+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11039 | |||||||||
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Title | bovine ATP synthase F1-peripheral stalk domain, state 2 | |||||||||
Map data | State 2 half mask 1 | |||||||||
Sample |
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Function / homology | Function and homology information angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / proton-transporting ATP synthase complex / heme biosynthetic process / : ...angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / proton-transporting ATP synthase complex / heme biosynthetic process / : / : / : / : / Mitochondrial protein degradation / : / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / proton motive force-driven mitochondrial ATP synthesis / aerobic respiration / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) / cattle (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||
Authors | Spikes T / Montgomery MG / Walker JE | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Structure of the dimeric ATP synthase from bovine mitochondria. Authors: Tobias E Spikes / Martin G Montgomery / John E Walker / Abstract: The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial ...The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains. | |||||||||
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_11039.map.gz | 446.2 MB | EMDB map data format | |
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Header (meta data) | emd-11039-v30.xml emd-11039.xml | 33.6 KB 33.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11039_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_11039.png | 49.1 KB | ||
Masks | emd_11039_msk_1.map | 476.8 MB | Mask map | |
Others | emd_11039_half_map_1.map.gz emd_11039_half_map_2.map.gz | 385.4 MB 385.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11039 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11039 | HTTPS FTP |
-Validation report
Summary document | emd_11039_validation.pdf.gz | 411.7 KB | Display | EMDB validaton report |
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Full document | emd_11039_full_validation.pdf.gz | 410.8 KB | Display | |
Data in XML | emd_11039_validation.xml.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11039 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11039 | HTTPS FTP |
-Related structure data
Related structure data | 6z1rMC 6yy0C 6z1uC 6zbbC 6zg7C 6zg8C 6zikC 6ziqC 6zitC 6ziuC 6zmrC 6znaC 6zpoC 6zqmC 6zqnC 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_11039.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | State 2 half mask 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 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_11039_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: State 2 half map 2
File | emd_11039_half_map_1.map | ||||||||||||
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Annotation | State 2 half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: atp synthase monomer mask
File | emd_11039_half_map_2.map | ||||||||||||
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Annotation | atp synthase monomer mask | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His
+Supramolecule #1: Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His
+Supramolecule #2: ATP synthase F1 domain
+Supramolecule #3: ATP synthase peripheral stalk
+Supramolecule #4: ATPase inhibitor, mitochondrial
+Macromolecule #1: ATP synthase subunit alpha, mitochondrial
+Macromolecule #2: ATP synthase subunit beta, mitochondrial
+Macromolecule #3: ATP synthase subunit gamma, mitochondrial
+Macromolecule #4: ATP synthase subunit delta, mitochondrial
+Macromolecule #5: ATP synthase subunit epsilon, mitochondrial
+Macromolecule #6: ATPase inhibitor, mitochondrial
+Macromolecule #7: ATP synthase F(0) complex subunit C2, mitochondrial
+Macromolecule #8: ATP synthase subunit O, mitochondrial
+Macromolecule #9: ATP synthase F(0) complex subunit B1, mitochondrial
+Macromolecule #10: ATP synthase-coupling factor 6, mitochondrial
+Macromolecule #11: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #12: MAGNESIUM ION
+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #14: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV Details: The sample was allowed to penetrate through the holey support and to distribute to both sides of the grid surface for ca. 15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting.. |
Details | Nickel affinity purified filled by gel filtration |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 12.0 sec. / Average electron dose: 4.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
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
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||
Output model | PDB-6z1r: |