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- EMDB-52782: Nitrogenase maturase NifEN in complex with the cofactor chaperone NifX -

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Basic information

Entry
Database: EMDB / ID: EMD-52782
TitleNitrogenase maturase NifEN in complex with the cofactor chaperone NifX
Map data
Sample
  • Complex: Ternary complex of NifENX for nitrogenase ion-molybdenum cofactor biosynthesis
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
    • Protein or peptide: Nitrogenase MoFe cofactor biosynthesis protein NifX
  • Ligand: FeFe cofactor
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordsnitrogenase cofactor maturase / METAL BINDING PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsSchneider FF / Martin del Campo JS / Zhang L / Dean DR / Einsle O
Funding supportEuropean Union, Germany, 2 items
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 FF / Martin del Campo JS / Zhang L / Dean DR / Einsle O
History
DepositionFeb 11, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52782.png

Downloads & links

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Map

FileDownload / File: emd_52782.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 240 pix.
= 183.048 Å		0.76 Å/pix.
x 240 pix.
= 183.048 Å		0.76 Å/pix.
x 240 pix.
= 183.048 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7627 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.14628392 - 0.38440588
Average (Standard dev.)0.0008639652 (±0.016444808)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 183.048 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52782_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Additional map: #1

Fileemd_52782_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_52782_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52782_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ternary complex of NifENX for nitrogenase ion-molybdenum cofactor...

EntireName: Ternary complex of NifENX for nitrogenase ion-molybdenum cofactor biosynthesis
Components
  • Complex: Ternary complex of NifENX for nitrogenase ion-molybdenum cofactor biosynthesis
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
    • Protein or peptide: Nitrogenase MoFe cofactor biosynthesis protein NifX
  • Ligand: FeFe cofactor
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Ternary complex of NifENX for nitrogenase ion-molybdenum cofactor...

SupramoleculeName: Ternary complex of NifENX for nitrogenase ion-molybdenum cofactor biosynthesis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)

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

MacromoleculeName: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Molecular weightTheoretical: 50.551762 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString: MKAKDIAELL DEPACSHNKK EKSGCAKPKP GATDGGCSFD GAQIALLPVA DVAHIVHGPI ACAGSSWDNR GTRSSGPDLY RIGMTTDLT ENDVIMGRAE KRLFHAIRQA VESYSPPAVF VYNTCVPALI GDDVDAVCKA AAERFGTPVI PVDSAGFYGT K NLGNRIAG ...String:
MKAKDIAELL DEPACSHNKK EKSGCAKPKP GATDGGCSFD GAQIALLPVA DVAHIVHGPI ACAGSSWDNR GTRSSGPDLY RIGMTTDLT ENDVIMGRAE KRLFHAIRQA VESYSPPAVF VYNTCVPALI GDDVDAVCKA AAERFGTPVI PVDSAGFYGT K NLGNRIAG EAMLKYVIGT REPDPLPVGS ERPGIRVHDV NLIGEYNIAG EFWHVLPLLD ELGLRVLCTL AGDARYREVQ TM HRAEVNM MVCSKAMLNV ARKLQETYGT PWFEGSFYGI TDTSQALRDF ARLLDDPDLT ARTEALIARE EAKVRAALEP WRA RLEGKR VLLYTGGVKS WSVVSALQDL GMKVVATGTK KSTEEDKARI RELMGDDVKM LDEGNARVLL KTVDEYQADI LIAG GRNMY TALKGRVPFL DINQEREFGY AGYDGMLELV RQLCITLECP VWEAVRRPAP WDIPA

UniProtKB: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE

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Macromolecule #2: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN

MacromoleculeName: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Molecular weightTheoretical: 48.463977 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString: AEIINRNKAL AVSPLKASQT MGAALAILGL ARSMPLFHGS QGCTAFAKVF FVRHFREPVP LQTTAMDQVS SVMGADENVV EALKTICER QNPSVIGLLT TGLSETQGCD LHTALHEFRT QYEEYKDVPI VPVNTPDFSG CFESGFAAAV KAIVETLVPE R RDQVGKRP ...String:
AEIINRNKAL AVSPLKASQT MGAALAILGL ARSMPLFHGS QGCTAFAKVF FVRHFREPVP LQTTAMDQVS SVMGADENVV EALKTICER QNPSVIGLLT TGLSETQGCD LHTALHEFRT QYEEYKDVPI VPVNTPDFSG CFESGFAAAV KAIVETLVPE R RDQVGKRP RQVNVLCSAN LTPGDLEYIA ESIESFGLRP LLIPDLSGSL DGHLDENRFN ALTTGGLSVA ELATAGQSVA TL VVGQSLA GAADALAERT GVPDRRFGML YGLDAVDAWL MALAEISGNP VPDRYKRQRA QLQDAMLDTH FMLSSARTAI AAD PDLLLG FDALLRSMGA HTVAAVVPAR AAALVDSPLP SVRVGDLEDL EHAARAGQAQ LVIGNSHALA SARRLGVPLL RAGF PQYDL LGGFQRCWSG YRGSSQVLFD LANLLVEHHQ GIQPYHSIYA QKPATEQ

UniProtKB: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN

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Macromolecule #3: Nitrogenase MoFe cofactor biosynthesis protein NifX

MacromoleculeName: Nitrogenase MoFe cofactor biosynthesis protein NifX / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Molecular weightTheoretical: 17.30751 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString:
MSSPTRQLQV LDSEDDGTLL KVAFASSDRE LVDQHFGSSR SFAIYGVNPE RSQLLSVVEF GELEQDGNED KLARKIDLLD GCVAVYCCA CGASAVRQLM AIGVQPIKVS EGARIAELIE ALQVELREGP SAWLAKAIQR TRGPDMRRFD AMAAEGWDE

UniProtKB: Nitrogenase MoFe cofactor biosynthesis protein NifX

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Macromolecule #4: FeFe cofactor

MacromoleculeName: FeFe cofactor / type: ligand / ID: 4 / Number of copies: 2 / Formula: S5Q
Molecular weightTheoretical: 747.356 Da
Chemical component information

ChemComp-S5Q:
FeFe cofactor

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 779 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 256875
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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