+Open data
-Basic information
Entry | Database: PDB / ID: 6zpo | |||||||||
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Title | bovine ATP synthase monomer state 1 (combined) | |||||||||
Components |
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Keywords | HYDROLASE / ATP synthase / mitochondria / mammalian / complex | |||||||||
Function / homology | Function and homology information Mitochondrial protein import / 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 import / 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 transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / aerobic respiration / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||
Authors | Spikes, T.E. / Montgomery, M.G. / Walker, J.E. | |||||||||
Funding support | United Kingdom, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zpo.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zpo.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 6zpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/6zpo ftp://data.pdbj.org/pub/pdb/validation_reports/zp/6zpo | HTTPS FTP |
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-Related structure data
Related structure data | 11342MC 6yy0C 6z1rC 6z1uC 6zbbC 6zg7C 6zg8C 6zikC 6ziqC 6zitC 6ziuC 6zmrC 6znaC 6zqmC 6zqnC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ATP synthase ... , 16 types, 27 molecules 8ABCDEFGHIKLMNOPQRSabdefgjk
#1: Protein | Mass: 7944.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P03929 | ||||||||||||||||||||||||||||
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#2: Protein | Mass: 55332.219 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P19483 #3: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P00829, H+-transporting two-sector ATPase #4: Protein | | Mass: 30300.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ATP synthase inhibitor protein IF1 residues 1-60 with 6His tag Source: (gene. exp.) Bos taurus (cattle) / Gene: ATP5C1, ATP5C / Production host: Escherichia coli (E. coli) / References: UniProt: P05631 #5: Protein | | Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P05630 #6: Protein/peptide | | Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P05632 #8: Protein | Mass: 7653.034 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P32876 #9: Protein | | Mass: 20959.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13621 #10: Protein | | Mass: 24801.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00847 #11: Protein | | Mass: 24702.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13619 #12: Protein | | Mass: 18588.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13620 #13: Protein | | Mass: 8205.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q00361 #14: Protein | | Mass: 10184.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28851 #15: Protein | | Mass: 11298.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: Q28852 #17: Protein | | Mass: 6846.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P14790 #18: Protein | | Mass: 6312.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: Q3ZBI7 |
-Protein , 2 types, 2 molecules Jh
#7: Protein | Mass: 7462.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: IF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01096 |
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#16: Protein | Mass: 8971.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P02721 |
-Non-polymers , 6 types, 33 molecules
#19: Chemical | #20: Chemical | ChemComp-MG / #21: Chemical | #22: Chemical | #23: Chemical | #24: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 1.2 MDa / Experimental value: YES | |||||||||||||||||||||||||||||||||||
Source (natural) |
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Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Nickel affinity purified filled by gel filtration | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 294 K 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. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 12 sec. / Electron dose: 4.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101165 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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