Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Mechanism of ATP hydrolysis dependent rotation of bacterial ATP synthase.
Journal, issue, pages	Nat Commun, Vol. 14, Issue 1, Page 4090, Year 2023
Publish date	Jul 10, 2023
Authors	Atsuki Nakano / Jun-Ichi Kishikawa / Kaoru Mitsuoka / Ken Yokoyama /
PubMed Abstract	F domain of ATP synthase is a rotary ATPase complex in which rotation of central γ-subunit proceeds in 120° steps against a surrounding αβ fueled by ATP hydrolysis. How the ATP hydrolysis ...F domain of ATP synthase is a rotary ATPase complex in which rotation of central γ-subunit proceeds in 120° steps against a surrounding αβ fueled by ATP hydrolysis. How the ATP hydrolysis reactions occurring in three catalytic αβ dimers are coupled to mechanical rotation is a key outstanding question. Here we describe catalytic intermediates of the F domain in FF synthase from Bacillus PS3 sp. during ATP mediated rotation captured using cryo-EM. The structures reveal that three catalytic events and the first 80° rotation occur simultaneously in F domain when nucleotides are bound at all the three catalytic αβ dimers. The remaining 40° rotation of the complete 120° step is driven by completion of ATP hydrolysis at αβ, and proceeds through three sub-steps (83°, 91°, 101°, and 120°) with three associated conformational intermediates. All sub-steps except for one between 91° and 101° associated with phosphate release, occur independently of the chemical cycle, suggesting that the 40° rotation is largely driven by release of intramolecular strain accumulated by the 80° rotation. Together with our previous results, these findings provide the molecular basis of ATP driven rotation of ATP synthases.
External links	Nat Commun / PubMed:37429854 / PubMed Central
Methods	EM (single particle)
Resolution	2.5 - 8.8 Å
Structure data	34748 8hh1 EMDB-34748: FoF1-ATPase from Bacillus PS3,hydrolyzable,highATP PDB-8hh1: FoF1-ATPase from Bacillus PS3, 81 degrees, highATP Method: EM (single particle) / Resolution: 2.9 Å 34749 8hh2 EMDB-34749, PDB-8hh2: F1 domain of FoF1-ATPase from Bacillus PS3,post-hyd,highATP Method: EM (single particle) / Resolution: 3.0 Å 34750 8hh3 EMDB-34750, PDB-8hh3: F1 domain of FoF1-ATPase from Bacillus PS3,90 degrees,highATP Method: EM (single particle) / Resolution: 4.3 Å 34751 8hh4 EMDB-34751, PDB-8hh4: F1 domain of FoF1-ATPase from Bacillus PS3,101 degrees, highATP Method: EM (single particle) / Resolution: 3.1 Å 34752 8hh5 EMDB-34752, PDB-8hh5: F1 domain of FoF1-ATPase from Bacillus PS3,120 degrees,highATP Method: EM (single particle) / Resolution: 2.9 Å 34753 8hh6 EMDB-34753, PDB-8hh6: F1 domain of FoF1-ATPase from Bacillus PS3,step waiting,highATP Method: EM (single particle) / Resolution: 2.9 Å 34754 8hh7 EMDB-34754, PDB-8hh7: F1 domain of FoF1-ATPase from Bacillus PS3, 81 degrees, lowATP Method: EM (single particle) / Resolution: 2.5 Å 34755 8hh8 EMDB-34755, PDB-8hh8: F1 domain of FoF1-ATPase from Bacillus PS3,post-hyd,lowATP Method: EM (single particle) / Resolution: 2.8 Å 34756 8hh9 EMDB-34756, PDB-8hh9: F1 domain of FoF1-ATPase from Bacillus PS3, 90 degrees, low ATP Method: EM (single particle) / Resolution: 3.6 Å 34757 8hha EMDB-34757, PDB-8hha: F1 domain of FoF1-ATPase from Bacillus PS3,120 degrees,lowATP Method: EM (single particle) / Resolution: 3.4 Å 34758 8hhb EMDB-34758, PDB-8hhb: F1 domain of FoF1-ATPase from Bacillus PS3,step waiting,lowATP Method: EM (single particle) / Resolution: 3.5 Å EMDB-34759: FoF1-ATPase from Bacillus PS3,hydrolyzable,state1,highATP Method: EM (single particle) / Resolution: 3.0 Å 34760 8hhc EMDB-34760, PDB-8hhc: F1 domain of FoF1-ATPase from Bacillus PS3,post-hyd',lowATP Method: EM (single particle) / Resolution: 3.3 Å EMDB-34761: FoF1-ATPase from Bacillus PS3,hydrolyzable,state2,highATP Method: EM (single particle) / Resolution: 