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- EMDB-76025: Cryo-EM structure of trimeric Nitrogenase MoFe protein from Metha... -

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Basic information

Entry
Database: EMDB / ID: EMD-76025
TitleCryo-EM structure of trimeric Nitrogenase MoFe protein from Methanosarcina acetivorans
Map data
Sample
  • Complex: Trimeric complex of MoFe protein bound to NifI inhibitor complex
    • Protein or peptide: Nitrogenase protein alpha chain
    • Protein or peptide: Nitrogenase molybdenum-iron protein beta chain
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: FE(8)-S(7) CLUSTER
KeywordsMetalloproteins / Nitrogenase / Oxidoreductase / Methanogen / cryo-EM
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / iron-sulfur cluster binding / metal ion binding / ATP binding
Similarity search - Function
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 molybdenum-iron protein beta chain / Nitrogenase protein alpha chain
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKashyap R / Antony E
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020965 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of trimeric Nitrogenase MoFe protein from Methanosarcina acetivorans
Authors: Kashyap R / Antony E
History
DepositionMar 11, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76025.png

Downloads & links

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Map

FileDownload / File: emd_76025.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 278.4 Å		0.93 Å/pix.
x 300 pix.
= 278.4 Å		0.93 Å/pix.
x 300 pix.
= 278.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.928 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00418
Minimum - Maximum-0.0016945726 - 2.247068
Average (Standard dev.)0.0010411227 (±0.02323185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 278.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_76025_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_76025_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 : Trimeric complex of MoFe protein bound to NifI inhibitor complex

EntireName: Trimeric complex of MoFe protein bound to NifI inhibitor complex
Components
  • Complex: Trimeric complex of MoFe protein bound to NifI inhibitor complex
    • Protein or peptide: Nitrogenase protein alpha chain
    • Protein or peptide: Nitrogenase molybdenum-iron protein beta chain
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: FE(8)-S(7) CLUSTER

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Supramolecule #1: Trimeric complex of MoFe protein bound to NifI inhibitor complex

SupramoleculeName: Trimeric complex of MoFe protein bound to NifI inhibitor complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methanosarcina acetivorans (archaea)

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Macromolecule #1: Nitrogenase protein alpha chain

MacromoleculeName: Nitrogenase protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 62.884285 KDa
SequenceString: MWSHPQFEKG GGSGGGSGGG SWSHPQFEKS GMGAEIEDKQ LIVDNILKVL PEKAARDRRK HIVVRDCAAE QHIEADDKVI PGILTNRGC AFAGTKGVVF GPIKDMVHLV HGPIGCAYFT WGTRRNLAKA EEGEDNYMNY SVCTDMKETD IVFGGEKKLK K AIDEVVKI ...String:
MWSHPQFEKG GGSGGGSGGG SWSHPQFEKS GMGAEIEDKQ LIVDNILKVL PEKAARDRRK HIVVRDCAAE QHIEADDKVI PGILTNRGC AFAGTKGVVF GPIKDMVHLV HGPIGCAYFT WGTRRNLAKA EEGEDNYMNY SVCTDMKETD IVFGGEKKLK K AIDEVVKI FNPGAITICA TCPVGLIGDD IESVAREAEE EHGIKVIPAR CEGYRGVSQS AGHHIASNSL MEHLIGTEDI KD PTPFDIN IFGEYNIGGD LWEIKPILEK IGYRIISSLT GDGSFHKISQ AHQAKLSILL CHRSINYTNR MMEEKYGVPW LKV NYIGTK GTEKSLRKMA EFFDDPELTR KTEEVIAEEK AKYADEIERY REKLQGKTAF IYAGGSRSHH YINLFEELGM KVVV AGYQF AHRDDYEGRQ IIPHIKEKAL GSILEDVHYE REENFKPSIN AERITELKEK IGLMDYEGLF PEMKDGTIVV DDLNH HETE FLVKALKPDI FCSGIKDKYW AQKIGVPSRQ IHSYDYSGRY TGFSGVLNFA RDIDMAIHSP TWRFINPPWK GEGAE

UniProtKB: Nitrogenase 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: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 49.478605 KDa
SequenceString: MLDYTPCEEV ERSAITINPA KICQPIGAVY AALGVHNCMP HSHGSQGCLS YLRMCLSRHY REAALATTSS FSEGTAVFGG AANLKEALV NLTTVYQPEV IAIHTTCVAE TIGDDVGVIL EDVSAEELID PSIKICAAST PSYVGTHITG YDNMVKSFVT T FASKSKPN ...String:
MLDYTPCEEV ERSAITINPA KICQPIGAVY AALGVHNCMP HSHGSQGCLS YLRMCLSRHY REAALATTSS FSEGTAVFGG AANLKEALV NLTTVYQPEV IAIHTTCVAE TIGDDVGVIL EDVSAEELID PSIKICAAST PSYVGTHITG YDNMVKSFVT T FASKSKPN GKLNIIPGFV EPADIREIKR ILSIMGISSI VFPDTTDVFD APLTKEHTFY PKGGTPIGDI EDSANSLGTI AL CRMAGGA AAKILESRYK VPAKIGPTPI GIRNTDRFIM NAAKLANVAI PPELEDERGR LVDMMTDAHP HYHGKKVAIY GDP DILSGL TSLVLEMGME PSVVLTGTQN SEFEKEIEAL IGSEYPDADI ISGGDLFMLH QIIKRKPVDL LIGNTYGKFI SRAE DVPLV RVGFPIMDRA NLHYFPIMGY AGAARLVERI GNTLLDRKDR DAPDWLLETI Q

UniProtKB: Nitrogenase molybdenum-iron protein beta chain

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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: 1 / 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: FE(8)-S(7) CLUSTER

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 4 / Number of copies: 1 / Formula: CLF
Molecular weightTheoretical: 671.215 Da
Chemical component information

ChemComp-CLF:
FE(8)-S(7) 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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 150000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 135383
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9p1x


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-11sx:
Cryo-EM structure of trimeric Nitrogenase MoFe protein from Methanosarcina acetivorans

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