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- EMDB-49753: CryoEM structure of ancestral nitrogenase MoFe-protein -

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Basic information

Entry
Database: EMDB / ID: EMD-49753
TitleCryoEM structure of ancestral nitrogenase MoFe-protein
Map data
Sample
  • Complex: Nitrogenase MoFe-protein
    • Protein or peptide: Nitrogenase MoFe-protein alpha chain
    • Protein or peptide: Nitrogenase MoFe-protein beta chain
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: FE (III) ION
  • Ligand: water
KeywordsMetalloprotein / OXIDOREDUCTASE
Biological speciesAzotobacter vinelandii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsShen Y / Warmack RA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143836 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152765 United States
CitationJournal: To Be Published
Title: CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes
Authors: Warmack RA
History
DepositionMar 17, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49753.png

Downloads & links

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Map

FileDownload / File: emd_49753.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 576 pix.
= 374.4 Å		0.65 Å/pix.
x 576 pix.
= 374.4 Å		0.65 Å/pix.
x 576 pix.
= 374.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.595
Minimum - Maximum-2.1293294 - 3.4486768
Average (Standard dev.)-0.000021175543 (±0.057623442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49753_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49753_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 : Nitrogenase MoFe-protein

EntireName: Nitrogenase MoFe-protein
Components
  • Complex: Nitrogenase MoFe-protein
    • Protein or peptide: Nitrogenase MoFe-protein alpha chain
    • Protein or peptide: Nitrogenase MoFe-protein beta chain
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: FE (III) ION
  • Ligand: water

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Supramolecule #1: Nitrogenase MoFe-protein

SupramoleculeName: Nitrogenase MoFe-protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ

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Macromolecule #1: Nitrogenase MoFe-protein alpha chain

MacromoleculeName: Nitrogenase MoFe-protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 55.73318 KDa
SequenceString: MTGMSRDEVE SLIQEVLEVY PEKAKKNREK HLSPNDPELE QSKKCITSNK KSLPGVMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEIE TLFPLNKGIS VQSECPIGLI G DDIEAVSK ...String:
MTGMSRDEVE SLIQEVLEVY PEKAKKNREK HLSPNDPELE QSKKCITSNK KSLPGVMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEIE TLFPLNKGIS VQSECPIGLI G DDIEAVSK QKGKEHGKTI VPVRCEGFRG VSQSLGHHIA NDAVRDWVLS ARDDDDSFET TDYDVAIIGD YNIGGDAWSS RI LLEEMGL RVVAQWSGDG TISEMELTPK VKLNLVHCYR SMNYISRHME EKYGIPWMEY NFFGPTKTIE SLRKIAAQFD ESI QKKCEE VIAKYQPEWE AVVAKYRPRL EGKRVMLYVG GLRPRHVIGA YEDLGMEVVG TGYEFGHNDD YDRTLKEMGD STLL YDDVT GYEFEEFVKK VKPDLIGSGI KEKYIFQKMG IPFRQMHSWD YSGPYHGFDG FAIFARDMDM TLNNPCWKKL QAPWK KSEQ ADEAVAASA

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Macromolecule #2: Nitrogenase MoFe-protein beta chain

MacromoleculeName: Nitrogenase MoFe-protein beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 60.071207 KDa
SequenceString: MSQQVDNIKP SYPLFRDQDY KDMLAKKRDN FEEKHPQEKI DEVFQWTTTE EYQELNFQRE ALTVNPAKAC QPLGAVLCSL GFEKTMPYV HGSQGCVAYF RTYFNRHFKE PISCVSDSMT EDAAVFGGQQ NMKDGLQNCK AIYKPDMIAV STTCMAEVIG D DLNAFINN ...String:
MSQQVDNIKP SYPLFRDQDY KDMLAKKRDN FEEKHPQEKI DEVFQWTTTE EYQELNFQRE ALTVNPAKAC QPLGAVLCSL GFEKTMPYV HGSQGCVAYF RTYFNRHFKE PISCVSDSMT EDAAVFGGQQ NMKDGLQNCK AIYKPDMIAV STTCMAEVIG D DLNAFINN SKKEGHIPDE FPVPFAHTPS FVGSHVTGWD NMFEGIARYF TLNYMEDKEV GSNGKINIVP GFETYLGNFR VI KRMMNEM NVDYTLLSDP EEVLDTPADG QFRMYAGGTT QDEMKDAPNA LNTLMLQPWQ LTKTTKFVKN TWKHEVPKLN IPM GLDWTD EFLMKVSEIS GQPIPESLAK ERGRLVDMMT DSHTWLHGKK FALWGDPDFV MGMTKFLLEL GCEPIHILCN NANK RWKKA MDAILAESPY GANSEVHIGK DLWHMRSLVF TNKPDFMIGN SYGKFIQRDT LYKGKEFEVP LIRIGFPIFD RHHLH RQTT LGYEGAMQIL TTLVNSVLER LDEETRGMQT TDYNYDLVR

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Macromolecule #3: iron-sulfur-molybdenum cluster with interstitial carbon

MacromoleculeName: iron-sulfur-molybdenum cluster with interstitial carbon
type: ligand / ID: 3 / 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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Macromolecule #4: 3-HYDROXY-3-CARBOXY-ADIPIC ACID

MacromoleculeName: 3-HYDROXY-3-CARBOXY-ADIPIC ACID / type: ligand / ID: 4 / 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 #5: FE(8)-S(7) CLUSTER

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 5 / 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 #6: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 1394 / 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

BufferpH: 7.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: -3.0 µm / Nominal defocus min: -0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192110
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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