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- PDB-11zk: Cryo-EM structure of NifI free Nitrogenase MoFe protein from Meth... -

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Basic information

Entry
Database: PDB / ID: 11zk
TitleCryo-EM structure of NifI free Nitrogenase MoFe protein from Methanosarcina acetivorans
Components
  • Nitrogenase molybdenum-iron protein beta chain
  • Nitrogenase protein alpha chain
KeywordsOXIDOREDUCTASE / Metalloproteins / Nitrogenase / 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
FE(8)-S(7) CLUSTER / Chem-ICS / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase protein alpha chain
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsKashyap, R. / Antony, E.
Funding support United States, 1items
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 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Nitrogenase protein alpha chain
A: Nitrogenase protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
D: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,1846
Polymers224,7264
Non-polymers1,4592
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Nitrogenase protein alpha chain


Mass: 62884.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: nifD, MA_3898 / Production host: Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJ90, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase


Mass: 49478.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJ89, nitrogenase
#3: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Trimeric complex of MoFe protein bound to NifI inhibitor complex
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 0.01 mm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
9PHENIX2.0-5936model refinement
13cryoSPARC4.7.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 591856 / Symmetry type: POINT
Atomic model buildingPDB-ID: 9P1X

9p1x


Accession code: 9P1X / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.02 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048989
ELECTRON MICROSCOPYf_angle_d0.71612189
ELECTRON MICROSCOPYf_dihedral_angle_d8.5831268
ELECTRON MICROSCOPYf_chiral_restr0.051369
ELECTRON MICROSCOPYf_plane_restr0.0051552

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