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Yorodumi- PDB-6tmi: Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tmi | |||||||||||||||
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Title | Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, peripheral stalk model | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / mitochondrial / ATP synthase / peripheral stalk / OSCP | |||||||||||||||
Function / homology | Function and homology information : / : / : / photosynthetic electron transport in photosystem I / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism ...: / : / : / photosynthetic electron transport in photosystem I / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / proton motive force-driven mitochondrial ATP synthesis / ADP binding / hydrolase activity / ATP binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Toxoplasma gondii (eukaryote) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Muhleip, A. / Kock Flygaard, R. / Amunts, A. | |||||||||||||||
Funding support | Sweden, 4items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6tmi.cif.gz | 237.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tmi.ent.gz | 175.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tmi_validation.pdf.gz | 1015 KB | Display | wwPDB validaton report |
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Full document | 6tmi_full_validation.pdf.gz | 1021.7 KB | Display | |
Data in XML | 6tmi_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 6tmi_validation.cif.gz | 63.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/6tmi ftp://data.pdbj.org/pub/pdb/validation_reports/tm/6tmi | HTTPS FTP |
-Related structure data
Related structure data | 10522MC 6tmgC 6tmhC 6tmjC 6tmkC 6tmlC 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: 61189.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) References: UniProt: S7UU80 |
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#2: Protein | Mass: 27669.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) References: UniProt: A0A125YKF8 |
#3: Protein | Mass: 61362.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) References: UniProt: S7V493 |
#4: Protein | Mass: 15400.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) References: UniProt: A0A125YKF7 |
#5: Protein | Mass: 64811.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) References: UniProt: S7V2T0 |
-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: Mitochondrial ATP synthase dimer, peripheral stalk / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.068 MDa / Experimental value: NO |
Source (natural) | Organism: Toxoplasma gondii GT1 (eukaryote) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: 3 seconds blot. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 4860 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 20 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203010 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |