+Open data
-Basic information
Entry | Database: PDB / ID: 6n2d | |||||||||
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Title | Bacillus PS3 ATP synthase membrane region | |||||||||
Components |
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Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bacillus sp. PS3 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Guo, H. / Rubinstein, J.L. | |||||||||
Funding support | Canada, Japan, 2items
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Citation | Journal: Elife / Year: 2019 Title: Structure of a bacterial ATP synthase. Authors: Hui Guo / Toshiharu Suzuki / John L Rubinstein / Abstract: ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest ...ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest form of the enzyme and because of the relative ease of genetic manipulation of these complexes. We expressed the PS3 ATP synthase in , purified it, and imaged it by cryo-EM, allowing us to build atomic models of the complex in three rotational states. The position of subunit shows how it is able to inhibit ATP hydrolysis while allowing ATP synthesis. The architecture of the membrane region shows how the simple bacterial ATP synthase is able to perform the same core functions as the equivalent, but more complicated, mitochondrial complex. The structures reveal the path of transmembrane proton translocation and provide a model for understanding decades of biochemical analysis interrogating the roles of specific residues in the enzyme. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6n2d.cif.gz | 167.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n2d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6n2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n2d_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6n2d_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6n2d_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 6n2d_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/6n2d ftp://data.pdbj.org/pub/pdb/validation_reports/n2/6n2d | HTTPS FTP |
-Related structure data
Related structure data | 9327MC 9333C 9334C 9335C 9336C 9337C 9338C 6n2yC 6n2zC 6n30C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 19249.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Strain: PS3 / Gene: atpF / Production host: Escherichia coli (E. coli) #2: Protein | | Mass: 26449.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Strain: PS3 / Gene: atpB / Production host: Escherichia coli (E. coli) #3: Protein | Mass: 7337.780 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Strain: PS3 / Gene: atpE, uncE / Production host: Escherichia coli (E. coli) / References: UniProt: P00845 |
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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: Membrane-embedded region of Bacillus PS3 ATP synthase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 110 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Bacillus sp. PS3 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 4 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 132075 X / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 60 sec. / Electron dose: 0.71 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
Image scans | Width: 4096 / Height: 4096 |
-Processing
Software | Name: PHENIX / Version: (1.13_2998: phenix.real_space_refine) / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1238140 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 895574 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 91.12 / Protocol: AB INITIO MODEL / Space: REAL |