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	How palytoxin transforms the Na,K pump into a cation channel.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 122, Issue 38, Page e2506450122, Year 2025
Publish date	Sep 23, 2025
Authors	Ryuta Kanai / Naoki Tsunekawa / Flemming Cornelius / Bente Vilsen / Chikashi Toyoshima /
PubMed Abstract	Palytoxin (PTX), a potent marine toxin, has long been known to transform Na,K-ATPase (NKA), an indispensable ion pump, into a nonselective cation channel. It has been postulated that PTX takes ...Palytoxin (PTX), a potent marine toxin, has long been known to transform Na,K-ATPase (NKA), an indispensable ion pump, into a nonselective cation channel. It has been postulated that PTX takes control of the two gates on either side of a channel-like pore. These gates normally open and close alternately, synchronized with chemical events, never opening simultaneously. A critical question is whether palytoxin takes over the control of the two gates or creates a new pathway. Here, we present structures of NKA with bound palytoxin in three different states. PTX binds to NKA in E2P, occupying the physiological Na exit pathway, similar to istaroxime, a new-generation cardiotonic steroid. Adding Na and ATP/ADP to the NKA·PTX complex induces an open channel traversing the entire membrane alongside the physiological ion pathway. As AlF, a stable transition state analog of phosphate replaces phosphate in the NKA·PTX complex preformed in E2P, the complex appears to undergo the normal reaction cycle from E2P to E1·Na. PTX occupies the space between the transmembrane helices M4 and M6, thereby preventing the closure of the extracellular half of the ion pathway. These structures demonstrate that the architecture of NKA is fundamentally different from "a pore with two gates." Each half of the ion pathway comprises three segments, including a movable component that plays a pivotal role in translocating the bound cations by connecting the constant part to an appropriate inlet. The ion pathway of NKA transforms dynamically, ensuring that the two halves never exist simultaneously.
External links	Proc Natl Acad Sci U S A / PubMed:40956884 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.3 - 3.79 Å
Structure data	65098 9viy EMDB-65098, PDB-9viy: Cryo-EM structure of palytoxin-bound Na+,K+-ATPase in the E2P state Method: EM (single particle) / Resolution: 3.3 Å 65099 9viz EMDB-65099, PDB-9viz: Cryo-EM structure of palytoxin-bound Na+,K+-ATPase in the transient state of dephosphorylation (E2~P) Method: EM (single particle) / Resolution: 3.4 Å 65100 9vj0 EMDB-65100, PDB-9vj0: Cryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ATP form) Method: EM (single particle) / Resolution: 3.7 Å 65101 9vj1 EMDB-65101, PDB-9vj1: Cryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ADP form) Method: EM (single particle) / Resolution: 3.4 Å PDB-9vj2: Crystal structure of palytoxin-bound Na+,K+-ATPase in the E2P state Method: X-RAY DIFFRACTION / Resolution: 3.79 Å
Chemicals	ChemComp-CLR: CHOLESTEROL ChemComp-PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipidYM ChemComp-MG: Unknown entry PDB-1ma6: TPY4 Tachyplesin I tyrosine mutant in the presence of dodecylphosphocholine micelles (300 mM) ChemComp-ALF: TETRAFLUOROALUMINATE ION ChemComp-NA: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose ChemComp-HOH*: WATER
Source	squalus acanthias (spiny dogfish) sus scrofa (pig)
Keywords	MEMBRANE PROTEIN / ion pump / P-type ATPase