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 basis for potassium transport in prokaryotes by KdpFABC.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 118, Issue 29, Year 2021
Publish date	Jul 20, 2021
Authors	Marie E Sweet / Casper Larsen / Xihui Zhang / Michael Schlame / Bjørn P Pedersen / David L Stokes /
PubMed Abstract	KdpFABC is an oligomeric K transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the superfamily of K ...KdpFABC is an oligomeric K transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the superfamily of K transporters and a pump-like subunit (KdpB) from the superfamily of P-type ATPases. Recent structural work has defined the architecture and generated contradictory hypotheses for the transport mechanism. Here, we use substrate analogs to stabilize four key intermediates in the reaction cycle and determine the corresponding structures by cryogenic electron microscopy. We find that KdpB undergoes conformational changes consistent with other representatives from the P-type superfamily, whereas KdpA, KdpC, and KdpF remain static. We observe a series of spherical densities that we assign as K or water and which define a pathway for K transport. This pathway runs through an intramembrane tunnel in KdpA and delivers ions to sites in the membrane domain of KdpB. Our structures suggest a mechanism where ATP hydrolysis is coupled to K transfer between alternative sites in KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K to the cytoplasm.
External links	Proc Natl Acad Sci U S A / PubMed:34272288 / PubMed Central
Methods	EM (single particle)
Resolution	2.9 - 3.76 Å
Structure data	12184 7bgy EMDB-12184, PDB-7bgy: Cryo-EM Structure of KdpFABC in E2Pi state with MgF4 Method: EM (single particle) / Resolution: 2.9 Å 12185 7bh1 EMDB-12185, PDB-7bh1: Cryo-EM Structure of KdpFABC in E1 state with K Method: EM (single particle) / Resolution: 3.38 Å 12186 7bh2 EMDB-12186, PDB-7bh2: Cryo-EM Structure of KdpFABC in E2Pi state with BeF3 and K+ Method: EM (single particle) / Resolution: 3.0 Å 23268 7lc3 EMDB-23268, PDB-7lc3: CryoEM Structure of KdpFABC in E1-ATP state Method: EM (single particle) / Resolution: 3.23 Å 23269 7lc6 EMDB-23269, PDB-7lc6: Cryo-EM Structure of KdpFABC in E2-P state with BeF3 Method: EM (single particle) / Resolution: 3.7 Å EMDB-23342: Cryo-EM Structure of KdpFABC in E1 state Method: EM (single particle) / Resolution: 3.57 Å EMDB-23343: Cryo-EM Structure of KdpFABC in E2Pi state with AlF4 Method: EM (single particle) / Resolution: 3.32 Å EMDB-23344: CryoEM Structure of KdpFABC in E2Pi state with AlF4 Method: EM (single particle) / Resolution: 3.76 Å EMDB-23346: CryoEM Structure of KdpFABC in E2Pi state with VO4 Method: EM (single particle) / Resolution: 3.6 Å EMDB-23347: CryoEM Structure of KdpFABC in E1 state Method: EM (single particle) / Resolution: 3.5 Å EMDB-23348: Cryo-EM Structure of KdpFABC in E2Pi state with VO4 and K+ Method: EM (single particle) / Resolution: 3.38 Å EMDB-23349: CryoEM Structure of KdpFABC in E1 state Method: EM (single particle) / Resolution: 3.32 Å EMDB-23353: Cryo-EM Structure of KdpFABC in E1ATP state with AMP-PCP Method: EM (single particle) / Resolution: 3.27 Å EMDB-23354: Cryo-EM Structure of KdpFABC in E2Pi state with BeF3 Method: EM (single particle) / Resolution: 3.21 Å
Chemicals	ChemComp-PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipidYM / Phosphatidylethanolamine ChemComp-9Y0: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate ChemComp-MG: Unknown entry ChemComp-MF4: TETRAFLUOROMAGNESATE(2-) ChemComp-HOH: WATER / Water ChemComp-K: Unknown entry ChemComp-BEF: BERYLLIUM TRIFLUORIDE ION ChemComp-ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogueYM
Source	escherichia coli k-12 (bacteria) escherichia coli (strain k12) (bacteria)
Keywords	MEMBRANE PROTEIN / P-type ATPase / ATP-dependent potassium pump