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- PDB-9i0h: CryoEM structure of transit-GmNifEN -

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Basic information

Entry
Database: PDB / ID: 9i0h
TitleCryoEM structure of transit-GmNifEN
ComponentsNitrogenase iron-molybdenum cofactor biosynthesis protein NifE
KeywordsMETAL BINDING PROTEIN / NITROGENASE COFACTOR MATURATION / PROTEIN BINDING / Metalloenzyme / Iron-Sulfur Cluster
Function / homology
Function and homology information


nitrogenase activity / protein-containing complex assembly
Similarity search - Function
Nitrogenase MoFe cofactor biosynthesis protein NifE / Nitrogenase molybdenum-iron cofactor biosynthesis protein / : / 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
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsPaya Tormo, L. / Nguyen, T.Q. / Fyfe, C. / Basbous, H. / Dobrzynska, K. / Echavarri-Erasun, C. / Martin, L. / Caserta, G. / Legrand, P. / Thorn, A. ...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 support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-02 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-17-EURE-0003 France
CitationJournal: Nature Chemical Biology / Year: 2025
Title: Dynamics driving the precursor in NifEN scaffold during nitrogenase FeMo-cofactor assembly
Authors: 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. ...Authors: 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.
History
DepositionJan 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,4696
Polymers200,2712
Non-polymers2,1984
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 100135.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (bacteria) / Strain: strain ATCC 53774 / DSM 7210 / GS-15 / Gene: nifEN, Gmet_0669 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q39XW3
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe4S4
#3: Chemical ChemComp-S5Q / FeFe cofactor


Mass: 747.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe8S9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: nitrogenase iron-molybdenum cofactor biosynthesis protein NifEN
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.199774 MDa / Experimental value: NO
Source (natural)Organism: Geobacter metallireducens (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
150 mMTris-HCl1
22 mMDTH1
3500 mMNaCl1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 mA / Grid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 100 % / Chamber temperature: 295 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 700 nm
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14397
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40 / Used frames/image: 2-40

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Processing

EM software
IDNameVersionCategory
7PHENIX1.21.1_5286:model fitting
12EMReady3D reconstruction
13PHENIX1.21.1_5286:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10391977
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 370821 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Holo-gmNifen / Source name: Other / Type: other

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