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	Cryoelectron microscopy of Na,K-ATPase in the two E2P states with and without cardiotonic steroids.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 119, Issue 15, Page e2123226119, Year 2022
Publish date	Apr 12, 2022
Authors	Ryuta Kanai / Flemming Cornelius / Bente Vilsen / Chikashi Toyoshima /
PubMed Abstract	Cryoelectron microscopy (cryo-EM) was applied to Na+,K+-ATPase (NKA) to determine the structures of two E2P states, one (E2PATP) formed by ATP and Mg2+ in the forward reaction, and the other (E2PPi) ...Cryoelectron microscopy (cryo-EM) was applied to Na+,K+-ATPase (NKA) to determine the structures of two E2P states, one (E2PATP) formed by ATP and Mg2+ in the forward reaction, and the other (E2PPi) formed by inorganic phosphate (Pi) and Mg2+ in the backward reaction, with and without ouabain or istaroxime, representatives of classical and new-generation cardiotonic steroids (CTSs). These two E2P states exhibit different biochemical properties. In particular, K+-sensitive acceleration of the dephosphorylation reaction is not observed with E2PPi, attributed to the presence of a Mg2+ ion in the transmembrane cation binding sites. The cryo-EM structures of NKA demonstrate that the two E2P structures are nearly identical but Mg2+ in the transmembrane binding cavity is identified only in E2PPi, corroborating the idea that it should be denoted as E2PPi·Mg2+. We can now explain why the absence of transmembrane Mg2+ in E2PATP confers the K+ sensitivity in dephosphorylation. In addition, we show that ATP bridges the actuator (A) and nucleotide binding (N) domains, stabilizing the E2PATP state; CTS binding causes hardly any changes in the structure of NKA, both in E2PATP and E2PPi·Mg2+, indicating that the binding mechanism is conformational selection; and istaroxime binds to NKA, extending its aminoalkyloxime group deep into the cation binding site. This orientation is upside down compared to that of classical CTSs with respect to the steroid ring. Notably, mobile parts of NKA are resolved substantially better in the electron microscopy (EM) maps than in previous X-ray structures, including sugars sticking out from the β-subunit and many phospholipid molecules.
External links	Proc Natl Acad Sci U S A / PubMed:35380894 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.9 - 3.9 Å
Structure data	32894 7wyu EMDB-32894, PDB-7wyu: Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP Method: EM (single particle) / Resolution: 3.4 Å 32895 7wyv EMDB-32895, PDB-7wyv: Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP in the presence of 40 mM Mg2+ Method: EM (single particle) / Resolution: 3.7 Å 32896 7wyw EMDB-32896, PDB-7wyw: Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by inorganic phosphate Method: EM (single particle) / Resolution: 3.8 Å 32897 7wyx EMDB-32897, PDB-7wyx: Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP with istaroxime Method: EM (single particle) / Resolution: 3.4 Å 32898 7wyy EMDB-32898, PDB-7wyy: Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by inorganic phosphate with istaroxime Method: EM (single particle) / Resolution: 3.9 Å 32899 7wyz EMDB-32899, PDB-7wyz: Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP with ouabain Method: EM (single particle) / Resolution: 3.4 Å 32900 7wz0 EMDB-32900, PDB-7wz0: Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by inorganic phosphate with ouabain Method: EM (single particle) / Resolution: 3.0 Å PDB-7wys: Crystal structures of Na+,K+-ATPase in complex with istaroxime Method: X-RAY DIFFRACTION / Resolution: 3.71 Å PDB-7wyt: Crystal structures of Na+,K+-ATPase in complex with ouabain Method: X-RAY DIFFRACTION / Resolution: 2.9 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-NA: Unknown entry ChemComp-PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipidYM ChemComp-7Q2: (3E,5S,8R,9S,10R,13S,14S)-3-(2-azanylethoxyimino)-10,13-dimethyl-1,2,4,5,7,8,9,11,12,14,15,16-dodecahydrocyclopenta[a]phenanthrene-6,17-dione / Istaroxime ChemComp-CLR: CHOLESTEROL / Cholesterol ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine ChemComp-HOH: WATER / Water ChemComp-OBN: OUABAIN / Ouabain ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate
Source	squalus acanthias (spiny dogfish) spiny dogfish (spiny dogfish) sus scrofa (pig)
Keywords	MEMBRANE PROTEIN / Na+ / K+-ATPase / ion transport / Cardiotonic steroids / TRANSPORT PROTEIN