+ Open data
Open data
- Basic information
Basic information
| Entry | Database: EMDB / ID: EMD-12402 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Title | Mycobacterium smegmatis ATP synthase state 2 | |||||||||
|  Map data | Msmeg F1Fo state 2 composite map | |||||||||
|  Sample | 
 | |||||||||
|  Keywords | complex / synthase / HYDROLASE | |||||||||
| Function / homology |  Function and homology information proton motive force-driven plasma membrane ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity ...proton motive force-driven plasma membrane ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
| Biological species |  Mycolicibacterium smegmatis MC2 155 (bacteria) /  Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) /  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
|  Authors | Montgomery MG / Petri J / Spikes TE / Walker JE | |||||||||
| Funding support |  United Kingdom, 2 items 
 | |||||||||
|  Citation |  Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structure of the ATP synthase from provides targets for treating tuberculosis. Authors: Martin G Montgomery / Jessica Petri / Tobias E Spikes / John E Walker /  Abstract: The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from This analysis confirms features in a prior description of the structure of the enzyme, ...The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from This analysis confirms features in a prior description of the structure of the enzyme, but it also describes other highly significant attributes not recognized before that are crucial for understanding the mechanism and regulation of the mycobacterial enzyme. First, we resolved not only the three main states in the catalytic cycle described before but also eight substates that portray structural and mechanistic changes occurring during a 360° catalytic cycle. Second, a mechanism of auto-inhibition of ATP hydrolysis involves not only the engagement of the C-terminal region of an α-subunit in a loop in the γ-subunit, as proposed before, but also a "fail-safe" mechanism involving the b'-subunit in the peripheral stalk that enhances engagement. A third unreported characteristic is that the fused bδ-subunit contains a duplicated domain in its N-terminal region where the two copies of the domain participate in similar modes of attachment of the two of three N-terminal regions of the α-subunits. The auto-inhibitory plus the associated "fail-safe" mechanisms and the modes of attachment of the α-subunits provide targets for development of innovative antitubercular drugs. The structure also provides support for an observation made in the bovine ATP synthase that the transmembrane proton-motive force that provides the energy to drive the rotary mechanism is delivered directly and tangentially to the rotor via a Grotthuss water chain in a polar L-shaped tunnel. | |||||||||
| History | 
 | 
- Structure visualization
Structure visualization
| Movie | 
 
 
  Movie viewer | 
|---|---|
| Structure viewer | EM map:  SurfView  Molmil  Jmol/JSmol | 
| Supplemental images | 
- Downloads & links
Downloads & links
-EMDB archive
| Map data |  emd_12402.map.gz | 8.3 MB |  EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) |  emd-12402-v30.xml  emd-12402.xml | 21.8 KB 21.8 KB | Display Display |  EMDB header | 
| Images |  emd_12402.png | 118.7 KB | ||
| Filedesc metadata |  emd-12402.cif.gz | 7.2 KB | ||
| Archive directory |  http://ftp.pdbj.org/pub/emdb/structures/EMD-12402  ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12402 | HTTPS FTP | 
-Validation report
| Summary document |  emd_12402_validation.pdf.gz | 360 KB | Display |  EMDB validaton report | 
|---|---|---|---|---|
| Full document |  emd_12402_full_validation.pdf.gz | 359.6 KB | Display | |
| Data in XML |  emd_12402_validation.xml.gz | 7.4 KB | Display | |
| Data in CIF |  emd_12402_validation.cif.gz | 8.5 KB | Display | |
| Arichive directory |  https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12402  ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12402 | HTTPS FTP | 
-Related structure data
| Related structure data |  7njpMC  7njkC  7njlC  7njmC  7njnC  7njoC  7njqC  7njrC  7njsC  7njtC  7njuC  7njvC  7njwC  7njxC  7njyC  7nk7C  7nk9C  7nkbC  7nkdC  7nkhC  7nkjC  7nkkC  7nklC  7nknC  7nkpC  7nkqC  7nl9C C: citing same article ( M: atomic model generated by this map | 
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| Similar structure data | 
- Links
Links
| EMDB pages |  EMDB (EBI/PDBe) /  EMDataResource | 
|---|---|
| Related items in Molecule of the Month | 
- Map
Map
| File |  Download / File: emd_12402.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Annotation | Msmeg F1Fo state 2 composite map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
 
 Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density | 
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML: 
 CCP4 map header: 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Supplemental data
- Sample components
Sample components
+Entire : Mycobacterium smegmatis ATP synthase
+Supramolecule #1: Mycobacterium smegmatis ATP synthase
+Macromolecule #1: ATP synthase subunit alpha
+Macromolecule #2: ATP synthase subunit beta
+Macromolecule #3: ATP synthase gamma chain
+Macromolecule #4: ATP synthase epsilon chain
+Macromolecule #5: ATP synthase subunit c
+Macromolecule #6: ATP synthase subunit a
+Macromolecule #7: ATP synthase subunit b
+Macromolecule #8: ATP synthase subunit b-delta
+Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #12: water
-Experimental details
-Structure determination
| Method | cryo EM | 
|---|---|
|  Processing | single particle reconstruction | 
| Aggregation state | particle | 
- Sample preparation
Sample preparation
| Buffer | pH: 8 | 
|---|---|
| Vitrification | Cryogen name: ETHANE | 
- Electron microscopy
Electron microscopy
| Microscope | FEI TITAN KRIOS | 
|---|---|
| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.86 e/Å2 | 
| Electron beam | Acceleration voltage: 300 kV / Electron source:  FIELD EMISSION GUN | 
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD | 
| Experimental equipment |  Model: Titan Krios / Image courtesy: FEI Company | 
- Image processing
Image processing
| Startup model | Type of model: INSILICO MODEL | 
|---|---|
| Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Details: resolution range 2.84-4.07 / Number images used: 17636 | 
| Initial angle assignment | Type: MAXIMUM LIKELIHOOD | 
| Final angle assignment | Type: MAXIMUM LIKELIHOOD | 
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