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- EMDB-52558: CryoEM structure of transit-GmNifEN -

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Basic information

Entry
Database: EMDB / ID: EMD-52558
TitleCryoEM structure of transit-GmNifEN
Map dataCryoEM structure of transit-GmNifEN sharped with EMready
Sample
  • Complex: nitrogenase iron-molybdenum cofactor biosynthesis protein NifEN
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FeFe cofactor
  • Ligand: water
KeywordsNITROGENASE COFACTOR MATURATION / PROTEIN BINDING / Metalloenzyme / Iron-Sulfur Cluster / METAL BINDING PROTEIN
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
Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsPaya Tormo L / Nguyen TQ / Fyfe C / Basbous H / Dobrzynska K / Echavarri-Erasun C / Martin L / Caserta G / Legrand P / Thorn A ...Paya Tormo L / Nguyen TQ / Fyfe C / Basbous H / Dobrzynska K / Echavarri-Erasun C / Martin L / Caserta G / Legrand P / Thorn A / Amara P / Schoehn G / Cherrier MV / Rubio LM / Nicolet Y
Funding support France, 3 items
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 TQ / Fyfe C / Basbous H / Dobrzynska K / Echavarri-Erasun C / Martin L / Caserta G / Legrand P / Thorn A / Amara P / Schoehn G / Cherrier MV / Rubio LM / Nicolet Y
History
DepositionJan 15, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52558.png

Downloads & links

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Map

FileDownload / File: emd_52558.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of transit-GmNifEN sharped with EMready
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 330 pix.
= 276.87 Å		0.84 Å/pix.
x 330 pix.
= 276.87 Å		0.84 Å/pix.
x 330 pix.
= 276.87 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-0.1287032 - 18.156507000000001
Average (Standard dev.)-0.031738177 (±0.48388728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 276.87 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CryoEM structure of transit-GmNifEN sharped

Fileemd_52558_additional_1.map
AnnotationCryoEM structure of transit-GmNifEN sharped
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoEM structure of transit-GmNifEN unsharped

Fileemd_52558_additional_2.map
AnnotationCryoEM structure of transit-GmNifEN unsharped
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM structure of transit-GmNifEN

Fileemd_52558_half_map_1.map
AnnotationCryoEM structure of transit-GmNifEN
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM structure of transit-GmNifEN

Fileemd_52558_half_map_2.map
AnnotationCryoEM structure of transit-GmNifEN
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : nitrogenase iron-molybdenum cofactor biosynthesis protein NifEN

EntireName: nitrogenase iron-molybdenum cofactor biosynthesis protein NifEN
Components
  • Complex: nitrogenase iron-molybdenum cofactor biosynthesis protein NifEN
    • Protein or peptide: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FeFe cofactor
  • Ligand: water

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Supramolecule #1: nitrogenase iron-molybdenum cofactor biosynthesis protein NifEN

SupramoleculeName: nitrogenase iron-molybdenum cofactor biosynthesis protein NifEN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Geobacter metallireducens (bacteria)
Molecular weightTheoretical: 199.774 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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Geobacter metallireducens (bacteria) / Strain: strain ATCC 53774 / DSM 7210 / GS-15
Molecular weightTheoretical: 100.135594 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAKPDYYDVS ECETHEKGAP KFCKKSEPGE GAERSCAYDG ARVVLMPITD VIHLVHGPIA CAGNSWDNRG ARSSDSQLYR RGFTTEMLE NDVVFGGEKK LYRAILELAE RYEGQAKAMF VYATCVTAMT GDDVEAVCAA AGKKVAIPLI PVNTPGFIGD K NIGNRLAG ...String:
MAKPDYYDVS ECETHEKGAP KFCKKSEPGE GAERSCAYDG ARVVLMPITD VIHLVHGPIA CAGNSWDNRG ARSSDSQLYR RGFTTEMLE NDVVFGGEKK LYRAILELAE RYEGQAKAMF VYATCVTAMT GDDVEAVCAA AGKKVAIPLI PVNTPGFIGD K NIGNRLAG EVLFKHVIGT AEPPVLGEYP INLIGEYNIA GDLWGMLPLF ERLGIQVLSC FSGDATFEEL RYAHRAKLNI II CSKSLTN LARKMQKNYG MPYLEESFYG MTDTAKALRD IARELDDAVG GLEKRIMQDR VEKLLEEEEA TCRERLAPYR ARL EGKRSV LFTGGVKTWS MVNALRELGV EILAAGTQNS TLEDFYRMKA LMHQDARIIE DTSSAGLLQV MYDKMPDLIV AGGK TKFLA LKTKTPFLDI NHGRSHPYAG YEGMVTFAKQ LDLTVNNPIW PVLNAKAPWE KTEEELTAAV ALAAGHARAC LDEDL KDST VKVPAKNATV NPQKNSPALG ATLAYLGIDQ MLALLHGAQG CSTFIRLQLS RHFKEPVALN STAMSEDTAI FGGWEN LKK GLKKVIEKFS PEVVGVMTSG LTETMGDDVR SAIVHFRQEY PEHDGVPVVW ASTPDYCGSL QEGYAATVEA IVRSVPE PG ETIPGQVTVL PGAHLTPADV EEVRELCEAF GLDPIIVPDI ANALDGHIDE TVSPLSTGGV SMARIRQAGQ SAATLFIG D SLAKAAEAMT ERCGMPSYGF TSLTGLAQVD RFMETLAAIA GRPIPEKFRR WRSRLMDAMV DSHYQFGLKK VTVALEGDN LKTLVNFLAG MGCEIQAAIA ATRVRGLDGL PARDIFVGDL EDLETAARGS DLIVANSNGR QAAAKLGIKA HLRAGLPVFD RLGAHQKMW VGYRGTMNLL FETANLFQAN AGEGQKLAHN

UniProtKB: Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE

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Macromolecule #2: IRON/SULFUR CLUSTER

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

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #3: FeFe cofactor

MacromoleculeName: FeFe cofactor / type: ligand / ID: 3 / Number of copies: 2 / Formula: S5Q
Molecular weightTheoretical: 747.356 Da
Chemical component information

ChemComp-S5Q:
FeFe cofactor

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 6 / 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

Concentration0.3 mg/mL
BufferpH: 8
Component:
ConcentrationName
50.0 mMTris-HCl
2.0 mMDTH
500.0 mMNaCl
GridModel: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 30 mA
VitrificationCryogen name: PROPANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Frames/image: 2-40 / Number grids imaged: 1 / Number real images: 14397 / Average exposure time: 1.5 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10391977
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold model of NifEN dimer
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 370821
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 2
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: Holo-gmNifen
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9i0h:
CryoEM structure of transit-GmNifEN

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