6TMH

Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, OSCP/F1/c-ring model


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria.

Muhleip, A.Kock Flygaard, R.Ovciarikova, J.Lacombe, A.Fernandes, P.Sheiner, L.Amunts, A.

(2021) Nat Commun 12: 120-120

  • DOI: https://doi.org/10.1038/s41467-020-20381-z
  • Primary Citation of Related Structures:  
    6TMG, 6TMH, 6TMI, 6TMJ, 6TMK, 6TML

  • PubMed 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 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 1 . 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.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibitor of F1A [auth i]145Toxoplasma gondii GT1Mutation(s): 0 
UniProt
Find proteins for A0A125YJP2 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupA0A125YJP2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha,subunit alphaB [auth A],
C [auth E],
D [auth C]
565Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for S7UU80 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupS7UU80
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit betaE [auth B],
F,
G [auth D]
560Toxoplasma gondii GT1Mutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0A125YYY4 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupA0A125YYY4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gammaH [auth g]314Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A125YUH0 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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UniProt GroupA0A125YUH0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit deltaI [auth d]183Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupA0A125YRE2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilonJ [auth e]73Toxoplasma gondii GT1Mutation(s): 0 
UniProt
Find proteins for S7VV10 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Oligomycin sensitivity conferring protein (OSCP)K [auth G]252Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A125YKF8 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
subunit c166Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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V [auth A],
X [auth E],
Z [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth B],
DA [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth C],
CA [auth B],
EA [auth D],
W [auth A],
Y [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17rc2-3612
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenNT_2015-04107
European Research CouncilSwedenERC-2018-StG-805230
Knut and Alice Wallenberg FoundationSweden2018.0080
European Molecular Biology OrganizationSwedenALTF 260-2017

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references