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- EMDB-19178: Cryo-EM structure of the molybdenum nitrogenase complexed with ir... -

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Basic information

Entry
Database: EMDB / ID: EMD-19178
TitleCryo-EM structure of the molybdenum nitrogenase complexed with iron protein (NifH) and Shethna protein II (FeSII)
Map dataunsharpened map
Sample
  • Complex: Supercomplex of NifDK-NifH-FeSII
    • Protein or peptide: Nitrogenase molybdenum-iron protein alpha chain
    • Protein or peptide: Nitrogenase molybdenum-iron protein beta chain
    • Protein or peptide: Protein FeSII
    • Protein or peptide: Nitrogenase iron protein 1
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: CALCIUM ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
Keywordsnitrogenase complex / OXIDOREDUCTASE
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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 molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain ...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 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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nitrogenase iron protein 1 / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Protein FeSII
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsFranke P / Zhang L / Einsle O
Funding supportEuropean Union, Germany, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)310656European Union
German Research Foundation (DFG)CRC 1381, project ID 403222702 Germany
German Research Foundation (DFG)RTG 1976, project ID 235777276 Germany
German Research Foundation (DFG)INST 35/134-1 FUGG Germany
CitationJournal: Nature / Year: 2025
Title: Conformational protection of molybdenum nitrogenase by Shethna protein II.
Authors: Philipp Franke / Simon Freiberger / Lin Zhang / Oliver Einsle /
Abstract: The oxygen-sensitive molybdenum-dependent nitrogenase of Azotobacter vinelandii is protected from oxidative damage by a reversible 'switch-off' mechanism. It forms a complex with a small ferredoxin, ...The oxygen-sensitive molybdenum-dependent nitrogenase of Azotobacter vinelandii is protected from oxidative damage by a reversible 'switch-off' mechanism. It forms a complex with a small ferredoxin, FeSII (ref. ) or the 'Shethna protein II', which acts as an O sensor and associates with the two component proteins of nitrogenase when its [2Fe:2S] cluster becomes oxidized. Here we report the three-dimensional structure of the protective ternary complex of the catalytic subunit of Mo-nitrogenase, its cognate reductase and the FeSII protein, determined by single-particle cryo-electron microscopy. The dimeric FeSII protein associates with two copies of each component to assemble a 620 kDa core complex that then polymerizes into large, filamentous structures. This complex is catalytically inactive, but the enzyme components are quickly released and reactivated upon oxygen depletion. The first step in complex formation is the association of FeSII with the more O-sensitive Fe protein component of nitrogenase during sudden oxidative stress. The action of this small ferredoxin represents a straightforward means of protection from O that may be crucial for the maintenance of recombinant nitrogenase in food crops.
History
DepositionDec 15, 2023-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19178.png

Downloads & links

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Map

FileDownload / File: emd_19178.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 320 pix.
= 280.96 Å		0.88 Å/pix.
x 320 pix.
= 280.96 Å		0.88 Å/pix.
x 320 pix.
= 280.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.20476466 - 0.9227391
Average (Standard dev.)0.000041667074 (±0.019668367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 280.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19178_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_19178_additional_1.map
Annotationsharpened map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_19178_half_map_1.map
Annotationhalf map A
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_19178_half_map_2.map
Annotationhalf map B
Projections & Slices
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Sample components

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Entire : Supercomplex of NifDK-NifH-FeSII

EntireName: Supercomplex of NifDK-NifH-FeSII
Components
  • Complex: Supercomplex of NifDK-NifH-FeSII
    • Protein or peptide: Nitrogenase molybdenum-iron protein alpha chain
    • Protein or peptide: Nitrogenase molybdenum-iron protein beta chain
    • Protein or peptide: Protein FeSII
    • Protein or peptide: Nitrogenase iron protein 1
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: CALCIUM ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: Supercomplex of NifDK-NifH-FeSII

SupramoleculeName: Supercomplex of NifDK-NifH-FeSII / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Azotobacter vinelandii (bacteria)
Molecular weightTheoretical: 611 KDa

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Macromolecule #1: Nitrogenase molybdenum-iron protein alpha chain

MacromoleculeName: Nitrogenase molybdenum-iron protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Azotobacter vinelandii (bacteria)
Molecular weightTheoretical: 55.363043 KDa
SequenceString: MTGMSREEVE SLIQEVLEVY PEKARKDRNK HLAVNDPAVT QSKKCIISNK KSQPGLMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEVE TLFPLNKGIS VQSECPIGLI G DDIESVSK ...String:
MTGMSREEVE SLIQEVLEVY PEKARKDRNK HLAVNDPAVT QSKKCIISNK KSQPGLMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEVE TLFPLNKGIS VQSECPIGLI G DDIESVSK VKGAELSKTI VPVRCEGFRG VSQSLGHHIA NDAVRDWVLG KRDEDTTFAS TPYDVAIIGD YNIGGDAWSS RI LLEEMGL RCVAQWSGDG SISEIELTPK VKLNLVHCYR SMNYISRHME EKYGIPWMEY NFFGPTKTIE SLRAIAAKFD ESI QKKCEE VIAKYKPEWE AVVAKYRPRL EGKRVMLYIG GLRPRHVIGA YEDLGMEVVG TGYEFAHNDD YDRTMKEMGD STLL YDDVT GYEFEEFVKR IKPDLIGSGI KEKFIFQKMG IPFREMHSWD YSGPYHGFDG FAIFARDMDM TLNNPCWKKL QAPWE ASEG AEKVAASA

