› 6ynx

Electron Microscopy
2.5Å resolution

Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - Fo-subcomplex

Released:
DOI: 10.2210/pdb6ynx/pdb
PDB entry 6ynx coloured by chain, front view.
PDB entry 6ynx coloured by chain, side view.
PDB entry 6ynx coloured by chain, top view.
Source organism: Tetrahymena thermophila
Primary publication:
Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.
Flygaard RK, Mühleip A, Tobiasson V, Amunts A
Nat Commun 11 5342 (2020)
PMID: 33093501
Related structures: EMD-10859

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 41-mer (preferred)
PDBe Complex ID:
PDB-CPX-125273 (preferred)
Entry contents:
21 distinct polypeptide molecules
Macromolecules (21 distinct):
Ymf66 Chains: A, a
Molecule details ›
Chains: A, a
Length: 446 amino acids
Theoretical weight: 52.56 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q951C1 (Residues: 1-446; Coverage: 100%)
Gene name: ymf66
Transmembrane protein, putative Chains: B, b
Molecule details ›
Chains: B, b
Length: 381 amino acids
Theoretical weight: 43.91 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7MJ84 (Residues: 1-381; Coverage: 100%)
Gene name: TTHERM_00127260
subunit d Chains: D, d
Molecule details ›
Chains: D, d
Length: 234 amino acids
Theoretical weight: 26.75 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q239R1 (Residues: 1-234; Coverage: 100%)
Gene name: TTHERM_01188360
Sequence domains: ATP synthase D chain, mitochondrial (ATP5H)
Transmembrane protein Chains: F, f
Molecule details ›
Chains: F, f
Length: 204 amino acids
Theoretical weight: 24.27 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q24I07 (Residues: 1-204; Coverage: 100%)
Gene name: TTHERM_00571670
Transmembrane protein, putative Chains: I, i
Molecule details ›
Chains: I, i
Length: 209 amino acids
Theoretical weight: 24.4 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7LZW2 (Residues: 1-209; Coverage: 100%)
Gene name: TTHERM_00529760
Transmembrane protein, putative Chains: K, k
Molecule details ›
Chains: K, k
Length: 179 amino acids
Theoretical weight: 20.96 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7LSX6 (Residues: 1-179; Coverage: 100%)
Gene name: TTHERM_00823660
Ymf56 Chains: C, c
Molecule details ›
Chains: C, c
Length: 100 amino acids
Theoretical weight: 12.3 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q950Y8 (Residues: 1-100; Coverage: 100%)
Gene name: ymf56
Transmembrane protein, putative Chains: G, g
Molecule details ›
Chains: G, g
Length: 286 amino acids
Theoretical weight: 34.72 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7M8Q3 (Residues: 1-286; Coverage: 100%)
Gene name: TTHERM_00136220
ATPTT4 Chains: H, h
Molecule details ›
Chains: H, h
Length: 268 amino acids
Theoretical weight: 32.48 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7MCZ0 (Residues: 1-268; Coverage: 100%)
Gene name: TTHERM_00486310
ATPTT5 Chains: J, j
Molecule details ›
Chains: J, j
Length: 273 amino acids
Theoretical weight: 31.67 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q228N4 (Residues: 1-273; Coverage: 100%)
Gene name: TTHERM_01528510
Transmembrane protein Chains: L, l
Molecule details ›
Chains: L, l
Length: 247 amino acids
Theoretical weight: 29.35 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7MCQ6 (Residues: 1-247; Coverage: 100%)
Gene name: TTHERM_00649060
Transmembrane protein Chains: M, m
Molecule details ›
Chains: M, m
Length: 221 amino acids
Theoretical weight: 26.36 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7M980 (Residues: 1-221; Coverage: 100%)
Gene name: TTHERM_00316290
ATPTT8 Chains: N, n
Molecule details ›
Chains: N, n
Length: 179 amino acids
Theoretical weight: 21.78 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7LVK6 (Residues: 1-179; Coverage: 100%)
Gene name: TTHERM_00289380
ATPTT9 Chains: O, o
Molecule details ›
Chains: O, o
Length: 154 amino acids
Theoretical weight: 18.2 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q24HK1 (Residues: 1-154; Coverage: 100%)
Gene name: TTHERM_01001220
Transmembrane protein Chains: P, p
Molecule details ›
Chains: P, p
Length: 152 amino acids
Theoretical weight: 17.43 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7LZE5 (Residues: 1-152; Coverage: 100%)
Gene name: TTHERM_00825290
Carrier domain-containing protein Chains: Q, q
Molecule details ›
Chains: Q, q
Length: 152 amino acids
Theoretical weight: 17.41 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22DV8 (Residues: 1-152; Coverage: 100%)
Gene name: TTHERM_00927010
Transmembrane protein Chains: R, r
Molecule details ›
Chains: R, r
Length: 149 amino acids
Theoretical weight: 17.34 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7M0G0 (Residues: 1-149; Coverage: 100%)
Gene name: TTHERM_00068120
ATPTT13 Chains: S, s
Molecule details ›
Chains: S, s
Length: 145 amino acids
Theoretical weight: 16.82 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7MLU7 (Residues: 1-145; Coverage: 100%)
Gene name: TTHERM_00444800
FAD/NAD(P)-binding domain-containing protein Chains: E, e
Molecule details ›
Chains: E, e
Length: 480 amino acids
Theoretical weight: 54.92 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7LVQ8 (Residues: 1-480; Coverage: 100%)
Gene name: TTHERM_00137990
Sequence domains: Pyridine nucleotide-disulphide oxidoreductase
Inhibitor of F1 (IF1) Chains: i1, i2
Molecule details ›
Chains: i1, i2
Length: 108 amino acids
Theoretical weight: 12.99 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7M7C0 (Residues: 1-108; Coverage: 100%)
Gene name: TTHERM_00145490
AB hydrolase-1 domain-containing protein Chain: t
Molecule details ›
Chain: t
Length: 460 amino acids
Theoretical weight: 54.34 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: I7M7B9 (Residues: 1-460; Coverage: 100%)
Gene name: TTHERM_00145440
Sequence domains: alpha/beta hydrolase fold

Ligands and Environments

8 bound ligands:
Ligand CDL 30 x CDL
Ligand PC1 6 x PC1
Ligand PO4 2 x PO4
Ligand UQ8 2 x UQ8
Ligand ATP 2 x ATP
Ligand MG 2 x MG
Ligand PEE 4 x PEE
Ligand NAD 2 x NAD
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.5Å
Relevant EMDB volumes: EMD-10859

Quick links

Citations

5 review citations

Redesigned and reversed: architectural and functional oddities of the trypanosomal ATP synthase.
Gahura et al. (2021)
4 more