9I0G | pdb_00009i0g

CryoEM structure of holo-GmNifEN


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dynamics driving the precursor in NifEN scaffold during nitrogenase FeMo-cofactor assembly.

Paya Tormo, L.Nguyen, T.Q.Fyfe, C.Basbous, H.Dobrzynska, K.Echavarri-Erasun, C.Martin, L.Caserta, G.Legrand, P.Thorn, A.Amara, P.Schoehn, G.Cherrier, M.V.Rubio, L.M.Nicolet, Y.

(2025) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-025-02070-4
  • Primary Citation of Related Structures:  
    9I0F, 9I0G, 9I0H

  • PubMed Abstract: 

    Nitrogenase catalyzes atmospheric nitrogen fixation, a critical biological process that depends on an intricate organometallic cofactor assembled by a dedicated multiprotein system. Here we uncover the structural basis for the function of NifEN, the scaffold protein that mediates the final stages of cofactor biosynthesis before its incorporation into nitrogenase. High-resolution structural analyses reveal that the cofactor precursor initially binds at a surface docking site before being transferred into a specialized cavity for further maturation. This process involves dynamic structural rearrangements, including coordinated domain motions and partial unfolding, enabling the scaffold to alternate between open and closed states. Additionally, a rear channel extends to the precursor-binding cavity, likely facilitating the entry of the modifying components molybdenum and homocitrate. These findings illuminate the dynamic mechanisms underlying FeMo-cofactor assembly and underscore the functional divergence between NifEN, the biosynthetic scaffold, and NifDK, the catalytic component of nitrogenase.


  • Organizational Affiliation
    • Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid e Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas, Madrid, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
A, B
919Geobacter metallireducensMutation(s): 0 
Gene Names: nifENGmet_0669
UniProt
Find proteins for Q39XW3 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39XW3 
Go to UniProtKB:  Q39XW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39XW3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-15-IDEX-02
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR-17-EURE-0003

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references