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- PDB-9nsv: CryoEM structure of ancestral nitrogenase MoFe-protein -

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Basic information

Entry
Database: PDB / ID: 9nsv
TitleCryoEM structure of ancestral nitrogenase MoFe-protein
Components(Nitrogenase MoFe-protein ...) x 2
KeywordsOXIDOREDUCTASE / Metalloprotein
Function / homologyFE(8)-S(7) CLUSTER / : / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS
Function and homology information
Biological speciesAzotobacter vinelandii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsShen, Y. / Warmack, R.A.
Funding support United States, 2items
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, R.A.
History
DepositionMar 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)235,05012
Polymers231,6094
Non-polymers3,4418
Water25,1131394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Nitrogenase MoFe-protein ... , 2 types, 4 molecules ACBD

#1: Protein Nitrogenase MoFe-protein alpha chain


Mass: 55733.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ
#2: Protein Nitrogenase MoFe-protein beta chain


Mass: 60071.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ

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Non-polymers , 5 types, 1402 molecules

#3: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1394 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: Nitrogenase MoFe-protein / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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 defocus max: -3000 nm / Nominal defocus min: -800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192110 / Symmetry type: POINT
RefinementHighest resolution: 2.19 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316521
ELECTRON MICROSCOPYf_angle_d0.50122437
ELECTRON MICROSCOPYf_dihedral_angle_d6.0612300
ELECTRON MICROSCOPYf_chiral_restr0.0422348
ELECTRON MICROSCOPYf_plane_restr0.0042884

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