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	Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 1213, Year 2022
Publish date	Mar 8, 2022
Authors	J Kishikawa / A Nakanishi / A Nakano / S Saeki / A Furuta / T Kato / K Mistuoka / K Yokoyama /
PubMed Abstract	V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FF ATP synthase. When powered by ATP hydrolysis, the V domain rotates the central rotor against the AB hexamer, ...V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FF ATP synthase. When powered by ATP hydrolysis, the V domain rotates the central rotor against the AB hexamer, composed of three catalytic AB dimers adopting different conformations (AB, AB, and AB). Here, we report the atomic models of 18 catalytic intermediates of the V domain of V/A-ATPase under different reaction conditions, determined by single particle cryo-EM. The models reveal that the rotor does not rotate immediately after binding of ATP to the V. Instead, three events proceed simultaneously with the 120˚ rotation of the shaft: hydrolysis of ATP in AB, zipper movement in AB by the binding ATP, and unzipper movement in AB with release of both ADP and Pi. This indicates the unidirectional rotation of V/A-ATPase by a ratchet-like mechanism owing to ATP hydrolysis in AB, rather than the power stroke model proposed previously for F-ATPase.
External links	Nat Commun / PubMed:35260556 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 6.3 Å
Structure data	EMDB-31841: Nucleotide-free V/A-ATPase from Thermus thermophilus, State1 Method: EM (single particle) / Resolution: 3.1 Å 31842 7vai EMDB-31842, PDB-7vai: V1EG of V/A-ATPase from Thermus thermophilus, state1-1 Method: EM (single particle) / Resolution: 3.1 Å 31843 7vaj EMDB-31843, PDB-7vaj: Nucleotide-free V1EG domain of V/A-ATPase from Thermus thermophilus, state1-2 Method: EM (single particle) / Resolution: 3.1 Å EMDB-31844: Nucleotide-free V/A-ATPase from Thermus thermophilus, state2 Method: EM (single particle) / Resolution: 4.7 Å 31845 7vak EMDB-31845, PDB-7vak: Nucleotide-free V1EG domain of V/A-ATPase from Thermus thermophilus, state2 Method: EM (single particle) / Resolution: 4.7 Å EMDB-31846: Nucleotide-free V/A-ATPase from Thermus thermophilus, state3 Method: EM (single particle) / Resolution: 6.3 Å EMDB-31847: V/A-ATPase from Thermus thermophilus, high ATP, state1-1 Method: EM (single particle) / Resolution: 3.5 Å EMDB-31848: V/A-ATPase ftom Thermus thermophilus, high ATP, state1-2 Method: EM (single particle) / Resolution: 3.6 Å 31849 7val EMDB-31849, PDB-7val: V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state1-1 Method: EM (single particle) / Resolution: 3.1 Å 31850 7vam EMDB-31850, PDB-7vam: V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state1-2 Method: EM (single particle) / Resolution: 3.2 Å EMDB-31851: V/A-ATPase from Thermus thermophilus, high ATP, state2-1 Method: EM (single particle) / Resolution: 3.3 Å EMDB-31852: V/A-ATPase from Thermus thermophilus, high ATP, state2-2 Method: EM (single particle) / Resolution: 4.0 Å 31853 7van EMDB-31853, PDB-7van: V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state2-1 Method: EM (single particle) / Resolution: 3.0 Å 31854 7vao EMDB-31854, PDB-7vao: V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state2-2 Method: EM (single particle) / Resolution: 3.4 Å EMDB-31855: V/A-ATPase from Thermus thermophilus, high ATP, state3-1 Method: EM (single particle) / Resolution: 3.3 Å EMDB-31856: V/A-ATPase from Thermus thermophilus, high ATP, state3-2 Method: EM (single particle) / Resolution: 4.5 Å 31857 7vap EMDB-31857, PDB-7vap: V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state2-2 Method: EM (single particle) / Resolution: 3.0 Å 31858 7vaq EMDB-31858, PDB-7vaq: V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state3-2 Method: EM (single particle) / Resolution: 3.6 Å EMDB-31859: V/A-ATPase from Thermus thermophilus at low ATP concentration, state1 Method: EM (single particle) / Resolution: 2.7 Å 31860 7var EMDB-31860, PDB-7var: V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP concentration, state1-1 Method: EM (single particle) / Resolution: 2.9 Å 31861 7vas EMDB-31861, PDB-7vas: V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP concentration, state1-2 Method: EM (single particle) / Resolution: 3.0 Å EMDB-31862: V/A-ATPase from Thermus thermophilus at low ATP concentration, state2 Method: EM (single particle) / Resolution: 3.3 Å 31863 7vat EMDB-31863, PDB-7vat: V1EG of V/A-ATPase from Thermus thermophilus at low ATP concentration, state2-1 Method: EM (single particle) / Resolution: 3.2 Å 31864 7vau EMDB-31864, PDB-7vau: V1EG of V/A-ATPase from Thermus thermophilus at low ATP concentration, state2-2 Method: EM (single particle) / Resolution: 3.3 Å EMDB-31865: V/A-ATPase from Thermus thermophilus at low ATP concentration, state3 Method: EM (single particle) / Resolution: 3.6 Å 31866 7vav EMDB-31866, PDB-7vav: V1EG of V/A-ATPase from Thermus thermophilus at low ATP concentration, state3 Method: EM (single particle) / Resolution: 2.8 Å EMDB-31867: V/A-ATPase from Thermus thermophilus at saturated ATP-gamma-S condition, state1 Method: EM (single particle) / Resolution: 2.7 Å 31868 7vaw EMDB-31868, PDB-7vaw: V1EG domain of V/A-ATPase from Thermus thermophilus at saturated ATP-gamma-S condition, state1-1 Method: EM (single particle) / Resolution: 2.7 Å 31869 7vax EMDB-31869, PDB-7vax: V1EG of V/A-ATPase from Thermus thermophilus at saturated ATP-gamma-S condition, state1-2 Method: EM (single particle) / Resolution: 2.9 Å EMDB-31870: V/A-ATPase from Thermus thermophilus at saturated ATP-gamma-S condition, state2 Method: EM (single particle) / Resolution: 3.3 Å 31871 7vay EMDB-31871, PDB-7vay: V1EG domain of V/A-ATPase from Thermus thermophilus at saturated ATP-gamma-S condition, state2 Method: EM (single particle) / Resolution: 3.3 Å EMDB-31872: V/A-ATPase from Thermus thermophilus at saturated ATP-gamma-S condition, state3 Method: EM (single particle) / Resolution: 3.6 Å 31873 7vb0 EMDB-31873, PDB-7vb0: V1EG domain of V/A-ATPase from Thermus thermophilus at saturated ATP-gamma-S condition, state3 Method: EM (single particle) / Resolution: 3.6 Å
Chemicals	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-PO4: PHOSPHATE ION ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM
Source	thermus thermophilus hb8 (bacteria)
Keywords	MOTOR PROTEIN / rotary ATPase / V-type ATPase / ATP synthase / Thermus thermophilus / chemo-mechanical coupling