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- EMDB-75567: CryoEM structure of Gluconacetobacter diazotrophicus MoFeP (C2 sy... -

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Basic information

Entry
Database: EMDB / ID: EMD-75567
TitleCryoEM structure of Gluconacetobacter diazotrophicus MoFeP (C2 symmetry)
Map dataGluconacetobacter diazotrophicus MoFeP (C2 symmetry) sharp map
Sample
  • Complex: Heterotetrameric MoFeP from Gluconacetobacter diazotrophicus
    • Protein or peptide: Nitrogenase MoFe protein beta subunit NifK
    • Protein or peptide: Nitrogenase MoFe protein alpha subunit NifD
  • Ligand: FE (III) ION
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
KeywordsNitrogenase / MoFeP / Gluconacetobacter diazotrophicus / molybdenum-iron protein / Oxidoreductase
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, alpha chain / 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 protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesGluconacetobacter diazotrophicus PA1 5 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsLi Y / Narehood SM / Cook BD / McGuire KL / Tezcan FA / Herzik Jr MA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM148607 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM138206 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10OD032471 United States
CitationJournal: Biochemistry / Year: 2026
Title: Structural and Functional Characterization of Heterologous Nitrogenase Complexes.
Authors: Yizhou Li / Sarah M Narehood / Brian D Cook / Kelly L McGuire / Mark A Herzik / F Akif Tezcan /
Abstract: Nitrogenase is the only known enzyme that catalyzes the reduction of dinitrogen to ammonia. The most prevalent isozyme, molybdenum nitrogenase, comprises the catalytic molybdenum-iron protein (MoFeP) ...Nitrogenase is the only known enzyme that catalyzes the reduction of dinitrogen to ammonia. The most prevalent isozyme, molybdenum nitrogenase, comprises the catalytic molybdenum-iron protein (MoFeP) and the ATP-dependent reductase iron protein (FeP). Although Mo-nitrogenases are widespread across bacteria and archaea and appear to share conserved mechanistic and structural features, FeP and MoFeP show considerable sequence variability across diazotrophs. This raises questions about the conservation of chemomechanical mechanisms coupling FeP-dependent ATP hydrolysis and electron transfer to MoFeP, and about the functional compatibility of nitrogenase components from divergent species. Previous studies showed that some heterologous FeP-MoFeP pairs can functionally complement each other, whereas other pairs lack catalytic activity, but the absence of structural information on such heterologous pairs has limited mechanistic understanding. To this end, we investigated the functional and structural compatibility of FeP and MoFeP from () and (), two phylogenetically and ecologically distinct species. Building on our prior work with -nitrogenase and recently developed cryogenic electron microscopy (cryoEM) protocols, we determined the ADP·BeF-trapped structure of the homologous FeP-MoFeP complex and showed that it adopted the same geometry as its counterpart. Activity measurements showed that heterologous combinations retained 60-80% of homologous catalytic activities despite 30-50% sequence divergence in FeP and MoFeP. High-resolution cryoEM structures of FeP-MoFeP and FeP-MoFeP corroborated these activities and revealed that functional complementation tolerates substantial sequence variation when the core structural elements supporting ATP binding/hydrolysis, protein-protein interaction, electron transfer, and substrate reduction are conserved.
History
DepositionFeb 12, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75567.png

Downloads & links

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Map

FileDownload / File: emd_75567.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluconacetobacter diazotrophicus MoFeP (C2 symmetry) sharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 448 pix.
= 418.88 Å		0.94 Å/pix.
x 448 pix.
= 418.88 Å		0.94 Å/pix.
x 448 pix.
= 418.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.5578254 - 3.3913677
Average (Standard dev.)-0.000033342458 (±0.040295716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 418.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75567_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Gluconacetobacter diazotrophicus MoFeP (C2 symmetry) map

Fileemd_75567_additional_1.map
AnnotationGluconacetobacter diazotrophicus MoFeP (C2 symmetry) map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Gluconacetobacter diazotrophicus MoFeP (C2 symmetry) half map

Fileemd_75567_half_map_1.map
AnnotationGluconacetobacter diazotrophicus MoFeP (C2 symmetry) half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Gluconacetobacter diazotrophicus MoFeP (C2 symmetry) half map

Fileemd_75567_half_map_2.map
AnnotationGluconacetobacter diazotrophicus MoFeP (C2 symmetry) half 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 : Heterotetrameric MoFeP from Gluconacetobacter diazotrophicus

EntireName: Heterotetrameric MoFeP from Gluconacetobacter diazotrophicus
Components
  • Complex: Heterotetrameric MoFeP from Gluconacetobacter diazotrophicus
    • Protein or peptide: Nitrogenase MoFe protein beta subunit NifK
    • Protein or peptide: Nitrogenase MoFe protein alpha subunit NifD
  • Ligand: FE (III) ION
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon

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Supramolecule #1: Heterotetrameric MoFeP from Gluconacetobacter diazotrophicus

SupramoleculeName: Heterotetrameric MoFeP from Gluconacetobacter diazotrophicus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Gluconacetobacter diazotrophicus PA1 5 (bacteria)
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: Nitrogenase MoFe protein beta subunit NifK

