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- PDB-9ian: Nitrogenase maturase NifEN in complex with the cofactor chaperone NifX -

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Basic information

Entry
Database: PDB / ID: 9ian
TitleNitrogenase maturase NifEN in complex with the cofactor chaperone NifX
Components
  • (Nitrogenase iron-molybdenum cofactor biosynthesis protein ...) x 2
  • Nitrogenase MoFe cofactor biosynthesis protein NifX
KeywordsMETAL BINDING PROTEIN / nitrogenase cofactor maturase
Function / homology
Function and homology information


nitrogenase activity / 4 iron, 4 sulfur cluster binding / protein-containing complex assembly / metal ion binding
Similarity search - Function
NifX-like domain / : / Dinitrogenase iron-molybdenum cofactor biosynthesis / Nitrogenase MoFe cofactor biosynthesis protein NifE / Nitrogenase molybdenum-iron cofactor biosynthesis protein / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / : / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. ...NifX-like domain / : / Dinitrogenase iron-molybdenum cofactor biosynthesis / Nitrogenase MoFe cofactor biosynthesis protein NifE / Nitrogenase molybdenum-iron cofactor biosynthesis protein / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / : / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
FeFe cofactor / IRON/SULFUR CLUSTER / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN / Nitrogenase MoFe cofactor biosynthesis protein NifX
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsSchneider, F.F. / Martin del Campo, J.S. / Zhang, L. / Dean, D.R. / Einsle, O.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Trafficking of a nitrogenase FeMo-cofactor assembly intermediate
Authors: Schneider, F.F. / Martin del Campo, J.S. / Zhang, L. / Dean, D.R. / Einsle, O.
History
DepositionFeb 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
B: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
C: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
D: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
E: Nitrogenase MoFe cofactor biosynthesis protein NifX
F: Nitrogenase MoFe cofactor biosynthesis protein NifX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,89312
Polymers232,6466
Non-polymers2,2476
Water14,034779
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Nitrogenase iron-molybdenum cofactor biosynthesis protein ... , 2 types, 4 molecules ABCD

#1: Protein Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE


Mass: 50551.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Gene: nifE, Avin_01450 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DH03
#2: Protein Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN


Mass: 48463.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Gene: nifN, Avin_01470 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DH04

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Protein , 1 types, 2 molecules EF

#3: Protein Nitrogenase MoFe cofactor biosynthesis protein NifX


Mass: 17307.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Gene: nifX, Avin_01480 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DH05

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Non-polymers , 4 types, 785 molecules

#4: Chemical ChemComp-S5Q / FeFe cofactor


Mass: 747.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe8S9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of NifENX for nitrogenase ion-molybdenum cofactor biosynthesis
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Source (recombinant)Organism: Azotobacter vinelandii DJ (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256875 / Symmetry type: POINT
RefinementHighest resolution: 2.16 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315309
ELECTRON MICROSCOPYf_angle_d0.59721135
ELECTRON MICROSCOPYf_dihedral_angle_d4.8722133
ELECTRON MICROSCOPYf_chiral_restr0.0462338
ELECTRON MICROSCOPYf_plane_restr0.0052721

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