› 8apj

Electron Microscopy
3.8Å resolution

rotational state 2d of Trypanosoma brucei mitochondrial ATP synthase

Released:
DOI: 10.2210/pdb8apj/pdb
PDB entry 8apj coloured by chain, front view.
PDB entry 8apj coloured by chain, side view.
PDB entry 8apj coloured by chain, top view.
Source organism: Trypanosoma brucei brucei
Primary publication:
An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.
Gahura O, Mühleip A, Hierro-Yap C, Panicucci B, Jain M, Hollaus D, Slapničková M, Zíková A, Amunts A
OpenAccess logo Nat Commun 13 5989 (2022)
PMID: 36220811
Related structures: EMD-15572

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 42-mer (preferred)
PDBe Complex ID:
PDB-CPX-103065 (preferred)
Entry contents:
25 distinct polypeptide molecules
Macromolecules (25 distinct):
subunit-e Chains: L, l
Molecule details ›
Chains: L, l
Length: 92 amino acids
Theoretical weight: 10.45 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q387J1 (Residues: 15-106; Coverage: 87%)
Gene name: Tb11.03.0475
T. brucei spp.-specific protein Chains: M, m
Molecule details ›
Chains: M, m
Length: 144 amino acids
Theoretical weight: 16.09 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: C9ZJA0 (Residues: 1-144; Coverage: 100%)
Gene name: TbgDal_II1950
ATP synthase subunit a Chain: a
Molecule details ›
Chain: a
Length: 231 amino acids
Theoretical weight: 28.71 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: P24499 (Residues: 1-22, 23-178, 179-229; Coverage: 100%)
Gene names: ATP6, MURF4
subunit-8 Chain: c
Molecule details ›
Chain: c
Length: 114 amino acids
Theoretical weight: 13.75 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q585K5 (Residues: 1-114; Coverage: 100%)
Gene names: Tb04.26G5.190, Tb927.4.3450
subunit-d Chain: d
Molecule details ›
Chain: d
Length: 370 amino acids
Theoretical weight: 43.38 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57ZW9 (Residues: 1-370; Coverage: 100%)
Gene names: Tb05.26K5.220, Tb927.5.2930
Letm1 RBD domain-containing protein Chain: e
Molecule details ›
Chain: e
Length: 396 amino acids
Theoretical weight: 46.88 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38CI8 (Residues: 1-396; Coverage: 100%)
Gene name: Tb10.70.7760
subunit-f Chain: f
Molecule details ›
Chain: f
Length: 145 amino acids
Theoretical weight: 17.18 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57ZE2 (Residues: 1-145; Coverage: 100%)
Gene names: Tb03.30P12.300, Tb927.3.1690
ATPTB3 Chain: g
Molecule details ›
Chain: g
Length: 269 amino acids
Theoretical weight: 27.65 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: A0A3L6KRX7 (Residues: 1-269; Coverage: 100%)
Gene name: DPX39_000041900
ATPTB4 Chain: h
Molecule details ›
Chain: h
Length: 157 amino acids
Theoretical weight: 17.22 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q389Z3 (Residues: 1-157; Coverage: 100%)
Gene name: Tb10.6k15.0480
subunit-i/j Chain: i
Molecule details ›
Chain: i
Length: 104 amino acids
Theoretical weight: 12.66 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57ZM4 (Residues: 1-104; Coverage: 100%)
Gene names: Tb03.27C5.274, Tb927.3.2880
Transmembrane protein Chain: j
Molecule details ›
Chain: j
Length: 169 amino acids
Theoretical weight: 20.31 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: D0A5R7 (Residues: 1-169; Coverage: 100%)
Gene name: TbgDal_XI1340
subunit-k Chain: k
Molecule details ›
Chain: k
Length: 124 amino acids
Theoretical weight: 14.53 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57VT0 (Residues: 1-124; Coverage: 100%)
Gene names: Tb07.29K4.425, Tb927.7.840
ATPTB11 Chain: n
Molecule details ›
Chain: n
Length: 156 amino acids
Theoretical weight: 17.93 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q582T1 (Residues: 1-156; Coverage: 100%)
Gene names: Tb03.48O8.780, Tb927.3.2180
ATPTB12 Chain: o
Molecule details ›
Chain: o
Length: 101 amino acids
Theoretical weight: 11.68 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57Z84 (Residues: 1-101; Coverage: 100%)
Gene names: Tb05.27M3.50, Tb927.5.3090
subunit-b Chain: p
Molecule details ›
Chain: p
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: C9ZLR9 (Residues: 65-169; Coverage: 62%)
Gene name: TbgDal_IV490
ATPEG3 Chain: q
Molecule details ›
Chain: q
Length: 98 amino acids
Theoretical weight: 12.29 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q583U4 (Residues: 1-98; Coverage: 100%)
Gene names: Tb06.3D8.274, Tb927.6.590
ATPEG4 Chain: r
Molecule details ›
Chain: r
Length: 62 amino acids
Theoretical weight: 7.65 KDa
Source organism: Trypanosoma brucei brucei
ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein Chain: H1
Molecule details ›
Chain: H1
Length: 182 amino acids
Theoretical weight: 20.17 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q586H1 (Residues: 1-182; Coverage: 100%)
Gene names: Tb06.30P15.500, Tb927.6.4990
Sequence domains: ATP synthase, Delta/Epsilon chain, beta-sandwich domain
ATP synthase subunit epsilon, mitochondrial Chain: I1
Molecule details ›
Chain: I1
Length: 75 amino acids
Theoretical weight: 8.71 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: P0DPG3 (Residues: 1-75; Coverage: 100%)
Gene name: Tb427.10.5050
Sequence domains: Mitochondrial ATP synthase epsilon chain
ATP synthase subunit p18, mitochondrial Chains: J1, K1, L1
Molecule details ›
Chains: J1, K1, L1
Length: 188 amino acids
Theoretical weight: 21.27 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: P0DPG4 (Residues: 1-188; Coverage: 100%)
Gene name: Tb427.05.1710
ATP synthase delta chain, mitochondrial Chain: M1
Molecule details ›
Chain: M1
Length: 255 amino acids
Theoretical weight: 28.87 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38AG1 (Residues: 1-255; Coverage: 100%)
Gene name: Tb10.6k15.2510
Sequence domains: ATP synthase delta (OSCP) subunit
V-ATPase proteolipid subunit C-like domain-containing protein Chains: O1, P1, Q1, R1, S1, T1, U1, V1, W1, X1
Molecule details ›
Chains: O1, P1, Q1, R1, S1, T1, U1, V1, W1, X1
Length: 118 amino acids
Theoretical weight: 12.4 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38C84 (Residues: 1-118; Coverage: 100%)
Gene name: Tb10.70.6340
Sequence domains: ATP synthase subunit C
ATP synthase subunit gamma, mitochondrial Chain: G1
Molecule details ›
Chain: G1
Length: 305 amino acids
Theoretical weight: 34.47 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: A0A161CM65 (Residues: 1-305; Coverage: 100%)
Sequence domains: ATP synthase
ATP synthase subunit alpha, mitochondrial Chains: A1, B1, C1
Molecule details ›
Chains: A1, B1, C1
Length: 584 amino acids
Theoretical weight: 63.57 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q9GS23 (Residues: 1-584; Coverage: 100%)
Gene names: Tb427.07.7420, Tb427.07.7430
Sequence domains:
ATP synthase subunit beta, mitochondrial Chains: D1, E1, F1
Molecule details ›
Chains: D1, E1, F1
Length: 519 amino acids
Theoretical weight: 55.84 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q9GPE9 (Residues: 1-519; Coverage: 100%)
Gene name: Tb427.03.1380
Sequence domains:

Ligands and Environments

9 bound ligands:
Ligand CDL 14 x CDL
Ligand PEE 3 x PEE
Ligand LMT 2 x LMT
Ligand Q7G 2 x Q7G
Ligand PC1 4 x PC1
Ligand UTP 1 x UTP
Ligand ATP 4 x ATP
Ligand MG 5 x MG
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-15572

Quick links

Citations

2 review citations

The mystery of massive mitochondrial complexes: the apicomplexan respiratory chain.
Maclean et al. (2022)
1 more