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- PDB-8pbb: CHAPSO treated partial catalytic component (comprising only AnfD ... -

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Basic information

Entry
Database: PDB / ID: 8pbb
TitleCHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus
Components
  • Nitrogenase iron-iron protein, beta subunit
  • Nitrogenase protein alpha chain
KeywordsOXIDOREDUCTASE / nitrogen fixation / Fe nitrogenase
Function / homology
Function and homology information


nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase iron-iron protein, alpha chain / Nitrogenase iron-iron, beta subunit / Nitrogenase alpha 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 / Nitrogenase protein alpha chain / Nitrogenase iron-iron protein, beta subunit
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 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
DepositionJun 9, 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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, beta subunit
C: Nitrogenase protein alpha chain
D: Nitrogenase iron-iron protein, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,3376
Polymers221,9954
Non-polymers1,3422
Water00
1


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

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Components

#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
#2: 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
#3: 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
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: CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Source (recombinant)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Buffer solutionpH: 7.8
Details: 37.5 mM TRIS (pH = 7.8) 150 mM NaCl 3.75 mM sodium dithionite 0.4 % (m/V) CHAPSO
SpecimenConc.: 0.75 mg/ml / Embedding 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-PROPANE / Humidity: 90 % / Chamber temperature: 281 K

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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 FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm
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
12cryoSPARC4.1.13D reconstruction
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7962489
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 927406 / Num. of class averages: 7 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00613632
ELECTRON MICROSCOPYf_angle_d0.72518450
ELECTRON MICROSCOPYf_dihedral_angle_d16.1615019
ELECTRON MICROSCOPYf_chiral_restr0.0512038
ELECTRON MICROSCOPYf_plane_restr0.0082356

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