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ion-translocating oxidoreductase complex subunit BG [auth B]174Azotobacter vinelandii DJMutation(s): 0 
Gene Names: rnfB1rnfBAvin_50970
EC: 7
Membrane Entity: Yes 
UniProt
Find proteins for C1DMA7 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
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UniProt GroupC1DMA7
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
I [auth A]
M [auth D]
N [auth D]
P [auth D]
Q [auth D]
I [auth A],
M [auth D],
N [auth D],
P [auth D],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
W [auth E],
X [auth E],
Y [auth E],
Z [auth E]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

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

Download Ideal Coordinates CCD File 
O [auth D]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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BA [auth B],
CA [auth B],
K [auth C],
L [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
H [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union310656
German Research Foundation (DFG)GermanyCRC 1381, project ID 403222702
German Research Foundation (DFG)GermanyCRC 992, project ID 192904750
German Research Foundation (DFG)GermanyRTG 2202, project ID 46710898
German Research Foundation (DFG)Germanygrant INST 35/134-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary