› 7y5b

Electron Microscopy
4.4Å resolution

Cryo-EM structure of F-ATP synthase from Mycolicibacterium smegmatis (rotational state 1)

Released:
DOI: 10.2210/pdb7y5b/pdb
PDB entry 7y5b coloured by chain, front view.
PDB entry 7y5b coloured by chain, side view.
PDB entry 7y5b coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis
Primary publication:
Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors.
Wong CF, Saw WG, Basak S, Sano M, Ueno H, Kerk HW, Litty D, Ragunathan P, Dick T, Müller V, Noji H, Grüber G
Antimicrob Agents Chemother e0105622 (2022)
PMID: 36445139
Related structures: EMD-33615

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 icosamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106416 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
ATP synthase subunit alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 548 amino acids
Theoretical weight: 58.95 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: A0R202 (Residues: 1-548; Coverage: 100%)
Gene names: MSMEG_4938, MSMEI_4811, atpA
Sequence domains:
ATP synthase subunit alpha Chain: C
Molecule details ›
Chain: C
Length: 548 amino acids
Theoretical weight: 58.51 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: A0R202 (Residues: 1-548; Coverage: 100%)
Gene names: MSMEG_4938, MSMEI_4811, atpA
Sequence domains:
ATP synthase subunit beta Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 481 amino acids
Theoretical weight: 52.5 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: A0R200 (Residues: 2-475; Coverage: 100%)
Gene names: MSMEG_4936, MSMEI_4809, atpD
Sequence domains:
ATP synthase gamma chain Chain: G
Molecule details ›
Chain: G
Length: 307 amino acids
Theoretical weight: 33.44 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: A0R201 (Residues: 1-307; Coverage: 100%)
Gene names: MSMEG_4937, MSMEI_4810, atpG
Sequence domains: ATP synthase
ATP synthase epsilon chain Chain: H
Molecule details ›
Chain: H
Length: 121 amino acids
Theoretical weight: 13.28 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: A0R1Z9 (Residues: 1-121; Coverage: 100%)
Gene names: MSMEG_4935, MSMEI_4808, atpC
Sequence domains: ATP synthase, Delta/Epsilon chain, beta-sandwich domain
ATP synthase subunit a Chain: a
Molecule details ›
Chain: a
Length: 252 amino acids
Theoretical weight: 27.57 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: A0R206 (Residues: 1-252; Coverage: 100%)
Gene names: MSMEG_4942, atpB
Sequence domains: ATP synthase A chain
ATP synthase subunit b Chain: b
Molecule details ›
Chain: b
Length: 170 amino acids
Theoretical weight: 17.64 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: A0R204 (Residues: 1-170; Coverage: 100%)
Gene names: MSMEG_4940, MSMEI_4813, atpF
Sequence domains: ATP synthase B/B' CF(0)
ATP synthase subunit b-delta Chain: d
Molecule details ›
Chain: d
Length: 445 amino acids
Theoretical weight: 47.5 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: A0R203 (Residues: 1-445; Coverage: 100%)
Gene names: MSMEG_4939, MSMEI_4812, atpF, atpFH, atpH
Sequence domains:
ATP synthase subunit c Chains: 1, 2, 3, 4, 5, 6, 7, 8, 9
Molecule details ›
Chains: 1, 2, 3, 4, 5, 6, 7, 8, 9
Length: 86 amino acids
Theoretical weight: 8.6 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: A0R205 (Residues: 1-86; Coverage: 100%)
Gene names: MSMEG_4941, atpE
Sequence domains: ATP synthase subunit C

Ligands and Environments

3 bound ligands:
Ligand ATP 5 x ATP
Ligand MG 5 x MG
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.4Å
Relevant EMDB volumes: EMD-33615
Expression system: Mycolicibacterium smegmatis

Quick links

Citations

1 citations in other articles

ATP binding by an F1Fo ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria.
Krah et al. (2023)

1 mention without citation

Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors.
Wong et al. (2022)