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Yorodumi- EMDB-28811: F1-focused map of yeast ATP synthase in conformation-1, at pH 6 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28811 | |||||||||
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Title | F1-focused map of yeast ATP synthase in conformation-1, at pH 6 | |||||||||
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Sample |
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Keywords | F-type ATP synthase / yeast / mitochondrial / MEMBRANE PROTEIN | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Sharma S / Patel H / Luo M / Mueller DM / Liao M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28811.map.gz | 56.8 MB | EMDB map data format | |
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Header (meta data) | emd-28811-v30.xml emd-28811.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_28811.png | 43.2 KB | ||
Filedesc metadata | emd-28811.cif.gz | 3.7 KB | ||
Others | emd_28811_half_map_1.map.gz emd_28811_half_map_2.map.gz | 49.3 MB 49.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28811 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28811 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28811.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_28811_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28811_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ATP synthase
Entire | Name: ATP synthase |
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Components |
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-Supramolecule #1: ATP synthase
Supramolecule | Name: ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#13, #1, #14-#18 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371073 |