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Yorodumi- PDB-8g08: Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g08 | ||||||
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Title | Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synthase rotational state 1 (backbone model) | ||||||
Components | (ATP synthase ...) x 8 | ||||||
Keywords | TRANSLOCASE/INHIBITOR / ATP synthase / mycobacterial / inhibitor / tuberculosis / antibiotic / HYDROLASE / TRANSLOCASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, catalytic core F(1) / photosynthetic electron transport in photosystem II / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity ...proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, catalytic core F(1) / photosynthetic electron transport in photosystem II / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / 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) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Courbon, G.M. / Rubinstein, J.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: EMBO J / Year: 2023 Title: Mechanism of mycobacterial ATP synthase inhibition by squaramides and second generation diarylquinolines. Authors: Gautier M Courbon / Paul R Palme / Lea Mann / Adrian Richter / Peter Imming / John L Rubinstein / Abstract: Mycobacteria, such as Mycobacterium tuberculosis, depend on the activity of adenosine triphosphate (ATP) synthase for growth. The diarylquinoline bedaquiline (BDQ), a mycobacterial ATP synthase ...Mycobacteria, such as Mycobacterium tuberculosis, depend on the activity of adenosine triphosphate (ATP) synthase for growth. The diarylquinoline bedaquiline (BDQ), a mycobacterial ATP synthase inhibitor, is an important medication for treatment of drug-resistant tuberculosis but suffers from off-target effects and is susceptible to resistance mutations. Consequently, both new and improved mycobacterial ATP synthase inhibitors are needed. We used electron cryomicroscopy and biochemical assays to study the interaction of Mycobacterium smegmatis ATP synthase with the second generation diarylquinoline TBAJ-876 and the squaramide inhibitor SQ31f. The aryl groups of TBAJ-876 improve binding compared with BDQ, while SQ31f, which blocks ATP synthesis ~10 times more potently than ATP hydrolysis, binds a previously unknown site in the enzyme's proton-conducting channel. Remarkably, BDQ, TBAJ-876, and SQ31f all induce similar conformational changes in ATP synthase, suggesting that the resulting conformation is particularly suited for drug binding. Further, high concentrations of the diarylquinolines uncouple the transmembrane proton motive force while for SQ31f they do not, which may explain why high concentrations of diarylquinolines, but not SQ31f, have been reported to kill mycobacteria. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g08.cif.gz | 589.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g08.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8g08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g08_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8g08_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8g08_validation.xml.gz | 101 KB | Display | |
Data in CIF | 8g08_validation.cif.gz | 173.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/8g08 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g08 | HTTPS FTP |
-Related structure data
Related structure data | 29649MC 8g07C 8g09C 8g0aC 8g0bC 8g0cC 8g0dC 8g0eC 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
-ATP synthase ... , 8 types, 20 molecules 978123456BCAEFDGHbda
#1: Protein | Mass: 8597.982 Da / Num. of mol.: 9 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R205 #2: Protein | Mass: 58951.461 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R202, H+-transporting two-sector ATPase #3: Protein | Mass: 51670.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R200, H+-transporting two-sector ATPase #4: Protein | | Mass: 33439.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R201 #5: Protein | | Mass: 13277.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R1Z9 #6: Protein | | Mass: 17636.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R204 #7: Protein | | Mass: 47504.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R203 #8: Protein | | Mass: 27568.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R206 |
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-Non-polymers , 4 types, 10 molecules
#9: Chemical | ChemComp-SQC / | ||||
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#10: Chemical | ChemComp-ATP / #11: Chemical | ChemComp-MG / #12: Chemical | ChemComp-PO4 / | |
-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: SQ31f-bound Mycobacterium smegmatis ATP synthase rotational state 1 Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 defocus max: 2000 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101399 / Symmetry type: POINT |