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Open data
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Basic information
Entry | Database: PDB / ID: 8fkj | ||||||
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Title | Yeast ATP Synthase in conformation-3, at pH 6 | ||||||
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Function / homology | ![]() cristae formation / mitochondrial proton-transporting ATP synthase, central stalk / Formation of ATP by chemiosmotic coupling / Cristae formation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]() | 677.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 29250MC ![]() 8f29C ![]() 8f39C ![]() 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 ... , 12 types, 25 molecules YABCDEFRSTKLMNOPQZ76UXGHI
#1: Protein | ![]() Mass: 17826.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() | ||||||||||||||||||||
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#2: Protein | ![]() Mass: 54748.148 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #3: Protein | ![]() Mass: 50752.641 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #4: Protein | ![]() Mass: 7532.048 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #5: Protein | | ![]() Mass: 17575.994 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) ![]() ![]() ![]() #10: Protein | | ![]() Mass: 25073.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #12: Protein | | ![]() Mass: 29898.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #13: Protein | | ![]() Mass: 14080.876 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #14: Protein | | ![]() Mass: 6388.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Protein/peptide , 2 types, 2 molecules 8J
#9: Protein/peptide | ![]() Mass: 5046.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#11: Protein/peptide | Mass: 4145.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: ATP Synthase![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
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: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction![]() | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15189 / Symmetry type: POINT | ||||||||||||||||||||||||
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