+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28835 | |||||||||
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Title | Yeast ATP synthase map in conformation-2, at pH 6 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | F-type ATP synthase / yeast / mitochondrial / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information : / : / : / 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 motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / 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 / proton transmembrane transport / ADP binding / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 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_28835.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-28835-v30.xml emd-28835.xml | 26.9 KB 26.9 KB | Display Display | EMDB header |
Images | emd_28835.png | 39.1 KB | ||
Filedesc metadata | emd-28835.cif.gz | 7.1 KB | ||
Others | emd_28835_half_map_1.map.gz emd_28835_half_map_2.map.gz | 49.4 MB 49.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28835 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28835 | HTTPS FTP |
-Validation report
Summary document | emd_28835_validation.pdf.gz | 842.2 KB | Display | EMDB validaton report |
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Full document | emd_28835_full_validation.pdf.gz | 841.8 KB | Display | |
Data in XML | emd_28835_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | emd_28835_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28835 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28835 | HTTPS FTP |
-Related structure data
Related structure data | 8f39MC 8f29C 8fkjC 8fl8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28835.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_28835_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28835_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : ATP synthase
+Supramolecule #1: ATP synthase
+Macromolecule #1: ATP synthase subunit gamma, mitochondrial
+Macromolecule #2: ATP synthase subunit 4, mitochondrial
+Macromolecule #3: ATP synthase subunit d, mitochondrial
+Macromolecule #4: ATP synthase subunit H, mitochondrial
+Macromolecule #5: ATP synthase subunit f, mitochondrial
+Macromolecule #6: ATP synthase subunit 9, mitochondrial
+Macromolecule #7: ATP synthase protein 8
+Macromolecule #8: ATP synthase subunit a
+Macromolecule #9: ATP synthase subunit J, mitochondrial
+Macromolecule #10: ATP synthase subunit 5, mitochondrial
+Macromolecule #11: ATP synthase subunit alpha, mitochondrial
+Macromolecule #12: ATP synthase subunit beta, mitochondrial
+Macromolecule #13: ATP synthase subunit delta, mitochondrial
+Macromolecule #14: ATP synthase subunit epsilon, mitochondrial
+Macromolecule #15: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #16: MAGNESIUM ION
-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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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99780 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |