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Yorodumi- EMDB-10523: Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10523 | |||||||||||||||
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Title | Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, rotor-stator map | |||||||||||||||
Map data | Toxoplasma gondii ATP synthase dimer, rotor-stator full map | |||||||||||||||
Sample |
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Keywords | mitochondrial / ATP synthase / rotor / stator / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information : / : / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton motive force-driven mitochondrial ATP synthesis / chloroplast thylakoid membrane / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / membrane Similarity search - Function | |||||||||||||||
Biological species | Toxoplasma gondii GT1 (eukaryote) / Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Muhleip A / Kock Flygaard R / Amunts A | |||||||||||||||
Funding support | Sweden, 4 items
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Citation | Journal: Nat Commun / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10523.map.gz | 378 MB | EMDB map data format | |
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Header (meta data) | emd-10523-v30.xml emd-10523.xml | 21.6 KB 21.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10523_fsc.xml | 19.9 KB | Display | FSC data file |
Images | emd_10523.png | 39 KB | ||
Masks | emd_10523_msk_1.map | 669.9 MB | Mask map | |
Filedesc metadata | emd-10523.cif.gz | 6.2 KB | ||
Others | emd_10523_half_map_1.map.gz emd_10523_half_map_2.map.gz | 538.6 MB 538.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10523 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10523 | HTTPS FTP |
-Validation report
Summary document | emd_10523_validation.pdf.gz | 678.8 KB | Display | EMDB validaton report |
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Full document | emd_10523_full_validation.pdf.gz | 678.3 KB | Display | |
Data in XML | emd_10523_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | emd_10523_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10523 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10523 | HTTPS FTP |
-Related structure data
Related structure data | 6tmjMC 6tmgC 6tmhC 6tmiC 6tmkC 6tmlC 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_10523.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Toxoplasma gondii ATP synthase dimer, rotor-stator full 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
File | emd_10523_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Halfmap 2
File | emd_10523_half_map_1.map | ||||||||||||
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Annotation | Halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Halfmap 1
File | emd_10523_half_map_2.map | ||||||||||||
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Annotation | Halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mitochondrial ATP synthase dimer, rotor-stator
Entire | Name: Mitochondrial ATP synthase dimer, rotor-stator |
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Components |
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-Supramolecule #1: Mitochondrial ATP synthase dimer, rotor-stator
Supramolecule | Name: Mitochondrial ATP synthase dimer, rotor-stator / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Toxoplasma gondii GT1 (eukaryote) |
Molecular weight | Theoretical: 127 KDa |
-Macromolecule #1: ATPTG11
Macromolecule | Name: ATPTG11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) Strain: ATCC 50853 / GT1 |
Molecular weight | Theoretical: 15.425367 KDa |
Sequence | String: MVRNQRYPAS PVQEIFLPEP VPFVQFDQTA PSPNSPPAPL PSPSLSQCEE QKDRYRDISS MFHRGVAGAE QVREAYNSMA KCFRRVSVA EVLESDPAFR QARNFTMDLK QAEDDQRYKQ LQYGRVPSIL TKYHL UniProtKB: Uncharacterized protein |
-Macromolecule #2: subunit a
Macromolecule | Name: subunit a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) Strain: ATCC 50853 / GT1 |
Molecular weight | Theoretical: 24.56257 KDa |
Sequence | String: MAAGSRFPFC TAARLSSRGT LPRLGEATFF AGAESQRSAG AFAKTLQRPF LRAPSTQLFP VGNRLGVSSA RALVANAMEP RRFFAAAAS AKATHALQPT GTGSVAFTRP GQGSNAQFQT SLADKTRGLL GVGFLRPTKM ASFAATFLLN FRFYFMYMAR T TFQAVRPL ...String: MAAGSRFPFC TAARLSSRGT LPRLGEATFF AGAESQRSAG AFAKTLQRPF LRAPSTQLFP VGNRLGVSSA RALVANAMEP RRFFAAAAS AKATHALQPT GTGSVAFTRP GQGSNAQFQT SLADKTRGLL GVGFLRPTKM ASFAATFLLN FRFYFMYMAR T TFQAVRPL LAFSVFGEVM KLVLATMSSG LFSFLFSFVL AFEVFYFFLQ CYISYTFLTM FFTVLF UniProtKB: Transmembrane protein |
-Macromolecule #3: ATP synthase subunit gamma
Macromolecule | Name: ATP synthase subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) Strain: ATCC 50853 / GT1 |
Molecular weight | Theoretical: 34.573031 KDa |
Sequence | String: MAGLASLSSV GALRGMRLVP AAHLLPLHSA FGQQTRNFGA GDLKIVAARM KSVKSIQKIT KAMKMVAASK LRMDQRRLEN GLPFATPVQ KLVQRIPVDP KEKGTLAVLA LSSDKGLCGG VNSFVAKQAR IVIKENEMAG NAVQVYGVGD KIRSALQRTF G DRFKRIMT ...String: MAGLASLSSV GALRGMRLVP AAHLLPLHSA FGQQTRNFGA GDLKIVAARM KSVKSIQKIT KAMKMVAASK LRMDQRRLEN GLPFATPVQ KLVQRIPVDP KEKGTLAVLA LSSDKGLCGG VNSFVAKQAR IVIKENEMAG NAVQVYGVGD KIRSALQRTF G DRFKRIMT EVTRFPWNFG QACIIADRLM QDNPARLMVI YNHFKSAVAY DTLTLNVLTP TQAAQSAKEQ LNTFEFEPEK TD VWKDLQD FYYACTVFGC MLDNIASEQS ARMSAMDNAS TNAGEMISSL TLRYNRARQA KITTELVEII SGANALE UniProtKB: ATP synthase subunit gamma, mitochondrial |
-Macromolecule #4: ATP synthase subunit delta
Macromolecule | Name: ATP synthase subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) Strain: ATCC 50853 / GT1 |
Molecular weight | Theoretical: 19.476082 KDa |
Sequence | String: MFARAFSRFA SLAAPAPQRG WNAFVLPSRH FATAAGGANP FKNQLLLTLS SPSEAIYVRT PVRSVTVPGS EGAMTMTNGH SQTVARLKA GEIIVRKGET GDEVERFFLS DGFVLFKSPE DDSGCCTAEV LGVEVVPVSM LDKESAATAL QELLQQGAGA T DEWTKART LLGQELLSSV IRAAP UniProtKB: Putative ATP synthase |
-Macromolecule #5: ATP synthase subunit epsilon
Macromolecule | Name: ATP synthase subunit epsilon / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) Strain: ATCC 50853 / GT1 |
Molecular weight | Theoretical: 8.492709 KDa |
Sequence | String: MWRSSGVSFT RYASEMAALL RQCLKEPYRT QAMQRNQIHL KETVYQQGQV LTRETFNDIK KAFEAAAKHA GEK UniProtKB: Putative atp synthase F1, epsilon subunit |
-Macromolecule #6: subunit c
Macromolecule | Name: subunit c / type: protein_or_peptide / ID: 6 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) Strain: ATCC 50853 / GT1 |
Molecular weight | Theoretical: 17.753504 KDa |
Sequence | String: MFFSRLSLSA LKAAPAREAL PGLLSRQSFS SAGFSQFSSQ KFFFSPSRNF SQSPLFQKHT PVHCNQRIAS ALVPTQQPAM TRQNPYAMQ VGARYDAGVA SLSAAIALMS VGGVAQGIGS LFAALVSGTA RNPSIKEDLF TYTLIGMGFL EFLGIICVLM S AVLLYS UniProtKB: Putative ATP synthase F0 subunit 9 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds blot.. |
-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: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6tmj: |