UniProtKB: Nitrogenase molybdenum-iron protein alpha chain

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Macromolecule #2: Nitrogenase molybdenum-iron protein beta chain

MacromoleculeName: Nitrogenase molybdenum-iron protein beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Azotobacter vinelandii (bacteria)
Molecular weightTheoretical: 59.535879 KDa
SequenceString: MSQQVDKIKA SYPLFLDQDY KDMLAKKRDG FEEKYPQDKI DEVFQWTTTK EYQELNFQRE ALTVNPAKAC QPLGAVLCAL GFEKTMPYV HGSQGCVAYF RSYFNRHFRE PVSCVSDSMT EDAAVFGGQQ NMKDGLQNCK ATYKPDMIAV STTCMAEVIG D DLNAFINN ...String:
MSQQVDKIKA SYPLFLDQDY KDMLAKKRDG FEEKYPQDKI DEVFQWTTTK EYQELNFQRE ALTVNPAKAC QPLGAVLCAL GFEKTMPYV HGSQGCVAYF RSYFNRHFRE PVSCVSDSMT EDAAVFGGQQ NMKDGLQNCK ATYKPDMIAV STTCMAEVIG D DLNAFINN SKKEGFIPDE FPVPFAHTPS FVGSHVTGWD NMFEGIARYF TLKSMDDKVV GSNKKINIVP GFETYLGNFR VI KRMLSEM GVGYSLLSDP EEVLDTPADG QFRMYAGGTT QEEMKDAPNA LNTVLLQPWH LEKTKKFVEG TWKHEVPKLN IPM GLDWTD EFLMKVSEIS GQPIPASLTK ERGRLVDMMT DSHTWLHGKR FALWGDPDFV MGLVKFLLEL GCEPVHILCH NGNK RWKKA VDAILAASPY GKNATVYIGK DLWHLRSLVF TDKPDFMIGN SYGKFIQRDT LHKGKEFEVP LIRIGFPIFD RHHLH RSTT LGYEGAMQIL TTLVNSILER LDEETRGMQA TDYNHDLVR

UniProtKB: Nitrogenase molybdenum-iron protein beta chain

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Macromolecule #3: Protein FeSII

MacromoleculeName: Protein FeSII / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii (bacteria)
Molecular weightTheoretical: 13.28933 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MATIYFSSPL MPHNKKVQAV AGKRSTLLGV AQENGVKIPF ECQDGNCGSC LVKITHLDGE RIKGMLLTDK ERNVLKSVGK LPKSEEERA AVRDLPPTYR LACQTIVTDE DLLVEFTGEP GGA

UniProtKB: Protein FeSII

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Macromolecule #4: Nitrogenase iron protein 1

MacromoleculeName: Nitrogenase iron protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Azotobacter vinelandii (bacteria)
Molecular weightTheoretical: 31.54824 KDa
SequenceString: MAMRQCAIYG KGGIGKSTTT QNLVAALAEM GKKVMIVGCD PKADSTRLIL HSKAQNTIME MAAEAGTVED LELEDVLKAG YGGVKCVES GGPEPGVGCA GRGVITAINF LEEEGAYEDD LDFVFYDVLG DVVCGGFAMP IRENKAQEIY IVCSGEMMAM Y AANNISKG ...String:
MAMRQCAIYG KGGIGKSTTT QNLVAALAEM GKKVMIVGCD PKADSTRLIL HSKAQNTIME MAAEAGTVED LELEDVLKAG YGGVKCVES GGPEPGVGCA GRGVITAINF LEEEGAYEDD LDFVFYDVLG DVVCGGFAMP IRENKAQEIY IVCSGEMMAM Y AANNISKG IVKYANSGSV RLGGLICNSR NTDREDELII ALANKLGTQM IHFVPRDNVV QRAEIRRMTV IEYDPKAKQA DE YRALARK VVDNKLLVIP NPITMDELEE LLMEFGIMEV EDESIVGKTA EEV

UniProtKB: Nitrogenase iron protein 1

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Macromolecule #5: FE(8)-S(7) CLUSTER

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 5 / Number of copies: 4 / Formula: CLF
Molecular weightTheoretical: 671.215 Da
Chemical component information

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

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Macromolecule #6: 3-HYDROXY-3-CARBOXY-ADIPIC ACID

MacromoleculeName: 3-HYDROXY-3-CARBOXY-ADIPIC ACID / type: ligand / ID: 6 / Number of copies: 4 / Formula: HCA
Molecular weightTheoretical: 206.15 Da
Chemical component information

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

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Macromolecule #7: iron-sulfur-molybdenum cluster with interstitial carbon

MacromoleculeName: iron-sulfur-molybdenum cluster with interstitial carbon
type: ligand / ID: 7 / Number of copies: 4 / Formula: ICS
Molecular weightTheoretical: 787.451 Da
Chemical component information

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

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #9: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 9 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #10: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 10 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 261829
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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