9CU2 | pdb_00009cu2

Azotobacter vinelandii filamentous 2:2:1 MoFeP:FeP:FeSII-Complex (C2 symmetry)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CU2

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 622.14 kDa 
  • Atom Count: 46,276 
  • Modeled Residue Count: 5,347 
  • Deposited Residue Count: 5,464 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chain
A, C, H, J
492Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii)
Explore P07328 
Go to UniProtKB:  P07328
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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, I, K
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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase iron protein 1
E, F, L, M
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
Find similar proteins by:|  3D Structure
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
Find similar proteins by:|  3D Structure
Entity ID: 5
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
DA [auth H],
HA [auth J],
P [auth A],
U [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
EA [auth H],
JA [auth K],
R [auth B],
V [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
KA [auth L],
NA [auth M],
W [auth E],
Z [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
MA [auth M],
Y [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HCA
(Subject of Investigation/LOI)

Query on HCA



Download:Ideal Coordinates CCD File
CA [auth H],
GA [auth J],
O [auth A],
T [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
BA [auth G],
PA [auth N]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
FA [auth I],
IA [auth K],
Q [auth B],
S [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
AA [auth F],
LA [auth L],
OA [auth M],
X [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2025-08-20
    Changes: Data collection, Experimental preparation