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- PDB-7uta: CryoEM structure of Azotobacter vinelandii nitrogenase complex (2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uta | |||||||||||||||
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Title | CryoEM structure of Azotobacter vinelandii nitrogenase complex (2:1 FeP:MoFeP) inhibited by BeFx during catalytic N2 reduction | |||||||||||||||
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![]() | OXIDOREDUCTASE / nitrogenase / MoFeP / nitrogen fixation | |||||||||||||||
Function / homology | ![]() molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||||||||
![]() | Rutledge, H.L. / Cook, B.D. / Nguyen, H.P.M. / Tezcan, F.A. / Herzik, M.A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the nitrogenase complex prepared under catalytic turnover conditions. Authors: Hannah L Rutledge / Brian D Cook / Hoang P M Nguyen / Mark A Herzik / F Akif Tezcan / ![]() Abstract: The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multielectron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ...The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multielectron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ATP-dependent energy transduction and dinitrogen reduction by nitrogenase are not well understood, requiring new strategies to monitor its structural dynamics during catalytic action. Here, we report cryo-electron microscopy structures of the nitrogenase complex prepared under enzymatic turnover conditions. We observe that asymmetry governs all aspects of the nitrogenase mechanism, including ATP hydrolysis, protein-protein interactions, and catalysis. Conformational changes near the catalytic iron-molybdenum cofactor are correlated with the nucleotide-hydrolysis state of the enzyme. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 599.8 KB | Display | ![]() |
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PDB format | ![]() | 486.6 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 | ![]() 26764MC ![]() 7ut6C ![]() 7ut7C ![]() 7ut8C ![]() 7ut9C ![]() 8dpnC M: map data used to model this data C: citing same article ( |
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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
-Nitrogenase molybdenum-iron protein ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 55363.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 59535.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein , 1 types, 4 molecules EFGH
#3: Protein | Mass: 31548.240 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 9 types, 77 molecules ![](data/chem/img/HCA.gif)
![](data/chem/img/ICS.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/0BE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ICS.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/0BE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-MG / #10: Chemical | ChemComp-ADP / #11: Chemical | ChemComp-0BE / #12: Water | ChemComp-HOH / | |
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-Details
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: BeFx inhibited Azotobacter vinelandii nitrogenase complex. Inhibition occurred during catalytic N2 reduction Type: COMPLEX Details: Wild-type MoFeP and FeP were purified from the native organism, Azotobacter vinelandii Entity ID: #1-#3 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.35921 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 8 Details: Solutions were prepared and filtered immediately prior to the experiment. | |||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 1.44 mg/mL MoFeP 3.6 mg/mL FeP | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K / Details: Custom manual plunger. Greater than 95% humidity. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 123 K / Temperature (min): 93 K |
Image recording | Electron dose: 65 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 8083 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2628629 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72125 / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4WZA Accession code: 4WZA / Source name: PDB / Type: experimental model |