+Open data
-Basic information
Entry | Database: PDB / ID: 6f36 | ||||||||||||
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Title | Polytomella Fo model | ||||||||||||
Components |
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Keywords | PROTON TRANSPORT / electron cryo-microscopy mitochondrial ATP synthase membrane protein energy conversion proton pathway | ||||||||||||
Function / homology | Function and homology information thylakoid / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / chloroplast thylakoid membrane / proton-transporting ATP synthase activity, rotational mechanism / lipid binding Similarity search - Function | ||||||||||||
Biological species | Polytomella sp. Pringsheim 198.80 (plant) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Yildiz, O. / Kuehlbrandt, W. / Klusch, N. / Murphy, B.J. / Mills, D.J. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Elife / Year: 2017 Title: Structural basis of proton translocation and force generation in mitochondrial ATP synthase. Authors: Niklas Klusch / Bonnie J Murphy / Deryck J Mills / Özkan Yildiz / Werner Kühlbrandt / Abstract: ATP synthases produce ATP by rotary catalysis, powered by the electrochemical proton gradient across the membrane. Understanding this fundamental process requires an atomic model of the proton ...ATP synthases produce ATP by rotary catalysis, powered by the electrochemical proton gradient across the membrane. Understanding this fundamental process requires an atomic model of the proton pathway. We determined the structure of an intact mitochondrial ATP synthase dimer by electron cryo-microscopy at near-atomic resolution. Charged and polar residues of the -subunit stator define two aqueous channels, each spanning one half of the membrane. Passing through a conserved membrane-intrinsic helix hairpin, the lumenal channel protonates an acidic glutamate in the -ring rotor. Upon ring rotation, the protonated glutamate encounters the matrix channel and deprotonates. An arginine between the two channels prevents proton leakage. The steep potential gradient over the sub-nm inter-channel distance exerts a force on the deprotonated glutamate, resulting in net directional rotation. | ||||||||||||
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 | 6f36.cif.gz | 180.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f36.ent.gz | 140.6 KB | Display | PDB format |
PDBx/mmJSON format | 6f36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f36_validation.pdf.gz | 694 KB | Display | wwPDB validaton report |
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Full document | 6f36_full_validation.pdf.gz | 701.7 KB | Display | |
Data in XML | 6f36_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 6f36_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/6f36 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f36 | HTTPS FTP |
-Related structure data
Related structure data | 4176MC 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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1 |
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-Components
#1: Protein | Mass: 12664.013 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D7P7X5 #2: Protein | | Mass: 34802.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: H8PGG3 #3: Protein | | Mass: 15904.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D7P897 |
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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: Polytommella mitochondrial ATP synthase Fo complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.11 MDa / Experimental value: NO |
Source (natural) | Organism: Polytomella sp. Pringsheim 198.80 (plant) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 282 K |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 82 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 30 |
Image scans | Width: 4096 / Height: 4096 / Movie frames/image: 45 / Used frames/image: 1-45 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90142 / Num. of class averages: 4 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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