+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4176 | ||||||||||||
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Title | Polytomella Fo model | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information thylakoid / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / intracellular membrane-bounded organelle / lipid binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Polytomella sp. Pringsheim 198.80 (plant) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Yildiz O / Kuehlbrandt W / Klusch N / Murphy BJ / Mills DJ | ||||||||||||
Funding support | Germany, 3 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4176.map.gz | 905.1 KB | EMDB map data format | |
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Header (meta data) | emd-4176-v30.xml emd-4176.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_4176.png | 218.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4176 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4176 | HTTPS FTP |
-Related structure data
Related structure data | 6f36MC M: atomic model generated by this map 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_4176.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.105 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 : Polytommella mitochondrial ATP synthase Fo complex
Entire | Name: Polytommella mitochondrial ATP synthase Fo complex |
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Components |
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-Supramolecule #1: Polytommella mitochondrial ATP synthase Fo complex
Supramolecule | Name: Polytommella mitochondrial ATP synthase Fo complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Polytomella sp. Pringsheim 198.80 (plant) |
Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: Mitochondrial ATP synthase subunit c
Macromolecule | Name: Mitochondrial ATP synthase subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Polytomella sp. Pringsheim 198.80 (plant) |
Molecular weight | Theoretical: 12.664013 KDa |
Sequence | String: MSVQRLSLGA ARCLSAGVAR VQASQALVAQ KAVAVAPTRA QAAPAEVAQV RSMSVLAASK MVGAGCATIA LAGVGAGLGV MFGSLINGA ARNPNIAKQL VGYALLGFAL TESIALFSLL VVFLILFA |
-Macromolecule #2: Mitochondrial ATP synthase subunit 6
Macromolecule | Name: Mitochondrial ATP synthase subunit 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Polytomella sp. Pringsheim 198.80 (plant) |
Molecular weight | Theoretical: 34.802344 KDa |
Sequence | String: MSVLSSVSMG SRIGSSLLGR SSAYLAQCGF STRSNLNGSI DTSSSVFQAL SSDNENKPAA SPLNVKLPGM SCSSILLPKT SRIAVPFGN QTMAMSSVRD VKTGSLPTNF LTGVYRFWRS QNPAEKPHDP VNDRLLPAVV DASDKRASIG TWATTFFCTI I SCNLLGLM ...String: MSVLSSVSMG SRIGSSLLGR SSAYLAQCGF STRSNLNGSI DTSSSVFQAL SSDNENKPAA SPLNVKLPGM SCSSILLPKT SRIAVPFGN QTMAMSSVRD VKTGSLPTNF LTGVYRFWRS QNPAEKPHDP VNDRLLPAVV DASDKRASIG TWATTFFCTI I SCNLLGLM PFNEAPTSGL GFATGLGVSV WATATILGLS KTGFKFPGHF IPGGTPWPMA FIFVPLETIS YTFRAVSLGV RL WVNMLAG HTLLHILTGM ALALPFSLGF FSMVPATFGV CCLLSALVGL EYLVAVLQSG VFSILSTVYV GEFNHDKFIG PAA KIVKKI H |
-Macromolecule #3: Mitochondrial ATP synthase subunit ASA6
Macromolecule | Name: Mitochondrial ATP synthase subunit ASA6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Polytomella sp. Pringsheim 198.80 (plant) |
Molecular weight | Theoretical: 15.90429 KDa |
Sequence | String: MMLRTLTRSS AVAGQAVRLF KTSAAAAEGN SVAGIIKSVN ETSGANLLSS LKTIKAQAAP IYPAAASSTG YSTQAKIALF GALSWILYR ADGQSKAHEW IVDLNLNVLQ AAWLISFSSL IPFRAVYFAF RGMAPATAST LNGLKTFSSI SL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 282 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-45 / Number grids imaged: 30 / Average exposure time: 0.2 sec. / Average electron dose: 82.0 e/Å2 |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Number classes used: 4 / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90142 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6f36: |