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- PDB-6tmi: Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase... -

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Basic information

Entry
Database: PDB / ID: 6tmi
TitleCryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, peripheral stalk model
Components
  • ATP synthase subunit alpha
  • ATPTG12
  • Oligomycin sensitivity conferring protein (OSCP)
  • subunit b
  • subunit d
KeywordsMEMBRANE PROTEIN / mitochondrial / ATP synthase / peripheral stalk / OSCP
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane / hydrolase activity / ATP binding
Similarity search - Function
ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATP synthase subunit alpha, N-terminal domain-like superfamily ...ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein / ATP synthase F1, delta subunit protein / ATP synthase subunit alpha / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMuhleip, A. / Kock Flygaard, R. / Amunts, A.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research CouncilERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Molecular Biology OrganizationALTF 260-2017 Sweden
CitationJournal: 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
DepositionDec 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Assembly

Deposited unit
C: ATP synthase subunit alpha
G: Oligomycin sensitivity conferring protein (OSCP)
A: subunit d
R: ATPTG12
B: subunit b


Theoretical massNumber of molelcules
Total (without water)230,4345
Polymers230,4345
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15720 Å2
ΔGint-137 kcal/mol
Surface area33290 Å2
MethodPISA

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Components

#1: Protein ATP synthase subunit alpha /


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
#2: Protein Oligomycin sensitivity conferring protein (OSCP)


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 subunit d


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 ATPTG12


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 subunit b


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial ATP synthase dimer, peripheral stalk / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.068 MDa / Experimental value: NO
Source (natural)Organism: Toxoplasma gondii GT1 (eukaryote)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: 3 seconds blot.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 4860
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2EPUimage acquisition
4GctfCTF correction
9PHENIX1.17rc2-3612model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203010 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingSpace: REAL

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