3.3 Å EMDB-34762: FoF1-ATPase from Bacillus PS3,post-hyd,state1,highATP Method: EM (single particle) / Resolution: 3.4 Å EMDB-34763: FoF1-ATPase from Bacillus PS3,hydrolyzable,state3,highATP Method: EM (single particle) / Resolution: 3.1 Å EMDB-34764: FoF1-ATPase from Bacillus PS3,post-hyd,state2,highATP Method: EM (single particle) / Resolution: 3.8 Å EMDB-34765: FoF1-ATPase from Bacillus PS3,post-hyd,state3,highATP Method: EM (single particle) / Resolution: 3.8 Å EMDB-34766: FoF1-ATPase from Bacillus PS3,90 degrees,state1,highATP Method: EM (single particle) / Resolution: 6.7 Å EMDB-34767: FoF1-ATPase from Bacillus PS3,90 degrees,state2,highATP Method: EM (single particle) / Resolution: 8.0 Å EMDB-34768: FoF1-ATPase from Bacillus PS3,100 degrees,state1,highATP Method: EM (single particle) / Resolution: 3.6 Å EMDB-34769: FoF1-ATPase from Bacillus PS3,100 degrees,state2,highATP Method: EM (single particle) / Resolution: 4.1 Å EMDB-34770: FoF1-ATPase from Bacillus PS3,100 degrees,state3,highATP Method: EM (single particle) / Resolution: 3.6 Å EMDB-34771: FoF1-ATPase from Bacillus PS3,120 degrees,state1,highATP Method: EM (single particle) / Resolution: 3.6 Å EMDB-34772: FoF1-ATPase from Bacillus PS3,120 degrees,state2,highATP Method: EM (single particle) / Resolution: 3.9 Å EMDB-34773: FoF1-ATPase from Bacillus PS3,120 degrees,state3,highATP Method: EM (single particle) / Resolution: 3.8 Å EMDB-34774: FoF1-ATPase from Bacillus PS3,step waiting, state1,highATP Method: EM (single particle) / Resolution: 3.3 Å EMDB-34775: FoF1-ATPase from Bacillus PS3,step waiting,state2,highATP Method: EM (single particle) / Resolution: 3.8 Å EMDB-34776: FoF1-ATPase from Bacillus PS3,step waiting,state3,highATP Method: EM (single particle) / Resolution: 3.6 Å EMDB-34777: FoF1-ATPase from Bacillus PS3, 81 degrees, state1,lowATP Method: EM (single particle) / Resolution: 2.9 Å EMDB-34778: FoF1-ATPase from Bacillus PS3,post-hyd,state1,lowATP Method: EM (single particle) / Resolution: 3.1 Å EMDB-34779: FoF1-ATPase from Bacillus PS3,81 degrees,state2,lowATP Method: EM (single particle) / Resolution: 3.0 Å EMDB-34780: FoF1-ATPase from Bacillus PS3,81 degrees,state3,lowATP Method: EM (single particle) / Resolution: 3.1 Å EMDB-34781: FoF1-ATPase from Bacillus PS3,post-hyd,state2,lowATP Method: EM (single particle) / Resolution: 3.2 Å EMDB-34782: FoF1-ATPase from Bacillus PS3,post-hyd',state1,lowATP Method: EM (single particle) / Resolution: 3.7 Å EMDB-34783: FoF1-ATPase from Bacillus PS3,post-hyd',state2,lowATP Method: EM (single particle) / Resolution: 4.2 Å EMDB-34784: FoF1-ATPase from Bacillus PS3,90 degrees,state1,lowATP Method: EM (single particle) / Resolution: 4.2 Å EMDB-34785: FoF1-ATPase from Bacillus PS3,90 degrees,state3,lowATP Method: EM (single particle) / Resolution: 4.2 Å EMDB-34786: FoF1-ATPase from Bacillus PS3,120 degrees,state1,lowATP Method: EM (single particle) / Resolution: 3.9 Å EMDB-34787: FoF1-ATPase from Bacillus PS3,120 degrees,state2,lowATP Method: EM (single particle) / Resolution: 4.2 Å EMDB-34788: FoF1-ATPase from Bacillus PS3,step waiting,state1,lowATP Method: EM (single particle) / Resolution: 3.9 Å EMDB-34789: FoF1-ATPase from Bacillus PS3,step waiting,state2,lowATP Method: EM (single particle) / Resolution: 4.2 Å EMDB-34790: FoF1-ATPase from Bacillus PS3,step waiting,state3,lowATP Method: EM (single particle) / Resolution: 7.0 Å EMDB-35373: FoF1-ATPase from Bacillus PS3,90 degrees,state3,highATP Method: EM (single particle) / Resolution: 8.8 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-PO4: PHOSPHATE ION ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM
Source	bacillus sp. ps3 (bacteria)
Keywords	MOTOR PROTEIN / ATP synthase / ATP synthase F1 / ATPase FoF1 / TRANSLOCASE/MOTOR PROTEIN / ATP synthase F1 ATPase FoF1 / TRANSLOCASE-MOTOR PROTEIN complex