9ONJ | pdb_00009onj

L-cluster free apo-NifEN expressed in E. coli

• PDB DOI: https://doi.org/10.2210/pdb9ONJ/pdb
• EM Map EMD-70642: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Azotobacter vinelandii DJ
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-15 Released: 2026-02-18 
• Deposition Author(s): Neumann, B., Brandon, K., Suder, D.S., Hu, Y., Ribbe, M.W., Gonen, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico

Literature

Structural insights into metallocluster trafficking in the nitrogenase assembly scaffold NifEN.

Neumann, B., Brandon, K.A., Quechol, R., Suder, D.S., Lee, C.C., Yang, Y., Gorecki, K., Wiig, J.A., Hu, Y., Gonen, S., Ribbe, M.W.

(2026) Nat Catal 9: 281-294

• PubMed: 41908675 
• DOI: https://doi.org/10.1038/s41929-026-01489-9
• Primary Citation Related Structures: 
  9ONJ, 9ONK


• PubMed Abstract: 
  

  Nitrogenase catalyses small-molecule activation, and has great relevance to agronomy, environment and energy. Understanding the assembly of the complex nitrogenase cofactor is a decades-long goal in the field, and structural insights into this process remain scarce. Here we report a cryogenic electron microscopy (cryo-EM) study of heterologously expressed NifEN, a key player converting the precursor (L-cluster) to a mature cofactor (M-cluster). Structural analyses of apo- and holo-NifEN demonstrate major conformational changes triggered by L-cluster incorporation. Further examinations of NifEN structures with inwardly and outwardly bound L-clusters, coupled with supporting mutational studies, AlphaFold 3 predictions and negative-stain EM analyses of NifEN complexed with upstream (NifB) and downstream (NifH) assembly partners, reveal a tunnel linking NifEN with NifB and NifH, with NifEN serving as a dynamic hub that coordinates L-cluster reception, maturation and delivery via conformation-gated metallocluster trafficking.

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Organizational Affiliation: 
• Department of Molecular Biology and Biochemistry, University of California, Irvine, CA USA.
Present Address: AbbVie, Irvine, CA USA.
Department of Chemistry, University of California, Irvine, CA USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 151.38 kDa 
• Atom Count: 7,264 
• Modeled Residue Count: 1,133 
• Deposited Residue Count: 1,397 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE	A	481	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 [auth C], C [auth B]	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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.2.1
MODEL REFINEMENT	PHENIX	1.21.2_5419:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-18 
Deposition Author(s): Neumann, B., Brandon, K., Suder, D.S., Hu, Y., Ribbe, M.W., Gonen, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM142797
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM67626
Department of Energy (DOE, United States)	United States	DE-SC0016510

Revision History  

• Version 1.0: 2026-02-18
  Type: Initial release
  
• Version 1.1: 2026-09-02
  Changes: Data collection, Database references