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Yorodumi- PDB-8dpn: CryoEM structure of Azotobacter vinelandii nitrogenase MoFeP duri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dpn | |||||||||||||||
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Title | CryoEM structure of Azotobacter vinelandii nitrogenase MoFeP during catalytic N2 reduction | |||||||||||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | |||||||||||||||
Keywords | OXIDOREDUCTASE / nitrogenase / MoFeP / nitrogen fixation | |||||||||||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Azotobacter vinelandii DJ (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||||||||
Authors | Rutledge, H.L. / Cook, B. / Tezcan, F.A. / Herzik, M.A. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Science / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dpn.cif.gz | 396.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dpn.ent.gz | 320.7 KB | Display | PDB format |
PDBx/mmJSON format | 8dpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dpn_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8dpn_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8dpn_validation.xml.gz | 68.8 KB | Display | |
Data in CIF | 8dpn_validation.cif.gz | 103.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/8dpn ftp://data.pdbj.org/pub/pdb/validation_reports/dp/8dpn | HTTPS FTP |
-Related structure data
Related structure data | 27639MC 7ut6C 7ut7C 7ut8C 7ut9C 7utaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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) Azotobacter vinelandii DJ (bacteria) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59535.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DGZ8, nitrogenase |
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-Non-polymers , 5 types, 48 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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 |
-Sample preparation
Component | Name: Azotobacter vinelandii nitrogenase MoFeP during catalytic N2 reduction Type: COMPLEX Details: Wild-type MoFeP was purified from the native organism, Azotobacter vinelandii. This map is the structure of free MoFeP from during catalytic N2 reduction. Entity ID: #1-#2 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.29621 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Azotobacter vinelandii DJ (bacteria) | |||||||||||||||
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: 1.4 mg/mL MoFeP 3.6 mg/mL FeP Note that this structure does not contain 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. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 135000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 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 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14903 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 19711170 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29181 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4WZA Accession code: 4WZA / Source name: PDB / Type: experimental model |