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- EMDB-73406: Negative stained A. vinelandii NifEN-B' fusion -

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Basic information

Entry
Database: EMDB / ID: EMD-73406
TitleNegative stained A. vinelandii NifEN-B' fusion
Map data
Sample
  • Complex: NifEN-B' fusion
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
    • Protein or peptide: FeMo cofactor biosynthesis protein NifB
KeywordsNitrogenase / Complex / Metal cluster / OXIDOREDUCTASE
Function / homology
Function and homology information


molybdopterin cofactor biosynthetic process / Lyases / nitrogenase activity / 4 iron, 4 sulfur cluster binding / protein-containing complex assembly / lyase activity / metal ion binding
Similarity search - Function
FeMo cofactor biosynthesis protein NifB, C-terminal / Nitrogenase cofactor biosynthesis protein NifB / 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 / MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / : ...FeMo cofactor biosynthesis protein NifB, C-terminal / Nitrogenase cofactor biosynthesis protein NifB / 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 / MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / : / : / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / Radical SAM superfamily / : / Radical SAM core domain profile. / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN / FeMo cofactor biosynthesis protein NifB
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 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: To Be Published
Title: Structural insights into metallocluster trafficking in nitrogenase assembly scaffold NifEN
Authors: Neumann B / Brandon K / Hu Y / Ribbe MW / Gonen S
History
DepositionOct 19, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73406.png

Downloads & links

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Map

FileDownload / File: emd_73406.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14678 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.083513 - 1.8541781
Average (Standard dev.)-0.028931603 (±0.12472511)
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_73406_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73406_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73406_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NifEN-B' fusion

EntireName: NifEN-B' fusion
Components
  • Complex: NifEN-B' fusion
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
    • Protein or peptide: FeMo cofactor biosynthesis protein NifB

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Supramolecule #1: NifEN-B' fusion

SupramoleculeName: NifEN-B' fusion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Molecular weightTheoretical: 280 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: FeMo cofactor biosynthesis protein NifB

MacromoleculeName: FeMo cofactor biosynthesis protein NifB / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
SequenceString: MELSVLGQNN GGQHSAGGCS SSSCGSTHDQ LSHLPENIRA KVQNHPCYSE EAHHYFARMH VAVAPACNI QCHYCNRKYD CANESRPGVV SEVLTPEQAV KKVKAVAAAI PQMSVLGIAG P GDPLANPK RTLDTFRMLS EQAPDMKLCV STNGLALPEC VEELAKHNID ...String:
MELSVLGQNN GGQHSAGGCS SSSCGSTHDQ LSHLPENIRA KVQNHPCYSE EAHHYFARMH VAVAPACNI QCHYCNRKYD CANESRPGVV SEVLTPEQAV KKVKAVAAAI PQMSVLGIAG P GDPLANPK RTLDTFRMLS EQAPDMKLCV STNGLALPEC VEELAKHNID HVTITINCVD PE IGAKIYP DLLEQQAHPR RQGRKILIEQ QQKGLEMLVA RGILVKVNSV MIPGVNDEHL KEV SKIVKA KGAFLHNVMP LIAEPEHGTF YGVMGQRSPE PEELQDLQDA CAGDMNMMRH CRQC RADAV GMLGEDRGDE FTLDKIESME IDYEAAMVKR AAIHAAIKEE L

UniProtKB: FeMo cofactor biosynthesis protein NifB

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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

Concentration0.075 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: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 14597
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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