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 6TML | pdb_00006tml

Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase hexamer, composite model


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 7,546.03 kDa 
  • Atom Count: 388,650 
  • Modeled Residue Count: 49,776 
  • Deposited Residue Count: 68,508 
  • Unique protein chains: 32

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG11134Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG7236Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG14133Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG5252Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit k157Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit a224Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit i/j229Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG13128Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG15126Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG6239Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG3325Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG17,ATPTG17,ATPTG1783Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit b571Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG12134Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG10138Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit f111Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG8208Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG1398Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG2310Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit 8205Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG9166Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG4267Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPTG16106Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit d536Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Oligomycin sensitivity conferring protein (OSCP)252Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Inhibitor of F1145Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha565Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit beta560Toxoplasma gondii GT1Mutation(s): 0 
EC: 7.1.2.2
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit gamma314Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit delta183Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilon73Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
subunit c166Toxoplasma gondii GT1Mutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.17rc2-3612

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
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary