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Yorodumi- EMDB-7036: Cryo-EM structure of the dimeric FO region of yeast mitochondrial... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7036 | ||||||||||||
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Title | Cryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase | ||||||||||||
Map data | Sharpened map of the dimeric FO region of yeast mitochondrial ATP synthase | ||||||||||||
Sample |
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Keywords | Complex / Dimer / Mitochondrial inner membrane / Proton translocation / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information : / : / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton transmembrane transport ...: / : / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton transmembrane transport / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / mitochondrion / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Guo H / Rubinstein JL | ||||||||||||
Funding support | Canada, United States, 3 items
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Citation | Journal: Science / Year: 2017 Title: Atomic model for the dimeric F region of mitochondrial ATP synthase. Authors: Hui Guo / Stephanie A Bueler / John L Rubinstein / Abstract: Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic ...Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded F region turns the rotor that drives ATP synthesis in the soluble F region. Although crystal structures of the F region have illustrated how this rotation leads to ATP synthesis, understanding how proton translocation produces the rotation has been impeded by the lack of an experimental atomic model for the F region. Using cryo-electron microscopy, we determined the structure of the dimeric F complex from at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7036.map.gz | 117.3 MB | EMDB map data format | |
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Header (meta data) | emd-7036-v30.xml emd-7036.xml | 30.2 KB 30.2 KB | Display Display | EMDB header |
Images | emd_7036.png | 138.4 KB | ||
Masks | emd_7036_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-7036.cif.gz | 6.8 KB | ||
Others | emd_7036_additional_1.map.gz emd_7036_additional_2.map.gz emd_7036_additional_3.map.gz | 115.6 MB 115.6 MB 62.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7036 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7036 | HTTPS FTP |
-Validation report
Summary document | emd_7036_validation.pdf.gz | 599.6 KB | Display | EMDB validaton report |
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Full document | emd_7036_full_validation.pdf.gz | 599.1 KB | Display | |
Data in XML | emd_7036_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_7036_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7036 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7036 | HTTPS FTP |
-Related structure data
Related structure data | 6b2zMC 7037C 7067C 6b8hC C: citing same article (ref.) M: atomic model generated by this map |
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Similar 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_7036.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map of the dimeric FO region of yeast mitochondrial ATP synthase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_7036_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Half map A of the dimeric FO region...
File | emd_7036_additional_1.map | ||||||||||||
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Annotation | Half map A of the dimeric FO region of yeast mitochondrial ATP synthase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half map B of the dimeric FO region...
File | emd_7036_additional_2.map | ||||||||||||
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Annotation | Half map B of the dimeric FO region of yeast mitochondrial ATP synthase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map of the dimeric FO region of...
File | emd_7036_additional_3.map | ||||||||||||
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Annotation | Unsharpened map of the dimeric FO region of yeast mitochondrial ATP synthase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yeast mitochondrial ATP synthase FO complex
+Supramolecule #1: Yeast mitochondrial ATP synthase FO complex
+Macromolecule #1: ATP synthase subunit c, mitochondrial
+Macromolecule #2: ATP synthase protein 8
+Macromolecule #3: ATP synthase subunit a
+Macromolecule #4: ATP synthase subunit b
+Macromolecule #5: ATP synthase subunit d, mitochondrial
+Macromolecule #6: ATP synthase subunit e, mitochondrial
+Macromolecule #7: ATP synthase subunit f, mitochondrial
+Macromolecule #8: ATP synthase subunit g
+Macromolecule #9: ATP synthase subunit j, mitochondrial
+Macromolecule #10: ATP synthase subunit k, mitochondrial
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Homemade / Material: COPPER/RHODIUM / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Details: blot for 26 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 2 / Number real images: 3023 / Average exposure time: 10.0 sec. / Average electron dose: 71.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-6b2z: |