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- EMDB-70642: L-cluster free apo-NifEN expressed in E. coli -

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Basic information

Entry
Database: EMDB / ID: EMD-70642
TitleL-cluster free apo-NifEN expressed in E. coli
Map data
Sample
  • Complex: NifEN
    • Complex: NifE
      • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
    • Complex: NifN
      • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
KeywordsNitrogenase / Complex / OXIDOREDUCTASE
Function / homology
Function and homology information


nitrogenase activity / 4 iron, 4 sulfur cluster binding / protein-containing complex assembly / metal ion binding
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
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 / cryo EM / Resolution: 3.72 Å
AuthorsNeumann B / Brandon K / Suder DS / 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: L-cluster free apo-NifEN expressed in E. coli
Authors: Neumann B / Brandon K / Suder DS / Hu Y / Ribbe MW / Gonen S
History
DepositionMay 15, 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_70642.png

Downloads & links

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Map

FileDownload / File: emd_70642.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 288 pix.
= 213.984 Å		0.74 Å/pix.
x 288 pix.
= 213.984 Å		0.74 Å/pix.
x 288 pix.
= 213.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.099681675 - 0.20285292
Average (Standard dev.)0.0006919892 (±0.0073897224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 213.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70642_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Mask #2

Fileemd_70642_msk_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Additional map: local res

Fileemd_70642_additional_1.map
Annotationlocal res
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: sharpened

Fileemd_70642_additional_2.map
Annotationsharpened
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: local filtered

Fileemd_70642_additional_3.map
Annotationlocal filtered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70642_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_70642_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : NifEN

EntireName: NifEN
Components
  • Complex: NifEN
    • Complex: NifE
      • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
    • Complex: NifN
      • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN

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Supramolecule #1: NifEN

SupramoleculeName: NifEN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Molecular weightTheoretical: 49 KDa

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Supramolecule #2: NifE

SupramoleculeName: NifE / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)

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Supramolecule #3: NifN

SupramoleculeName: NifN / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Molecular weightTheoretical: 52.77709 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHKAK DIAELLDEPA CSHNKKEKSG CAKPKPGATD GGCSFDGAQI ALLPVADVAH IVHGPIACAG SSWDNRGTRS SGPDLYRIG MTTDLTENDV IMGRAEKRLF HAIRQAVESY SPPAVFVYNT CVPALIGDDV DAVCKAAAER FGTPVIPVDS A GFYGTKNL ...String:
MHHHHHHKAK DIAELLDEPA CSHNKKEKSG CAKPKPGATD GGCSFDGAQI ALLPVADVAH IVHGPIACAG SSWDNRGTRS SGPDLYRIG MTTDLTENDV IMGRAEKRLF HAIRQAVESY SPPAVFVYNT CVPALIGDDV DAVCKAAAER FGTPVIPVDS A GFYGTKNL GNRIAGEAML KYVIGTREPD PLPVGSERPG IRVHDVNLIG EYNIAGEFWH VLPLLDELGL RVLCTLAGDA RY REVQTMH RAEVNMMVCS KAMLNVARKL QETYGTPWFE GSFYGITDTS QALRDFARLL DDPDLTARTE ALIAREEAKV RAA LEPWRA RLEGKRVLLY TGGVKSWSVV SALQDLGMKV VATGTKKSTE EDKARIRELM GDDVKMLDEG NARVLLKTVD EYQA DILIA GGRNMYTALK GRVPFLDINQ EREFGYAGYD GMLELVRQLC ITLECPVWEA VRRPAPWDIP ASQDAAPSAP ARSAN A

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: 49.301969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEIINRNKA LAVSPLKASQ TMGAALAILG LARSMPLFHG SQGCTAFAKV FFVRHFREPV PLQTTAMDQV SSVMGADENV VEALKTICE RQNPSVIGLL TTGLSETQGC DLHTALHEFR TQYEEYKDVP IVPVNTPDFS GCFESGFAAA VKAIVETLVP E RRDQVGKR ...String:
MAEIINRNKA LAVSPLKASQ TMGAALAILG LARSMPLFHG SQGCTAFAKV FFVRHFREPV PLQTTAMDQV SSVMGADENV VEALKTICE RQNPSVIGLL TTGLSETQGC DLHTALHEFR TQYEEYKDVP IVPVNTPDFS GCFESGFAAA VKAIVETLVP E RRDQVGKR PRQVNVLCSA NLTPGDLEYI AESIESFGLR PLLIPDLSGS LDGHLDENRF NALTTGGLSV AELATAGQSV AT LVVGQSL AGAADALAER TGVPDRRFGM LYGLDAVDAW LMALAEISGN PVPDRYKRQR AQLQDAMLDT HFMLSSARTA IAA DPDLLL GFDALLRSMG AHTVAAVVPA RAAALVDSPL PSVRVGDLED LEHAARAGQA QLVIGNSHAL ASARRLGVPL LRAG FPQYD LLGGFQRCWS GYRGSSQVLF DLANLLVEHH QGIQPYHSIY AQKPATEQPQ WRH

UniProtKB: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN

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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

Concentration0.75 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
500.0 mMNaClsodium clhoride
50.0 mMC4H13Cl2NO3Tris-HCl
1.0 %C3H8O3glycerol
GridModel: Quantifoil R1.2/1.3 / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: negatively glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Plunged inside an anaerobic chamber.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
SoftwareName: SerialEM
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 3 / Number real images: 16536 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 126644
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

l_v4


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX
Output model

PDB-9onj:
L-cluster free apo-NifEN expressed in E. coli

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