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Yorodumi- PDB-6b2z: Cryo-EM structure of the dimeric FO region of yeast mitochondrial... -
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-Basic information
Entry | Database: PDB / ID: 6b2z | ||||||||||||
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Title | Cryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Complex / Dimer / Mitochondrial inner membrane / Proton translocation | ||||||||||||
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) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Guo, H. / Rubinstein, J.L. | ||||||||||||
Funding support | Canada, United States, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6b2z.cif.gz | 583 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b2z.ent.gz | 468.7 KB | Display | PDB format |
PDBx/mmJSON format | 6b2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b2z_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6b2z_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6b2z_validation.xml.gz | 66.6 KB | Display | |
Data in CIF | 6b2z_validation.cif.gz | 110 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/6b2z ftp://data.pdbj.org/pub/pdb/validation_reports/b2/6b2z | HTTPS FTP |
-Related structure data
Related structure data | 7036MC 7037C 7067C 6b8hC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-ATP synthase subunit ... , 9 types, 36 molecules 1234567890CDEFGHIJKBaMbNdOePfQ...
#1: Protein | Mass: 7762.375 Da / Num. of mol.: 20 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P61829 #3: Protein | Mass: 27900.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P00854 #4: Protein | Mass: 23194.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: W303-1A / References: UniProt: P05626 #5: Protein | Mass: 19709.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P30902 #6: Protein/peptide | Mass: 4188.154 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c #7: Protein | Mass: 10584.166 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q06405 #8: Protein | Mass: 9039.134 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: W303-1A #9: Protein | Mass: 6696.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P81450 #10: Protein | Mass: 7546.778 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P81451 |
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-Protein/peptide , 1 types, 2 molecules AL
#2: Protein/peptide | Mass: 5825.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P00856 |
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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
Component | Name: Yeast mitochondrial ATP synthase FO complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.4 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303-1A / Cellular location: Inner membrane of mitochondria / Organelle: Mitochondria |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid type: Homemade |
Vitrification | Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 26 seconds before plunging |
-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 / Nominal magnification: 130000 X / Calibrated magnification: 47170 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 71 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3023 |
EM imaging optics | Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 446259 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 238848 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||
Refine LS restraints |
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