+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9338 | |||||||||
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Title | Bacillus PS3 ATP synthase FO region class 3 | |||||||||
Map data | ATP synthase FO region class 3 | |||||||||
Sample |
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Biological species | Bacillus sp. PS3 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Guo H / Rubinstein JL | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9338.map.gz | 116.3 MB | EMDB map data format | |
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Header (meta data) | emd-9338-v30.xml emd-9338.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9338_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_9338.png | 25.7 KB | ||
Masks | emd_9338_msk_1.map | 125 MB | Mask map | |
Others | emd_9338_half_map_1.map.gz emd_9338_half_map_2.map.gz | 98.1 MB 98.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9338 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9338 | HTTPS FTP |
-Validation report
Summary document | emd_9338_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_9338_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_9338_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9338 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9338 | HTTPS FTP |
-Related structure data
Related structure data | 9327C 9333C 9334C 9335C 9336C 9337C 6n2dC 6n2yC 6n2zC 6n30C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9338.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ATP synthase FO region class 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_9338_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: ATP synthase FO region class 3
File | emd_9338_half_map_1.map | ||||||||||||
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Annotation | ATP synthase FO region class 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ATP synthase FO region class 3
File | emd_9338_half_map_2.map | ||||||||||||
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Annotation | ATP synthase FO region class 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacillus PS3 ATP synthase FO region class 3
Entire | Name: Bacillus PS3 ATP synthase FO region class 3 |
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Components |
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-Supramolecule #1: Bacillus PS3 ATP synthase FO region class 3
Supramolecule | Name: Bacillus PS3 ATP synthase FO region class 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9 |
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Source (natural) | Organism: Bacillus sp. PS3 (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 160 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.4 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 60.0 sec. / Average electron dose: 0.71 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 132075 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |