6YO0

Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1/peripheral stalk


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.

Flygaard, R.K.Muhleip, A.Tobiasson, V.Amunts, A.

(2020) Nat Commun 11: 5342-5342

  • DOI: https://doi.org/10.1038/s41467-020-18993-6
  • Primary Citation of Related Structures:  
    6YNV, 6YNW, 6YNX, 6YNY, 6YNZ, 6YO0

  • PubMed Abstract: 

    Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF 1 . Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.


  • 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
Oligomycin sensitivity-conferring protein (OSCP)A [auth G1]219Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I7MMI7 (Tetrahymena thermophila (strain SB210))
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UniProt GroupI7MMI7
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gammaB [auth g1]299Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q22Z05 (Tetrahymena thermophila (strain SB210))
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UniProt GroupQ22Z05
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alphaC [auth C1],
E [auth B1],
G [auth A1]
546Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q24HY8 (Tetrahymena thermophila (strain SB210))
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UniProt GroupQ24HY8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit betaD [auth D1],
F [auth F1],
H [auth E1]
497Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I7LZV1 (Tetrahymena thermophila (strain SB210))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibitor of F1 (IF1)I [auth i1]108Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for I7M7C0 (Tetrahymena thermophila (strain SB210))
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UniProt GroupI7M7C0
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT13J [auth s]145Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
subunit bK [auth b]381Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I7MJ84 (Tetrahymena thermophila (strain SB210))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
subunit dL [auth d]234Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for Q239R1 (Tetrahymena thermophila (strain SB210))
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
M [auth C1],
Q [auth B1],
S [auth A1]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
O [auth D1],
U [auth E1]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth C1],
P [auth D1],
R [auth B1],
T [auth A1],
V [auth E1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenNT_2015-04107
European Research Council (ERC)SwedenERC-2018-StG-805230
Knut and Alice Wallenberg FoundationSweden2018.0080

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references