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- PDB-8pbb: CHAPSO treated partial catalytic component (comprising only AnfD ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pbb | |||||||||
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Title | CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus | |||||||||
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![]() | OXIDOREDUCTASE / nitrogen fixation / Fe nitrogenase | |||||||||
Function / homology | ![]() nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||
![]() | Schmidt, F.V. / Schulz, L. / Zarzycki, J. / Prinz, S. / Erb, T.J. / Rebelein, J.G. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 303.2 KB | Display | ![]() |
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PDB format | ![]() | 241.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 17583MC ![]() 8oieC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 60221.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: anfD / Production host: ![]() #2: Protein | Mass: 50776.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: anfK, RCAP_rcc00588 / Production host: ![]() #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 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 |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.8 Details: 37.5 mM TRIS (pH = 7.8) 150 mM NaCl 3.75 mM sodium dithionite 0.4 % (m/V) CHAPSO |
Specimen | Conc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 7962489 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 927406 / Num. of class averages: 7 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
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