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- PDB-8dbx: CryoEM structure of partially oxidized MoFe-protein on ultrathin ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dbx | ||||||||||||
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Title | CryoEM structure of partially oxidized MoFe-protein on ultrathin carbon | ||||||||||||
![]() | (Nitrogenase molybdenum-iron protein ...) x 2 | ||||||||||||
![]() | METAL BINDING PROTEIN / OXIDOREDUCTASE / Nitrogenase / metalloenzyme | ||||||||||||
Function / homology | ![]() molybdenum-iron nitrogenase complex / 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: 1.92 Å | ||||||||||||
![]() | Warmack, R.A. / Rees, D.C. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural consequences of turnover-induced homocitrate loss in nitrogenase. Authors: Rebeccah A Warmack / Ailiena O Maggiolo / Andres Orta / Belinda B Wenke / James B Howard / Douglas C Rees / ![]() Abstract: Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation that is essential for sustaining life. The active site FeMo-cofactor ...Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation that is essential for sustaining life. The active site FeMo-cofactor contains a [7Fe:1Mo:9S:1C] metallocluster coordinated with an R-homocitrate (HCA) molecule. Here, we establish through single particle cryoEM and chemical analysis of two forms of the Azotobacter vinelandii MoFe-protein - a high pH turnover inactivated species and a ∆NifV variant that cannot synthesize HCA - that loss of HCA is coupled to α-subunit domain and FeMo-cofactor disordering, and formation of a histidine coordination site. We further find a population of the ∆NifV variant complexed to an endogenous protein identified through structural and proteomic approaches as the uncharacterized protein NafT. Recognition by endogenous NafT demonstrates the physiological relevance of the HCA-compromised form, perhaps for cofactor insertion or repair. Our results point towards a dynamic active site in which HCA plays a role in enabling nitrogenase catalysis by facilitating activation of the FeMo-cofactor from a relatively stable form to a state capable of reducing dinitrogen under ambient conditions. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 421.4 KB | Display | ![]() |
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PDB format | ![]() | 338.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 77.4 KB | Display | |
Data in CIF | ![]() | 120 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27316MC ![]() 8crsC ![]() 8enlC ![]() 8enmC ![]() 8ennC ![]() 8enoC 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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-Non-polymers , 6 types, 924 molecules ![](data/chem/img/ICS.gif)
![](data/chem/img/HCA.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/1CL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HCA.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/1CL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: Heterotetrameric nitrogenase MoFe-protein / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
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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 defocus max: -3000 nm / Nominal defocus min: -800 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219537 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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