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- EMDB-22311: Cryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22311 | |||||||||
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Title | Cryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP synthase rotational state 1 | |||||||||
![]() | Locally sharpened map. | |||||||||
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![]() | Bedaquiline / Sirturo / TMC207 / T207910 / ATP synthase / mycobacteria / tuberculosis / TRANSLOCASE | |||||||||
Function / homology | ![]() proton motive force-driven plasma membrane ATP synthesis / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem II / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / membrane => GO:0016020 ...proton motive force-driven plasma membrane ATP synthesis / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem II / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / membrane => GO:0016020 / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Guo H / Courbon GM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline. Authors: Hui Guo / Gautier M Courbon / Stephanie A Bueler / Juntao Mai / Jun Liu / John L Rubinstein / ![]() Abstract: Tuberculosis-the world's leading cause of death by infectious disease-is increasingly resistant to current first-line antibiotics. The bacterium Mycobacterium tuberculosis (which causes tuberculosis) ...Tuberculosis-the world's leading cause of death by infectious disease-is increasingly resistant to current first-line antibiotics. The bacterium Mycobacterium tuberculosis (which causes tuberculosis) can survive low-energy conditions, allowing infections to remain dormant and decreasing their susceptibility to many antibiotics. Bedaquiline was developed in 2005 from a lead compound identified in a phenotypic screen against Mycobacterium smegmatis. This drug can sterilize even latent M. tuberculosis infections and has become a cornerstone of treatment for multidrug-resistant and extensively drug-resistant tuberculosis. Bedaquiline targets the mycobacterial ATP synthase, which is an essential enzyme in the obligate aerobic Mycobacterium genus, but how it binds the intact enzyme is unknown. Here we determined cryo-electron microscopy structures of M. smegmatis ATP synthase alone and in complex with bedaquiline. The drug-free structure suggests that hook-like extensions from the α-subunits prevent the enzyme from running in reverse, inhibiting ATP hydrolysis and preserving energy in hypoxic conditions. Bedaquiline binding induces large conformational changes in the ATP synthase, creating tight binding pockets at the interface of subunits a and c that explain the potency of this drug as an antibiotic for tuberculosis. #1: ![]() Title: Structure of mycobacterial ATP synthase with the TB drug bedaquiline Authors: Guo H / Courbon GM / Bueler SA / Mai J / Liu J / Rubinstein JL | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 57.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 34.1 KB 34.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 105.9 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 7.9 KB | ||
Others | ![]() ![]() ![]() ![]() | 62.6 MB 62.6 MB 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jg5MC ![]() 7jg6C ![]() 7jg7C ![]() 7jg8C ![]() 7jg9C ![]() 7jgaC ![]() 7jgbC ![]() 7jgcC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Locally sharpened map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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-Additional map: Unsharpened map.
File | emd_22311_additional.map | ||||||||||||
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Annotation | Unsharpened map. | ||||||||||||
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-Additional map: Unsharpened map.
File | emd_22311_additional_1.map | ||||||||||||
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Annotation | Unsharpened map. | ||||||||||||
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-Half map: Half map 2.
File | emd_22311_half_map_1.map | ||||||||||||
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Annotation | Half map 2. | ||||||||||||
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Density Histograms |
-Half map: Half map 1.
File | emd_22311_half_map_2.map | ||||||||||||
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Annotation | Half map 1. | ||||||||||||
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Sample components
+Entire : ATP synthase from Mycobacterium smegmatis
+Supramolecule #1: ATP synthase from Mycobacterium smegmatis
+Macromolecule #1: ATP synthase subunit alpha
+Macromolecule #2: ATP synthase subunit alpha,ATP synthase subunit alpha
+Macromolecule #3: ATP synthase subunit beta
+Macromolecule #4: ATP synthase gamma chain
+Macromolecule #5: ATP synthase epsilon chain
+Macromolecule #6: ATP synthase subunit a
+Macromolecule #7: ATP synthase subunit b
+Macromolecule #8: ATP synthase subunit b-delta
+Macromolecule #9: ATP synthase subunit c
+Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: PHOSPHATE ION
+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Homemade / Material: COPPER/RHODIUM / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 7691 / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.3000000000000003 µm / Calibrated defocus min: 0.8 µm / 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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7jg5: |