9I0F | pdb_00009i0f

Revisited AvNifEN crystal structure

• PDB DOI: https://doi.org/10.2210/pdb9I0F/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Azotobacter vinelandii DJ
• Expression System: Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 2025-01-15 Released: 2025-12-03 
• Deposition Author(s): 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.
• Funding Organization(s): Agence Nationale de la Recherche (ANR), French Infrastructure for Integrated Structural Biology (FRISBI), Grenoble Alliance for Integrated Structural Cell Biology (GRAL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.304 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: in silico

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3PDI

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 

• PubMed: 41238839 
• 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.

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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.
Univ. Grenoble-Alpes, CNRS, CEA, IBS, Metalloproteins Unit, Grenoble, France.
Synanthra, Évry-Courcouronnes, France.
Institut für Chemie, Technische Universität Berlin, Berlin, Germany.
SOLEIL synchrotron, Gif-sur-Yvette, France.
Department AI and Biomolecular Structures, Helmholtz-Zentrum Berlin, Berlin, Germany.
Univ. Grenoble-Alpes, CNRS, CEA, IBS, Electron Microscopy and Methods Unit, Grenoble, France.
Univ. Grenoble-Alpes, CNRS, CEA, IBS, Metalloproteins Unit, Grenoble, France. [e-mail].
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. [e-mail].
Univ. Grenoble-Alpes, CNRS, CEA, IBS, Metalloproteins Unit, Grenoble, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 426.2 kDa 
• Atom Count: 29,802 
• Modeled Residue Count: 3,661 
• Deposited Residue Count: 3,764 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE	A, C, E, G	483	Azotobacter vinelandii DJ	Mutation(s): 0  Gene Names: nifE, Avin_01450
UniProt
Find proteins for C1DH03 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DH03  Go to UniProtKB:  C1DH03

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN	B, D, F, H	458	Azotobacter vinelandii DJ	Mutation(s): 0  Gene Names: nifN, Avin_01470
UniProt
Find proteins for C1DH04 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DH04  Go to UniProtKB:  C1DH04

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S5Q (Subject of Investigation/LOI)	HD [auth E], J [auth A], SE [auth G], WB [auth C]	FeFe cofactor C Fe8 S9 ARHQIUGQOSHZFD-UHFFFAOYSA-N
SF4	GD [auth E], I [auth A], RE [auth G], VB [auth C]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
1PE	NA [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	IE [auth F], LB [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	HF [auth G], LE [auth F], MD [auth E], PE [auth F], QA [auth A], QE [auth F], RA [auth A], UF [auth H], VF [auth H], XB [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	FD [auth D], IF [auth H], JC [auth D], JF [auth H], K [auth A], KC [auth D], KF [auth H], L [auth A], LC [auth D], LF [auth H], M [auth A], MA [auth A], MB [auth B], MC [auth D], NB [auth B], OA [auth A], QC [auth D], R [auth A], TA [auth B], UA [auth B], UB [auth B], VA [auth B], WC [auth D], WE [auth G], YD [auth F], YE [auth G], ZB [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	AA [auth A], AB [auth B], AC [auth C], AD [auth D], AE [auth F], AF [auth G], BA [auth A], BB [auth B], BC [auth C], BD [auth D], BE [auth F], BF [auth G], CA [auth A], CB [auth B], CC [auth C], CD [auth D], CE [auth F], CF [auth G], DA [auth A], DB [auth B], DC [auth C], DD [auth D], DE [auth F], DF [auth G], EA [auth A], EB [auth B], EC [auth C], ED [auth D], EE [auth F], EF [auth G], FA [auth A], FB [auth B], FC [auth C], FE [auth F], FF [auth G], GA [auth A], GB [auth B], GE [auth F], GF [auth G], HA [auth A], HB [auth B], HC [auth D], HE [auth F], IA [auth A], IB [auth B], IC [auth D], ID [auth E], JA [auth A], JB [auth B], JD [auth E], JE [auth F], KA [auth A], KB [auth B], KD [auth E], KE [auth F], LA [auth A], LD [auth E], ME [auth F], MF [auth H], N [auth A], NC [auth D], ND [auth E], NE [auth F], NF [auth H], O [auth A], OB [auth B], OC [auth D], OD [auth E], OE [auth F], OF [auth H], P [auth A], PA [auth A], PB [auth B], PC [auth D], PD [auth E], PF [auth H], Q [auth A], QB [auth B], QD [auth E], QF [auth H], RB [auth B], RC [auth D], RD [auth E], RF [auth H], S [auth A], SB [auth B], SC [auth D], SF [auth H], T [auth A], TB [auth B], TC [auth D], TE [auth G], TF [auth H], U [auth A], UC [auth D], UD [auth F], UE [auth G], V [auth A], VC [auth D], VD [auth F], VE [auth G], W [auth A], WA [auth B], WD [auth F], X [auth A], XA [auth B], XC [auth D], XD [auth F], XE [auth G], Y [auth A], YA [auth B], YB [auth C], YC [auth D], Z [auth A], ZA [auth B], ZC [auth D], ZD [auth F], ZE [auth G]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	GC [auth D], SA [auth B], SD [auth F], TD [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.304 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.07	α = 90
b = 95.22	β = 95.5
c = 149.98	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
Blu-Ice	data collection
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): 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.

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

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release