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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11196 | |||||||||
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Title | bovine ATP synthase rotor domain state 2 | |||||||||
![]() | State 2 rotor main map | |||||||||
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Function / homology | ![]() 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 transmembrane transporter activity ...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 transmembrane transporter activity / proton motive force-driven ATP synthesis / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / proton motive force-driven mitochondrial ATP synthesis / aerobic respiration / mitochondrial inner membrane / lipid binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
![]() | Spikes T / Montgomery MG / Walker JE | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 442.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.8 KB 23.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.7 KB | Display | ![]() |
Images | ![]() | 45.7 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Others | ![]() ![]() | 383.3 MB 383.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 322 KB | Display | ![]() |
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Full document | ![]() | 321.1 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zg8MC ![]() 6yy0C ![]() 6z1rC ![]() 6z1uC ![]() 6zbbC ![]() 6zg7C ![]() 6zikC ![]() 6ziqC ![]() 6zitC ![]() 6ziuC ![]() 6zmrC ![]() 6znaC ![]() 6zpoC ![]() 6zqmC ![]() 6zqnC C: citing same article ( M: atomic model generated by this map |
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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 | State 2 rotor main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: State 2 rotor half map 1
File | emd_11196_half_map_1.map | ||||||||||||
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Annotation | State 2 rotor half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State 2 rotor half map 2
File | emd_11196_half_map_2.map | ||||||||||||
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Annotation | State 2 rotor half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : bovine dimeric ATP synthase
Entire | Name: bovine dimeric ATP synthase |
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Components |
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-Supramolecule #1: bovine dimeric ATP synthase
Supramolecule | Name: bovine dimeric ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 112 KDa |
-Supramolecule #2: bovine ATP synthase rotor domain state 2
Supramolecule | Name: bovine ATP synthase rotor domain state 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: ATP synthase subunit gamma, mitochondrial
Macromolecule | Name: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 30.30076 KDa |
Sequence | String: ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARVYGVGSLA LYEKADIKTP EDKKKHLIIG VSSDRGLCGA IHSSVAKQM KSEAANLAAA GKEVKIIGVG DKIRSILHRT HSDQFLVTFK EVGRRPPTFG DASVIALELL NSGYEFDEGS I IFNRFRSV ...String: ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARVYGVGSLA LYEKADIKTP EDKKKHLIIG VSSDRGLCGA IHSSVAKQM KSEAANLAAA GKEVKIIGVG DKIRSILHRT HSDQFLVTFK EVGRRPPTFG DASVIALELL NSGYEFDEGS I IFNRFRSV ISYKTEEKPI FSLDTISSAE SMSIYDDIDA DVLRNYQEYS LANIIYYSLK ESTTSEQSAR MTAMDNASKN AS EMIDKLT LTFNRTRQAV ITKELIEIIS GAAALD |
-Macromolecule #2: ATP synthase subunit delta, mitochondrial
Macromolecule | Name: ATP synthase subunit delta, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.074813 KDa |
Sequence | String: AEAAAAQAPA AGPGQMSFTF ASPTQVFFNS ANVRQVDVPT QTGAFGILAA HVPTLQVLRP GLVVVHAEDG TTSKYFVSSG SVTVNADSS VQLLAEEAVT LDMLDLGAAK ANLEKAQSEL LGAADEATRA EIQIRIEANE ALVKALE |
-Macromolecule #3: ATP synthase subunit epsilon, mitochondrial
Macromolecule | Name: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 5.662693 KDa |
Sequence | String: VAYWRQAGLS YIRYSQICAK AVRDALKTEF KANAMKTSGS TIKIVKVKKE |
-Macromolecule #4: ATP synthase F(0) complex subunit C2, mitochondrial
Macromolecule | Name: ATP synthase F(0) complex subunit C2, mitochondrial / type: protein_or_peptide / ID: 4 Details: residue 43 is tri-methyl lysine. A post translational modification Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 7.653034 KDa |
Sequence | String: DIDTAAKFIG AGAATVGVAG SGAGIGTVFG SLIIGYARNP SL(M3L)QQLFSYA ILGFALSEAM GLFCLMVAFL ILFAM |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4.5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER Details: Post glow-discharging, the grids were PEGylated with 5 mM mercaptopoly(ethylene glycol)carboxylic acid (PEGthiol) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV Details: The sample was allowed to penetrate through the holes support and to distribute to both sides of the grid surface for ~15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting.. |
Details | Nickel affinity purified followed by gel filtration |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 12.0 sec. / Average electron dose: 4.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |