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Open data
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Basic information
Entry | Database: PDB / ID: 7njn | |||||||||
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Title | Mycobacterium smegmatis ATP synthase state 1d | |||||||||
![]() | (ATP synthase ...) x 8 | |||||||||
![]() | HYDROLASE / complex / synthase | |||||||||
Function / homology | ![]() proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem I / 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 / 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 / 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 / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å | |||||||||
![]() | Montgomery, M.G. / Petri, J. / Spikes, T.E. / Walker, J.E. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12392MC ![]() 7njkC ![]() 7njlC ![]() 7njmC ![]() 7njoC ![]() 7njpC ![]() 7njqC ![]() 7njrC ![]() 7njsC ![]() 7njtC ![]() 7njuC ![]() 7njvC ![]() 7njwC ![]() 7njxC ![]() 7njyC ![]() 7nk7C ![]() 7nk9C ![]() 7nkbC ![]() 7nkdC ![]() 7nkhC ![]() 7nkjC ![]() 7nkkC ![]() 7nklC ![]() 7nknC ![]() 7nkpC ![]() 7nkqC ![]() 7nl9C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-ATP synthase ... , 8 types, 20 molecules ABCDEFGHLMNOPQRSTabd
#1: Protein | Mass: 58951.461 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: atpA, MSMEG_4938, MSMEI_4811 / Production host: ![]() References: UniProt: A0R202, H+-transporting two-sector ATPase #2: Protein | Mass: 51670.453 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: UNIPROT A0R200. The crossref box is missing. Source: (gene. exp.) ![]() Gene: atpD, MSMEG_4936, MSMEI_4809 / Production host: ![]() References: UniProt: A0R200, H+-transporting two-sector ATPase #3: Protein | | Mass: 33439.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: UNIPROT A0R201. The crossref box is missing Source: (gene. exp.) ![]() Gene: atpG, MSMEG_4937, MSMEI_4810 / Production host: ![]() #4: Protein | | Mass: 13277.741 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Uniprot A0R1Z9. The crossref box is missing Source: (gene. exp.) ![]() Gene: atpC, MSMEG_4935, MSMEI_4808 / Production host: ![]() #5: Protein | Mass: 8597.982 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Details: Uniprot A0R205. The cross ref box is missing Source: (gene. exp.) ![]() Gene: atpE, MSMEG_4941 / Production host: ![]() #6: Protein | | Mass: 27568.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Uniprot A0R206. The crossref box is missing Source: (gene. exp.) ![]() Gene: atpB, MSMEG_4942 / Production host: ![]() #7: Protein | | Mass: 19018.170 Da / Num. of mol.: 1 / Mutation: C-ter 10His tag Source method: isolated from a genetically manipulated source Details: Uniprot A0R204. The crossref box is missing. C-ter 10His tag Source: (gene. exp.) ![]() Gene: atpF, MSMEG_4940, MSMEI_4813 / Production host: ![]() #8: Protein | | Mass: 47504.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Uniprot A0R203. The crossref box is missing. Source: (gene. exp.) ![]() Gene: atpFH, atpF, atpH, MSMEG_4939, MSMEI_4812 / Production host: ![]() |
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-Non-polymers , 4 types, 27 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#9: Chemical | ChemComp-ATP / #10: Chemical | ChemComp-MG / #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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 |
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Sample preparation
Component | Name: Mycobacterium smegmatis ATP synthase / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Molecular weight | Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 59.86 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21966 / Details: resolution range is 2.64-3.99 / Symmetry type: POINT |