MacromoleculeName: Nitrogenase MoFe protein beta subunit NifK / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Gluconacetobacter diazotrophicus PA1 5 (bacteria)
Molecular weightTheoretical: 57.094352 KDa
SequenceString: MPQNVDKILD HAPLFREPEY QEMLAGKAKL ENMPPADKVV EIADWTKSWE YREKNFARES LSVNPAKACQ PLGAVFVASG FERTMSFVH GSQGCVAYYR SHLSRHFKEP SSAVSSSMTE DAAVFGGLNN MVDGLANTYK LYDPKMIAVS TTCMAEVIGD D LHAFIQTA ...String:
MPQNVDKILD HAPLFREPEY QEMLAGKAKL ENMPPADKVV EIADWTKSWE YREKNFARES LSVNPAKACQ PLGAVFVASG FERTMSFVH GSQGCVAYYR SHLSRHFKEP SSAVSSSMTE DAAVFGGLNN MVDGLANTYK LYDPKMIAVS TTCMAEVIGD D LHAFIQTA KGKGSVPEEF DVPFAHTPAF VGSHVTGYDN MLKGILEHFW KGRTPVPNRS VNIIPGFDGF AVGNNRELKR IL GMMGVQY TILSDVSDQF DTPSDGEYRM YDGGTKIEAA RDAVNADYTI SLQEYCTPKT LEYCQSFGQK TASFHYPLGI GAT DDLLQK LSEISGKPVP QELEMERGRL VDALADSQAY LHGKTYAIYG DPDFVYGMAR FILETGGEPK HCLATNGSKA WEAQ MQELF DSSPFGVGCK AWGGKDLWHM RSLLATEKVD LLIGNSYGKY LERDTDTPLI RLMFPIFDRH HHHRFPVWGY QGALR VLVT LLDKIFDKLD DDTIQAGVTD YSFDLTR

UniProtKB: Nitrogenase molybdenum-iron protein beta chain

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Macromolecule #2: Nitrogenase MoFe protein alpha subunit NifD

MacromoleculeName: Nitrogenase MoFe protein alpha subunit NifD / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Gluconacetobacter diazotrophicus PA1 5 (bacteria)
Molecular weightTheoretical: 56.095453 KDa
SequenceString: MSLDEDKTND SAFHARLIAE VLEAYPDKAR KRRQKHLNVA GQAEAEAQDA GEEGVMLSEC DVKSNVKSVP GVMTIRGCAY AGSKGVVWG PVKDMVHISH GPVGCGQYSW SQRRNYYIGN TGVDSFVTMQ FTSDFQEKDI VFGGDKKLEK IIDEIDELFP L AKGISVQS ...String:
MSLDEDKTND SAFHARLIAE VLEAYPDKAR KRRQKHLNVA GQAEAEAQDA GEEGVMLSEC DVKSNVKSVP GVMTIRGCAY AGSKGVVWG PVKDMVHISH GPVGCGQYSW SQRRNYYIGN TGVDSFVTMQ FTSDFQEKDI VFGGDKKLEK IIDEIDELFP L AKGISVQS ECPIGLIGDD IEAVSRKKKK EIGKTIVPVR CEGFRGVSQS LGHHIANDAI RDWVFDGEDK HAAFETTPYD VN VIGDYNI GGDAWSSRIL LEEMGLRVVG NWSGDATLAE IERAPKAKLN LIHCYRSMNY ICRHMEEKYN IPWTEYNFFG PSQ IAASLR KIAALFDEKI QEGAERVIAK YQPLVDAVIE KFRPRLAGKK VMLYVGGLRP RHVVNAYNDL GMEIVGTGYE FGHN DDYQR TGHYVREGTL IYDDVTGYEL EKFIEGIRPD LVGSGIKEKY PVQKMGIPFR QMHSWDYSGP YHGYDGFAIF ARDMD LAIN NPVWSMFKAP WKNAA

UniProtKB: Nitrogenase protein alpha chain

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Macromolecule #3: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #4: FE(8)-S(7) CLUSTER

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: CLF
Molecular weightTheoretical: 671.215 Da
Chemical component information

ChemComp-CLF:
FE(8)-S(7) CLUSTER

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Macromolecule #5: 3-HYDROXY-3-CARBOXY-ADIPIC ACID

MacromoleculeName: 3-HYDROXY-3-CARBOXY-ADIPIC ACID / type: ligand / ID: 5 / Number of copies: 2 / Formula: HCA
Molecular weightTheoretical: 206.15 Da
Chemical component information

ChemComp-HCA:
3-HYDROXY-3-CARBOXY-ADIPIC ACID

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Macromolecule #6: iron-sulfur-molybdenum cluster with interstitial carbon

MacromoleculeName: iron-sulfur-molybdenum cluster with interstitial carbon
type: ligand / ID: 6 / Number of copies: 2 / Formula: ICS
Molecular weightTheoretical: 787.451 Da
Chemical component information

ChemComp-ICE:
iron-sulfur-molybdenum cluster with interstitial carbon

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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

Concentration6.9 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
25.0 mMNaClSodium chloride
10.0 mMNa2S2O4Sodium dithionite

Details: Solutions were prepared, filtered, and degassed to Ar immediately prior to the experiment.
GridModel: Quantifoil Active R1.2/0.8 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 298 K / Instrument: SPT LABTECH CHAMELEON
Details: Samples were covered by Al's oil and frozen with the SPT Labtech chameleon..
DetailsHomogeneous Gd-MoFeP purified from a gel filtration column(SEC).

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2371 / Average exposure time: 5.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 674977
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

26757

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 211731
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-10zl:
CryoEM structure of Gluconacetobacter diazotrophicus MoFeP (C2 symmetry)

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