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Open data
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Basic information
Entry | Database: PDB / ID: 8f29 | ||||||
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Title | Yeast ATP synthase in conformation-1 at pH 6 | ||||||
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![]() | MEMBRANE PROTEIN / F-type ATP synthase / yeast / mitochondrial | ||||||
Function / homology | ![]() : / cristae formation / : / : / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / : ...: / cristae formation / : / : / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / : / mitochondrial nucleoid / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial intermembrane space / ADP binding / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
![]() | Sharma, S. / Patel, H. / Luo, M. / Mueller, D.M. / Liao, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational ensemble of yeast ATP synthase at low pH reveals unique intermediates and plasticity in F-F coupling. Authors: Stuti Sharma / Min Luo / Hiral Patel / David M Mueller / Maofu Liao / ![]() ![]() ![]() Abstract: Mitochondrial adenosine triphosphate (ATP) synthase uses the proton gradient across the inner mitochondrial membrane to synthesize ATP. Structural and single molecule studies conducted mostly at ...Mitochondrial adenosine triphosphate (ATP) synthase uses the proton gradient across the inner mitochondrial membrane to synthesize ATP. Structural and single molecule studies conducted mostly at neutral or basic pH have provided details of the reaction mechanism of ATP synthesis. However, pH of the mitochondrial matrix is slightly acidic during hypoxia and pH-dependent conformational changes in the ATP synthase have been reported. Here we use single-particle cryo-EM to analyze the conformational ensemble of the yeast (Saccharomyces cerevisiae) ATP synthase at pH 6. Of the four conformations resolved in this study, three are reaction intermediates. In addition to canonical catalytic dwell and binding dwell structures, we identify two unique conformations with nearly identical positions of the central rotor but different catalytic site conformations. These structures provide new insights into the catalytic mechanism of the ATP synthase and highlight elastic coupling between the catalytic and proton translocating domains. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 848.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 28809MC ![]() 8f39C ![]() 8fkjC ![]() 8fl8C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-ATP synthase subunit ... , 13 types, 26 molecules YGHIZ76USTKLMNOPQRXJABCDEF
#1: Protein | Mass: 20199.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
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#2: Protein | Mass: 28984.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
#3: Protein | Mass: 14080.876 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
#4: Protein | Mass: 6388.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
#5: Protein | Mass: 17561.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
#6: Protein | Mass: 19509.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
#7: Protein | Mass: 10090.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
#8: Protein | Mass: 9383.837 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
#9: Protein | Mass: 7663.243 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | | Mass: 25073.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein/peptide | | Mass: 4145.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 54748.148 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 50752.641 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P00830, H+-transporting two-sector ATPase |
-Protein/peptide , 1 types, 1 molecules 8
#10: Protein/peptide | Mass: 5046.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 3 types, 11 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
#15: Chemical | ChemComp-ADP / #16: Chemical | ChemComp-MG / #17: Chemical | ChemComp-PO4 / | |
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-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 |
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Sample preparation
Component | Name: ATP synthase / Type: COMPLEX / Entity ID: #2-#12, #1, #13-#14 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 6 |
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 / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146826 / Symmetry type: POINT | ||||||||||||||||||||||||
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