8RHO | pdb_00008rho

[2Fe:2S] ferredoxin FeSII from Azotobacter vinelandii, reduced form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.182 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Conformational protection of molybdenum nitrogenase by Shethna protein II.

Franke, P.Freiberger, S.Zhang, L.Einsle, O.

(2025) Nature 637: 998-1004

  • DOI: https://doi.org/10.1038/s41586-024-08355-3
  • Primary Citation of Related Structures:  
    8RHO, 8RHP

  • PubMed Abstract: 

    The oxygen-sensitive molybdenum-dependent nitrogenase of Azotobacter vinelandii is protected from oxidative damage by a reversible 'switch-off' mechanism 1 . It forms a complex with a small ferredoxin, FeSII (ref.  2 ) or the 'Shethna protein II' 3 , which acts as an O 2 sensor and associates with the two component proteins of nitrogenase when its [2Fe:2S] cluster becomes oxidized 4,5 . Here we report the three-dimensional structure of the protective ternary complex of the catalytic subunit of Mo-nitrogenase, its cognate reductase and the FeSII protein, determined by single-particle cryo-electron microscopy. The dimeric FeSII protein associates with two copies of each component to assemble a 620 kDa core complex that then polymerizes into large, filamentous structures. This complex is catalytically inactive, but the enzyme components are quickly released and reactivated upon oxygen depletion. The first step in complex formation is the association of FeSII with the more O 2 -sensitive Fe protein component of nitrogenase during sudden oxidative stress. The action of this small ferredoxin represents a straightforward means of protection from O 2 that may be crucial for the maintenance of recombinant nitrogenase in food crops.


  • Organizational Affiliation
    • Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin
A, B
122Azotobacter vinelandii DJMutation(s): 0 
Gene Names: Avin_39700
UniProt
Find proteins for Q44501 (Azotobacter vinelandii)
Explore Q44501 
Go to UniProtKB:  Q44501
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ44501
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download Ideal Coordinates CCD File 
E [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A],
I [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
H [auth A],
K [auth B],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.182 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.955α = 90
b = 60.955β = 90
c = 139.414γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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)GermanyRTG 1976, project ID 235777276
German Research Foundation (DFG)GermanyCRC 1381, project ID 403222702

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Database references
  • Version 1.2: 2025-01-22
    Changes: Database references
  • Version 1.3: 2025-02-05
    Changes: Database references