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- EMDB-73407: Negative stained A. vinelandii NifEN/NifH ADPxAIF4- stabilized complex -

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Basic information

Entry
Database: EMDB / ID: EMD-73407
TitleNegative stained A. vinelandii NifEN/NifH ADPxAIF4- stabilized complex
Map data
Sample
  • Complex: NifEN/NifH ADPxAIF4- stabilized complex
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
    • Protein or peptide: Nitrogenase iron protein
KeywordsNitrogenase / Complex / Metal cluster / OXIDOREDUCTASE
Function / homology
Function and homology information


nitrogenase / nitrogenase activity / protein-containing complex assembly / ATP binding
Similarity search - Function
Nitrogenase MoFe cofactor biosynthesis protein NifE / Nitrogenase molybdenum-iron cofactor biosynthesis protein / : / Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. ...Nitrogenase MoFe cofactor biosynthesis protein NifE / Nitrogenase molybdenum-iron cofactor biosynthesis protein / : / Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nitrogenase iron protein / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 14.8 Å
AuthorsNeumann B / Brandon K / Hu Y / Ribbe MW / Gonen S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142797 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM67626 United States
Department of Energy (DOE, United States)DE-SC0016510 United States
CitationJournal: Nat Catal / Year: 2026
Title: Structural insights into metallocluster trafficking in the nitrogenase assembly scaffold NifEN.
Authors: Bryan Neumann / Kristal A Brandon / Robert Quechol / Diana S Suder / Chi Chung Lee / Yimo Yang / Kamil Górecki / Jared A Wiig / Yilin Hu / Shane Gonen / Markus W Ribbe /
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 ...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.
History
DepositionOct 19, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73407.png

Downloads & links

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Map

FileDownload / File: emd_73407.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 320 pix.
= 366.97 Å		1.15 Å/pix.
x 320 pix.
= 366.97 Å		1.15 Å/pix.
x 320 pix.
= 366.97 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14678 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-1.2161322 - 1.9969031
Average (Standard dev.)-0.013945952 (±0.16454819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 366.9696 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73407_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_73407_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_73407_half_map_2.map
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Sample components

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Entire : NifEN/NifH ADPxAIF4- stabilized complex

EntireName: NifEN/NifH ADPxAIF4- stabilized complex
Components
  • Complex: NifEN/NifH ADPxAIF4- stabilized complex
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
    • Protein or peptide: Nitrogenase iron protein

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Supramolecule #1: NifEN/NifH ADPxAIF4- stabilized complex

SupramoleculeName: NifEN/NifH ADPxAIF4- stabilized complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Molecular weightTheoretical: 330 KDa

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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 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
SequenceString: MKAKDIAELL DEPACSHNKK EKSGCAKPKP GATDGGCSFD GAQIALLPVA DVAHIVHGPI ACAGSSWDN RGTRSSGPDL YRIGMTTDLT ENDVIMGRAE KRLFHAIRQA VESYSPPAVF V YNTCVPAL IGDDVDAVCK AAAERFGTPV IPVDSAGFYG TKNLGNRIAG ...String:
MKAKDIAELL DEPACSHNKK EKSGCAKPKP GATDGGCSFD GAQIALLPVA DVAHIVHGPI ACAGSSWDN RGTRSSGPDL YRIGMTTDLT ENDVIMGRAE KRLFHAIRQA VESYSPPAVF V YNTCVPAL IGDDVDAVCK AAAERFGTPV IPVDSAGFYG TKNLGNRIAG EAMLKYVIGT RE PDPLPVG SERPGIRVHD VNLIGEYNIA GEFWHVLPLL DELGLRVLCT LAGDARYREV QTM HRAEVN MMVCSKAMLN VARKLQETYG TPWFEGSFYG ITDTSQALRD FARLLDDPDL TART EALIA REEAKVRAAL EPWRARLEGK RVLLYTGGVK SWSVVSALQD LGMKVVATGT KKSTE EDKA RIRELMGDDV KMLDEGNARV LLKTVDEYQA DILIAGGRNM YTALKGRVPF LDINQE REF GYAGYDGMLE LVRQLCITLE CPVWEAVRRP APWDIPASQD AAPSAPARSA NA

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 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
SequenceString: MAEIINRNKA LAVSPLKASQ TMGAALAILG LARSMPLFHG SQGCTAFAKV FFVRHFREPV PLQTTAMDQ VSSVMGADEN VVEALKTICE RQNPSVIGLL TTGLSETQGC DLHTALHEFR T QYEEYKDV PIVPVNTPDF SGCFESGFAA AVKAIVETLV PERRDQVGKR ...String:
MAEIINRNKA LAVSPLKASQ TMGAALAILG LARSMPLFHG SQGCTAFAKV FFVRHFREPV PLQTTAMDQ VSSVMGADEN VVEALKTICE RQNPSVIGLL TTGLSETQGC DLHTALHEFR T QYEEYKDV PIVPVNTPDF SGCFESGFAA AVKAIVETLV PERRDQVGKR PRQVNVLCSA NL TPGDLEY IAESIESFGL RPLLIPDLSG SLDGHLDENR FNALTTGGLS VAELATAGQS VAT LVVGQS LAGAADALAE RTGVPDRRFG MLYGLDAVDA WLMALAEISG NPVPDRYKRQ RAQL QDAML DTHFMLSSAR TAIAADPDLL LGFDALLRSM GAHTVAAVVP ARAAALVDSP LPSVR VGDL EDLEHAARAG QAQLVIGNSH ALASARRLGV PLLRAGFPQY DLLGGFQRCW SGYRGS SQV LFDLANLLVE HHQGIQPYHS IYAQKPATEQ PQWRH

UniProtKB: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN

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Macromolecule #3: Nitrogenase iron protein

MacromoleculeName: Nitrogenase iron protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
SequenceString: MAMRQCAIYG KGGIGKSTTT QNLVAALAEM GKKVMIVGCD PKADSTRLIL HSKAQNTIME MAAEAGTVE DLELEDVLKA GYGGVKCVES GGPEPGVGCA GRGVITAINF LEEEGAYEDD L DFVFYDVL GDVVCGGFAM PIRENKAQEI YIVCSGEMMA MYAANNISKG ...String:
MAMRQCAIYG KGGIGKSTTT QNLVAALAEM GKKVMIVGCD PKADSTRLIL HSKAQNTIME MAAEAGTVE DLELEDVLKA GYGGVKCVES GGPEPGVGCA GRGVITAINF LEEEGAYEDD L DFVFYDVL GDVVCGGFAM PIRENKAQEI YIVCSGEMMA MYAANNISKG IVKYANSGSV RL GGLICNS RNTDREDELI IALANKLGTQ MIHFVPRDNV VQRAEIRRMT VIEYDPKAKQ ADE YRALAR KVVDNKLLVI PNPITMDELE ELLMEFGIME VEDESIVGKT AEEV

UniProtKB: Nitrogenase iron protein

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
StainingType: NEGATIVE / Material: uranyl formate
GridModel: EMS Formvar Carbon / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR

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Electron microscopy

MicroscopeJEOL 2100F
Image recordingFilm or detector model: OTHER / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 18448
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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