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- PDB-8oie: Iron Nitrogenase Complex from Rhodobacter capsulatus -

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Basic information

Entry
Database: PDB / ID: 8oie
TitleIron Nitrogenase Complex from Rhodobacter capsulatus
Components
  • (Nitrogenase iron-iron ...) x 2
  • Nitrogenase iron protein
  • Nitrogenase protein alpha chain
KeywordsOXIDOREDUCTASE / nitrogen fixation / Fe nitrogenase
Function / homology
Function and homology information


nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / iron ion binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase iron-iron, delta subunit / Nitrogenase iron-iron protein, alpha chain / Nitrogenase iron-iron, beta subunit / Vanadium/alternative nitrogenase delta subunit / Vanadium/alternative nitrogenase delta subunit / Nitrogenase alpha chain / Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family ...Nitrogenase iron-iron, delta subunit / Nitrogenase iron-iron protein, alpha chain / Nitrogenase iron-iron, beta subunit / Vanadium/alternative nitrogenase delta subunit / Vanadium/alternative nitrogenase delta subunit / Nitrogenase 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 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / FE(8)-S(7) CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / FeFe cofactor / IRON/SULFUR CLUSTER / Nitrogenase iron protein / Nitrogenase protein alpha chain / Nitrogenase iron-iron protein delta chain / Nitrogenase iron-iron protein, beta subunit
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsSchmidt, F.V. / Schulz, L. / Zarzycki, J. / Prinz, S. / Erb, T.J. / Rebelein, J.G.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)446841743 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural insights into the iron nitrogenase complex.
Authors: Frederik V Schmidt / Luca Schulz / Jan Zarzycki / Simone Prinz / Niels N Oehlmann / Tobias J Erb / Johannes G Rebelein /
Abstract: Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO) and carbon monoxide ...Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the three nitrogenase isozymes, the iron nitrogenase has the highest wild-type activity for the reduction of CO, but the molecular architecture facilitating these activities has remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the ADP·AlF-stabilized iron nitrogenase complex from Rhodobacter capsulatus, revealing an [FeSC-(R)-homocitrate] cluster in the active site. The enzyme complex suggests that the iron nitrogenase G subunit is involved in cluster stabilization and substrate channeling and confers specificity between nitrogenase reductase and catalytic component proteins. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intrasubunit 'communication' and thus the nitrogenase mechanism.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogenase protein alpha chain
B: Nitrogenase iron-iron protein delta chain
C: Nitrogenase iron-iron protein, beta subunit
D: Nitrogenase iron protein
E: Nitrogenase iron protein
F: Nitrogenase protein alpha chain
G: Nitrogenase iron-iron protein delta chain
H: Nitrogenase iron-iron protein, beta subunit
I: Nitrogenase iron protein
J: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,76930
Polymers369,67410
Non-polymers6,09520
Water8,377465
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 6 molecules AFDEIJ

#1: Protein Nitrogenase protein alpha chain /


Mass: 60221.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria)
Gene: anfD / Production host: Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ANJ7
#4: Protein
Nitrogenase iron protein / Nitrogenase Fe protein / Nitrogenase component II / Nitrogenase reductase


Mass: 30212.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria)
Gene: anfH, nifH, RCAP_rcc00585 / Production host: Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ANJ6, nitrogenase

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Nitrogenase iron-iron ... , 2 types, 4 molecules BGCH

#2: Protein Nitrogenase iron-iron protein delta chain / Nitrogenase component I


Mass: 13414.546 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria)
Gene: anfG, RCAP_rcc00587 / Production host: Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ANJ8, nitrogenase
#3: Protein Nitrogenase iron-iron protein, beta subunit


Mass: 50776.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria)
Gene: anfK, RCAP_rcc00588 / Production host: Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ANJ9, nitrogenase

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Non-polymers , 8 types, 485 molecules

#5: Chemical ChemComp-S5Q / FeFe cofactor


Mass: 747.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe8S9 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF3
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Iron Nitrogenase Complex from Rhodobacter capsulatus / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.36 MDa / Experimental value: YES
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Source (recombinant)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Buffer solutionpH: 7.8
Details: 50 mM TRIS (pH = 7.8) 200 mM NaCl 5 mM sodium dithionite
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
4cryoSPARC4.1.1CTF correction
9cryoSPARC4.1.1initial Euler assignment
10cryoSPARC4.1.1final Euler assignment
11cryoSPARC4.1.1classification
12cryoSPARC3D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3014316
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218653 / Symmetry type: POINT

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