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	Structure of ATP synthase under strain during catalysis.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 2232, Year 2022
Publish date	Apr 25, 2022
Authors	Hui Guo / John L Rubinstein /
PubMed Abstract	ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor ...ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor subcomplex and are held stationary relative to each other by a peripheral stalk. Structures of resting mitochondrial ATP synthases revealed a left-handed curvature of the peripheral stalk even though rotation of the rotor, driven by either ATP hydrolysis in F or proton translocation through F, would apply a right-handed bending force to the stalk. We used cryoEM to image yeast mitochondrial ATP synthase under strain during ATP-hydrolysis-driven rotary catalysis, revealing a large deformation of the peripheral stalk. The structures show how the peripheral stalk opposes the bending force and suggests that during ATP synthesis proton translocation causes accumulation of strain in the stalk, which relaxes by driving the relative rotation of the rotor through six sub-steps within F, leading to catalysis.
External links	Nat Commun / PubMed:35468906 / PubMed Central
Methods	EM (single particle)
Resolution	3.2 - 8.4 Å
Structure data	25930 7tjs EMDB-25930, PDB-7tjs: Yeast ATP synthase F1 region State 1-3catalytic beta_tight closed without exogenous ATP Method: EM (single particle) / Resolution: 3.2 Å 25931 7tjt EMDB-25931, PDB-7tjt: Yeast ATP synthase F1 region State 1-3catalytic beta_tight open without exogenous ATP Method: EM (single particle) / Resolution: 3.2 Å 25932 7tju EMDB-25932, PDB-7tju: Yeast ATP synthase F1 region State 1-3binding beta_tight open without exogenous ATP Method: EM (single particle) / Resolution: 3.3 Å 25933 7tjv EMDB-25933, PDB-7tjv: Yeast ATP synthase F1 region State 1catalytic(a) with 10 mM ATP Method: EM (single particle) / Resolution: 3.6 Å 25934 7tjw EMDB-25934, PDB-7tjw: Yeast ATP synthase F1 region State 1catalytic(e-h) with 10 mM ATP Method: EM (single particle) / Resolution: 4.0 Å EMDB-25935: Yeast ATP synthase F1 region State 1catalytic beta_tight closed without exogenous ATP Method: EM (single particle) / Resolution: 3.4 Å EMDB-25936: Yeast ATP synthase F1 region State 1catalytic beta_tight open without exogenous ATP Method: EM (single particle) / Resolution: 3.5 Å EMDB-25937: Yeast ATP synthase F1 region State 1binding beta_tight open without exogenous ATP Method: EM (single particle) / Resolution: 3.7 Å EMDB-25938: Yeast ATP synthase F1 region State 2catalytic beta_tight closed without exogenous ATP Method: EM (single particle) / Resolution: 3.4 Å 25939 7tjx EMDB-25939, PDB-7tjx: Yeast ATP synthase F1 region State 1binding(a-d) with 10 mM ATP Method: EM (single particle) / Resolution: 4.0 Å EMDB-25940: Yeast ATP synthase F1 region State 2catalytic beta_tight open without exogenous ATP Method: EM (single particle) / Resolution: 3.5 Å EMDB-25941: Yeast ATP synthase F1 region State 2binding beta_tight open without exogenous ATP Method: EM (single particle) / Resolution: 3.4 Å EMDB-25942: Yeast ATP synthase F1 region State 3catalytic beta_tight closed without exogenous ATP Method: EM (single particle) / Resolution: 3.6 Å EMDB-25943: Yeast ATP synthase F1 region State 3catalytic beta_tight open without exogenous ATP Method: EM (single particle) / Resolution: 3.4 Å EMDB-25944: Yeast ATP synthase F1 region State 3binding beta_tight open without exogenous ATP Method: EM (single particle) / Resolution: 3.7 Å EMDB-25945: Yeast ATP synthase OSCP without exogenous ATP Method: EM (single particle) / Resolution: 3.3 Å 25946 7tjy EMDB-25946, PDB-7tjy: Yeast ATP synthase State 1catalytic(a) without exogenous ATP backbone model Method: EM (single particle) / Resolution: 3.8 Å 25947 7tjz EMDB-25947, PDB-7tjz: Yeast ATP synthase State 1catalytic(b) without exogenous ATP backbone model Method: EM (single particle) / Resolution: 4.4 Å 25948 7tk0 EMDB-25948, PDB-7tk0: Yeast ATP synthase State 1catalytic(c) without exogenous ATP backbone model Method: EM (single particle) / Resolution: 4.4 Å 25949 7tk1 EMDB-25949, PDB-7tk1: Yeast ATP synthase State 1catalytic(d) without exogenous ATP backbone model Method: EM (single particle) / Resolution: 7.1 Å EMDB-25950: Yeast ATP synthase peripheral stalk without exogenous ATP Method: EM (single particle) / Resolution: 3.7 Å EMDB-25951: Yeast ATP synthase FO region without exogenous ATP Method: EM (single particle) / Resolution: 3.7 Å EMDB-25952: Yeast ATP synthase composite map without exogenous ATP Method: EM (single particle) / Resolution: 3.3 Å EMDB-25953: Yeast ATP synthase with 10 mM ATP showing strained peripheral stalk determined by a screening microscope Method: EM (single particle) / Resolution: 8.4 Å 25954 7tk2 EMDB-25954, PDB-7tk2: Yeast ATP synthase State 1binding(a) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 6.5 Å 25955 7tk3 EMDB-25955, PDB-7tk3: Yeast ATP synthase State 1binding(b) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 6.3 Å 25956 7tk4 EMDB-25956, PDB-7tk4: Yeast ATP synthase State 1binding(c) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.0 Å 25957 7tk5 EMDB-25957, PDB-7tk5: Yeast ATP synthase State 1binding(d) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.8 Å 25958 7tk6 EMDB-25958, PDB-7tk6: Yeast ATP synthase State 1catalytic(a) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 6.5 Å 25959 7tk7 EMDB-25959, PDB-7tk7: Yeast ATP synthase State 1catalytic(b) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 6.7 Å 25960 7tk8 EMDB-25960, PDB-7tk8: Yeast ATP synthase State 1catalytic(c) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 4.7 Å 25961 7tk9 EMDB-25961, PDB-7tk9: Yeast ATP synthase State 1catalytic(d) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 6.0 Å 25962 7tka EMDB-25962, PDB-7tka: Yeast ATP synthase State 1catalytic(e) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.1 Å 25963 7tkb EMDB-25963, PDB-7tkb: Yeast ATP synthase State 1catalytic(f) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 6.3 Å 25964 7tkc EMDB-25964, PDB-7tkc: Yeast ATP synthase State 1catalytic(g) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 5.8 Å 25965 7tkd EMDB-25965, PDB-7tkd: Yeast ATP synthase State 1catalytic(h) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.7 Å 25966 7tke EMDB-25966, PDB-7tke: Yeast ATP synthase State 2binding(a) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.1 Å 25967 7tkf EMDB-25967, PDB-7tkf: Yeast ATP synthase State 2binding(b) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.1 Å 25968 7tkg EMDB-25968, PDB-7tkg: Yeast ATP synthase State 2catalytic(a) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 4.5 Å 25969 7tkh EMDB-25969, PDB-7tkh: Yeast ATP synthase State 2catalytic(b) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 4.4 Å 25970 7tki EMDB-25970, PDB-7tki: Yeast ATP synthase State 2catalytic(c) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.1 Å 25971 7tkj EMDB-25971, PDB-7tkj: Yeast ATP synthase State 2catalytic(d) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.5 Å 25972 7tkk EMDB-25972, PDB-7tkk: Yeast ATP synthase State 2catalytic(e) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.3 Å 25973 7tkl EMDB-25973, PDB-7tkl: Yeast ATP synthase State 3binding(a) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 6.4 Å 25974 7tkm EMDB-25974, PDB-7tkm: Yeast ATP synthase State 3binding(b) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 4.5 Å 25975 7tkn EMDB-25975, PDB-7tkn: Yeast ATP synthase State 3binding(c) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.1 Å 25976 7tko EMDB-25976, PDB-7tko: Yeast ATP synthase State 3catalytic(a) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 4.8 Å 25977 7tkp EMDB-25977, PDB-7tkp: Yeast ATP synthase State 3catalytic(b) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 4.6 Å 25978 7tkq EMDB-25978, PDB-7tkq: Yeast ATP synthase State 3catalytic(c) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 4.5 Å 25979 7tkr EMDB-25979, PDB-7tkr: Yeast ATP synthase State 3catalytic(d) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 6.5 Å 25980 7tks EMDB-25980, PDB-7tks: Yeast ATP synthase State 3catalytic(e) with 10 mM ATP backbone model Method: EM (single particle) / Resolution: 7.5 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-PO4: PHOSPHATE ION / Phosphate
Source	saccharomyces cerevisiae (brewer's yeast)
Keywords	HYDROLASE / F1-ATPase / ATP Synthase / Nanomotor / Complex