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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3164 | |||||||||
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Title | Bovine mitochondrial ATP synthase state 1a | |||||||||
![]() | Reconstruction of detergent-solubilized bovine mitochondrial ATP synthase | |||||||||
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![]() | ATP synthase / rotary ATPase | |||||||||
Function / homology | ![]() Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / proton-transporting ATP synthase complex / : / : / : / : ...Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / proton-transporting ATP synthase complex / : / : / : / : / Mitochondrial protein degradation / proton-transporting ATP synthase complex, coupling factor F(o) / : / 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 / ADP binding / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
![]() | Zhou A / Rohou A / Schep DG / Bason JV / Montgomery MG / Walker JE / Grigorieff N / Rubinstein JL | |||||||||
![]() | ![]() Title: Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM. Authors: Anna Zhou / Alexis Rohou / Daniel G Schep / John V Bason / Martin G Montgomery / John E Walker / Nikolaus Grigorieff / John L Rubinstein / ![]() ![]() ![]() Abstract: Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic ...Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 54.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.2 KB 16.2 KB | Display Display | ![]() |
Images | ![]() ![]() | 132.7 KB 132.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5araMC ![]() 3165C ![]() 3166C ![]() 3167C ![]() 3168C ![]() 3169C ![]() 3170C ![]() 3181C ![]() 5areC ![]() 5arhC ![]() 5ariC ![]() 5fijC ![]() 5fikC ![]() 5filC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of detergent-solubilized bovine mitochondrial ATP synthase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Bovine mitochondrial ATP synthase
Entire | Name: Bovine mitochondrial ATP synthase |
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Components |
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-Supramolecule #1000: Bovine mitochondrial ATP synthase
Supramolecule | Name: Bovine mitochondrial ATP synthase / type: sample / ID: 1000 / Details: Detergent-solubilized protein complex Oligomeric state: One hetero-oligomeric ATP synthase complex Number unique components: 1 |
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Molecular weight | Experimental: 600 KDa |
-Macromolecule #1: ATP synthase
Macromolecule | Name: ATP synthase / type: protein_or_peptide / ID: 1 / Name.synonym: ATPase, complex V / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 600 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 8 mg/mL |
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Buffer | pH: 7.2 Details: 20 mM Tris-HCl, 100 mM NaCl, 0.05% (wt/v) dodecylmaltoside, 2 mM ATP, 0.02% (wt/v) NaN3 |
Grid | Details: Home made holey carbon on 400 square mesh Cu/Rh grid, glow-discharged 2 mins |
Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 27 seconds before plunging |
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Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Temperature | Average: 80 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 18,000x magnification (before detector post-magnification) |
Details | K2 Summit direct detector device (Gatan Inc.) operated in super-resolution mode with a 1.64 angstrom physical pixel and 0.82 angstrom super-resolution pixel. With no specimen present, the rate of exposure of the detector was 8 electrons/pixel/second. Exposure- fractionated movies of 20.1 s were recorded as stacks of 67 frames, so that selected specimen areas were exposed with a total of 60.3 electrons/square angstrom. |
Date | Mar 15, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 5867 / Average electron dose: 60.3 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 30487 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 18000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #2
Microscopy ID | 2 |
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Microscope | FEI TITAN KRIOS |
Temperature | Average: 80 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 18,000x magnification (before detector post-magnification) |
Details | K2 Summit direct detector device (Gatan Inc.) operated in super-resolution mode with a 1.64 angstrom physical pixel and 0.82 angstrom super-resolution pixel. With no specimen present, the rate of exposure of the detector was 8 electrons/pixel/second. Exposure- fractionated movies of 20.1 s were recorded as stacks of 67 frames, so that selected specimen areas were exposed with a total of 60.3 electrons/square angstrom. |
Date | Sep 28, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 5867 / Average electron dose: 60.3 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 30487 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 18000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | The particles were selected using an automatic selection program. |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: OTHER / Software - Name: Relion, FREALIGN Details: To avoid noise bias, only data up to a resolution of 10 angstrom were used during refinement. Number images used: 20104 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: S |
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Software | Name: Chimera, MDFF |
Details | Rigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF). |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-5ara: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: J / Chain - #1 - Chain ID: K / Chain - #2 - Chain ID: L / Chain - #3 - Chain ID: M / Chain - #4 - Chain ID: N / Chain - #5 - Chain ID: O / Chain - #6 - Chain ID: P / Chain - #7 - Chain ID: Q |
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Software | Name: Chimera, MDFF |
Details | Rigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF). |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-5ara: |
-Atomic model buiding 3
Initial model | PDB ID: Chain - #0 - Chain ID: D / Chain - #1 - Chain ID: E / Chain - #2 - Chain ID: F |
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Software | Name: Chimera, MDFF |
Details | Rigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF). |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-5ara: |