9CU0

Azotobacter vinelandii 1:1:1 MoFeP:FeP:FeSII-Complex (C1 symmetry)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for the conformational protection of nitrogenase from O 2 .

Narehood, S.M.Cook, B.D.Srisantitham, S.Eng, V.H.Shiau, A.A.McGuire, K.L.Britt, R.D.Herzik Jr., M.A.Tezcan, F.A.

(2025) Nature 637: 991-997

  • DOI: https://doi.org/10.1038/s41586-024-08311-1
  • Primary Citation of Related Structures:  
    9CTZ, 9CU0, 9CU1, 9CU2

  • PubMed Abstract: 

    The low reduction potentials required for the reduction of dinitrogen (N 2 ) render metal-based nitrogen-fixation catalysts vulnerable to irreversible damage by dioxygen (O 2 ) 1-3 . Such O 2 sensitivity represents a major conundrum for the enzyme nitrogenase, as a large fraction of nitrogen-fixing organisms are either obligate aerobes or closely associated with O 2 -respiring organisms to support the high energy demand of catalytic N 2 reduction 4 . To counter O 2 damage to nitrogenase, diazotrophs use O 2 scavengers, exploit compartmentalization or maintain high respiration rates to minimize intracellular O 2 concentrations 4-8 . A last line of damage control is provided by the 'conformational protection' mechanism 9 , in which a [2Fe:2S] ferredoxin-family protein termed FeSII (ref.  10 ) is activated under O 2 stress to form an O 2 -resistant complex with the nitrogenase component proteins 11,12 . Despite previous insights, the molecular basis for the conformational O 2 protection of nitrogenase and the mechanism of FeSII activation are not understood. Here we report the structural characterization of the Azotobacter vinelandii FeSII-nitrogenase complex by cryo-electron microscopy. Our studies reveal a core complex consisting of two molybdenum-iron proteins (MoFePs), two iron proteins (FePs) and one FeSII homodimer, which polymerize into extended filaments. In this three-protein complex, FeSII mediates an extensive network of interactions with MoFeP and FeP to position their iron-sulphur clusters in catalytically inactive but O 2 -protected states. The architecture of the FeSII-nitrogenase complex is confirmed by solution studies, which further indicate that the activation of FeSII involves an oxidation-induced conformational change.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chain
A, C
492Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii)
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Go to UniProtKB:  P07328
Entity Groups  
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UniProt GroupP07328
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chain
B, D
523Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii)
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UniProt GroupP07329
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron protein 1
E, F
290Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii)
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UniProt GroupP00459
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FeSII122Azotobacter vinelandiiMutation(s): 0 
Gene Names: fesII
UniProt
Find proteins for Q44501 (Azotobacter vinelandii)
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UniProt GroupQ44501
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS (Subject of Investigation/LOI)
Query on ICS

Download Ideal Coordinates CCD File 
I [auth A],
N [auth C]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
CLF (Subject of Investigation/LOI)
Query on CLF

Download Ideal Coordinates CCD File 
J [auth A],
O [auth D]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
P [auth E],
S [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
R [auth F]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HCA (Subject of Investigation/LOI)
Query on HCA

Download Ideal Coordinates CCD File 
H [auth A],
M [auth C]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
U [auth G]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
Q [auth E],
T [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM148607-02
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R35GM138206
Other privateSearle Scholars

Revision History  (Full details and data files)

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