+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11510 | |||||||||
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Title | bovine ATP synthase dimer state2:state3e | |||||||||
Map data | bovine ATP synthase dimer s2:s3e main map | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of mitochondrial ATP synthesis coupled proton transport / 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 / : / : ...negative regulation of mitochondrial ATP synthesis coupled proton transport / 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 / proton-transporting ATP synthase complex, coupling factor F(o) / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial 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 / aerobic respiration / proton transmembrane transport / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / mitochondrial inner membrane / calmodulin binding / 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) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 18.1 Å | |||||||||
Authors | Spikes TE / Montgomery MG / Walker JE | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Interface mobility between monomers in dimeric bovine ATP synthase participates in the ultrastructure of inner mitochondrial membranes. Authors: Tobias E Spikes / Martin G Montgomery / John E Walker / Abstract: The ATP synthase complexes in mitochondria make the ATP required to sustain life by a rotary mechanism. Their membrane domains are embedded in the inner membranes of the organelle, and they dimerize ...The ATP synthase complexes in mitochondria make the ATP required to sustain life by a rotary mechanism. Their membrane domains are embedded in the inner membranes of the organelle, and they dimerize via interactions between their membrane domains. The dimers form extensive chains along the tips of the cristae with the two rows of monomeric catalytic domains extending into the mitochondrial matrix at an angle to each other. Disruption of the interface between dimers by mutation affects the morphology of the cristae severely. By analysis of particles of purified dimeric bovine ATP synthase by cryo-electron microscopy, we have shown that the angle between the central rotatory axes of the monomeric complexes varies between ca. 76 and 95°. These particles represent active dimeric ATP synthase. Some angular variations arise directly from the catalytic mechanism of the enzyme, and others are independent of catalysis. The monomer-monomer interaction is mediated mainly by j subunits attached to the surface of wedge-shaped protein-lipid structures in the membrane domain of the complex, and the angular variation arises from rotational and translational changes in this interaction, and combinations of both. The structures also suggest how the dimeric ATP synthases might be interacting with each other to form the characteristic rows along the tips of the cristae via other interwedge contacts, molding themselves to the range of oligomeric arrangements observed by tomography of mitochondrial membranes, and at the same time allowing the ATP synthase to operate under the range of physiological conditions that influence the structure of the 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_11510.map.gz | 34.5 MB | EMDB map data format | |
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Header (meta data) | emd-11510-v30.xml emd-11510.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
Images | emd_11510.png | 38.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11510 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11510 | HTTPS FTP |
-Validation report
Summary document | emd_11510_validation.pdf.gz | 193.8 KB | Display | EMDB validaton report |
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Full document | emd_11510_full_validation.pdf.gz | 193 KB | Display | |
Data in XML | emd_11510_validation.xml.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11510 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11510 | HTTPS FTP |
-Related structure data
Related structure data | 7ajbC 7ajcC 7ajdC 7ajeC 7ajfC 7ajgC 7ajhC 7ajiC 7ajjC C: citing same article (ref.) |
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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_11510.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | bovine ATP synthase dimer s2:s3e main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Bovine ATP synthase dimer
Entire | Name: Bovine ATP synthase dimer |
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Components |
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-Supramolecule #1: Bovine ATP synthase dimer
Supramolecule | Name: Bovine ATP synthase dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18 / Details: bovine ATP synthase inhibited by IF1 1-60His |
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Molecular weight | Experimental: 7.441 KDa |
-Supramolecule #2: monomeric bovine ATP synthase
Supramolecule | Name: monomeric bovine ATP synthase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #7-#18 Details: monomeric bovine ATP synthase inhibited by IF1 1-60His |
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Source (natural) | Organism: Bos taurus (cattle) |
-Supramolecule #3: Bovine ATP synthase IF1
Supramolecule | Name: Bovine ATP synthase IF1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6 / Details: residues 1-60 of IF1 with a 6His tag |
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Source (natural) | Organism: Bos taurus (cattle) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-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
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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