Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Conformational ensemble of yeast ATP synthase at low pH reveals unique intermediates and plasticity in F-F coupling.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 31, Issue 4, Page 657-666, Year 2024
Publish date	Feb 5, 2024
Authors	Stuti Sharma / Min Luo / Hiral Patel / David M Mueller / Maofu Liao /
PubMed 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.
External links	Nat Struct Mol Biol / PubMed:38316880
Methods	EM (single particle)
Resolution	2.7 - 4.5 Å
Structure data	EMDB-28685: Yeast ATP synthase consensus map in conformation-0 at pH 6 Method: EM (single particle) / Resolution: 4.5 Å EMDB-28687: Yeast ATP synthase F1-focused map in conformation-0 at pH 6 Method: EM (single particle) / Resolution: 2.9 Å EMDB-28689: Yeast ATP synthase Fo-focused map in conformation-0 at pH 6 Method: EM (single particle) / Resolution: 3.5 Å 28809 8f29 EMDB-28809: Yeast ATP synthase map in conformation-1 at pH 6 PDB-8f29: Yeast ATP synthase in conformation-1 at pH 6 Method: EM (single particle) / Resolution: 4.0 Å EMDB-28811: F1-focused map of yeast ATP synthase in conformation-1, at pH 6 Method: EM (single particle) / Resolution: 2.7 Å EMDB-28814: Fo and central rotor focused map of yeast ATP synthase in conformation-1, at pH 6 Method: EM (single particle) / Resolution: 3.7 Å 28835 8f39 EMDB-28835: Yeast ATP synthase map in conformation-2, at pH 6 PDB-8f39: Yeast ATP synthase in conformation-2, at pH 6 Method: EM (single particle) / Resolution: 3.5 Å EMDB-28836: F1-focused map of yeast ATP synthase in conformation-2, at pH 6 Method: EM (single particle) / Resolution: 2.8 Å EMDB-28837: Fo and central rotor focused map of yeast ATP synthase in conformation-2, at pH 6 Method: EM (single particle) / Resolution: 3.7 Å 29250 8fkj EMDB-29250, PDB-8fkj: Yeast ATP Synthase in conformation-3, at pH 6 Method: EM (single particle) / Resolution: 4.2 Å EMDB-29251: Fo and central rotor focused map of yeast ATP Synthase in conformation-3, at pH 6 Method: EM (single particle) / Resolution: 4.1 Å 29270 8fl8 EMDB-29270: Yeast ATP Synthase map in presence of MgATP PDB-8fl8: Yeast ATP Synthase structure in presence of MgATP Method: EM (single particle) / Resolution: 4.2 Å EMDB-29278: F1-focused map of yeast ATP Synthase in presence of MgATP Method: EM (single particle) / Resolution: 3.2 Å
Chemicals	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-PO4: PHOSPHATE ION ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM
Source	saccharomyces cerevisiae (brewer's yeast)
Keywords	MEMBRANE PROTEIN / F-type ATP synthase / yeast / mitochondrial / F-type / ATP Synthase