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- EMDB-10524: Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10524 | |||||||||||||||
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Title | Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, consensus map | |||||||||||||||
![]() | Local resolution filtered full dimer map | |||||||||||||||
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Function / homology | ![]() : / : / mitochondrial electron transport, ubiquinol to cytochrome c / : / : / : / photosynthetic electron transport in photosystem I / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis ...: / : / mitochondrial electron transport, ubiquinol to cytochrome c / : / : / : / photosynthetic electron transport in photosystem I / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / photosynthetic electron transport in photosystem II / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / electron transfer activity / hydrolase activity / lipid binding / heme binding / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
![]() | Muhleip A / Kock Flygaard R / Amunts A | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria. Authors: Alexander Mühleip / Rasmus Kock Flygaard / Jana Ovciarikova / Alice Lacombe / Paula Fernandes / Lilach Sheiner / Alexey Amunts / ![]() ![]() Abstract: Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has ...Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has been observed, but its structural basis is unknown. Here, we report that the apicomplexan ATP synthase assembles into cyclic hexamers, essential to shape their distinct cristae. Cryo-EM was used to determine the structure of the hexamer, which is held together by interactions between parasite-specific subunits in the lumenal region. Overall, we identified 17 apicomplexan-specific subunits, and a minimal and nuclear-encoded subunit-a. The hexamer consists of three dimers with an extensive dimer interface that includes bound cardiolipins and the inhibitor IF. Cryo-ET and subtomogram averaging revealed that hexamers arrange into ~20-megadalton pentagonal pyramids in the curved apical membrane regions. Knockout of the linker protein ATPTG11 resulted in the loss of pentagonal pyramids with concomitant aberrantly shaped cristae. Together, this demonstrates that the unique macromolecular arrangement is critical for the maintenance of cristae morphology in Apicomplexa. | |||||||||||||||
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 | ![]() | 370.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 51.3 KB 51.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.8 KB | Display | ![]() |
Images | ![]() | 83.8 KB | ||
Masks | ![]() | 669.9 MB | ![]() | |
Others | ![]() ![]() | 535.4 MB 538.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tmkMC ![]() 6tmgC ![]() 6tmhC ![]() 6tmiC ![]() 6tmjC ![]() 6tmlC 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 | Local resolution filtered full dimer map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 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: Full dimer halfmap 1
File | emd_10524_half_map_1.map | ||||||||||||
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Annotation | Full dimer halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Full dimer halfmap 2
File | emd_10524_half_map_2.map | ||||||||||||
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Annotation | Full dimer halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Mitochondrial ATP synthase dimer, composite model
+Supramolecule #1: Mitochondrial ATP synthase dimer, composite model
+Macromolecule #1: ATPTG11
+Macromolecule #2: ATPTG7
+Macromolecule #3: ATPTG14
+Macromolecule #4: ATPTG5
+Macromolecule #5: subunit k
+Macromolecule #6: subunit a
+Macromolecule #7: subunit i/j
+Macromolecule #8: ATPTG13
+Macromolecule #9: ATPTG15
+Macromolecule #10: ATPTG6
+Macromolecule #11: ATPTG3
+Macromolecule #12: ATPTG17
+Macromolecule #13: subunit b
+Macromolecule #14: ATPTG12
+Macromolecule #15: ATPTG10
+Macromolecule #16: subunit f
+Macromolecule #17: ATPTG8
+Macromolecule #18: ATPTG1
+Macromolecule #19: ATPTG2
+Macromolecule #20: subunit 8
+Macromolecule #21: ATPTG9
+Macromolecule #22: ATPTG4
+Macromolecule #23: ATPTG16
+Macromolecule #24: subunit d
+Macromolecule #25: Inhibitor of F1
+Macromolecule #26: ATP synthase subunit alpha,subunit alpha
+Macromolecule #27: ATP synthase subunit beta
+Macromolecule #28: ATP synthase subunit gamma
+Macromolecule #29: ATP synthase subunit delta
+Macromolecule #30: ATP synthase subunit epsilon
+Macromolecule #31: Oligomycin sensitivity conferring protein (OSCP)
+Macromolecule #32: subunit c
+Macromolecule #33: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #34: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #35: CARDIOLIPIN
+Macromolecule #36: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #37: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #38: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds blot.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 4860 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-6tmk: |