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	Ligand-mediated Structural Dynamics of a Mammalian Pancreatic K Channel.
Journal, issue, pages	J Mol Biol, Vol. 434, Issue 19, Page 167789, Year 2022
Publish date	Aug 11, 2022
Authors	Min Woo Sung / Camden M Driggers / Barmak Mostofian / John D Russo / Bruce L Patton / Daniel M Zuckerman / Show-Ling Shyng /
PubMed Abstract	Regulation of pancreatic K channels involves orchestrated interactions of their subunits, Kir6.2 and SUR1, and ligands. Previously we reported K channel cryo-EM structures in the presence and absence ...Regulation of pancreatic K channels involves orchestrated interactions of their subunits, Kir6.2 and SUR1, and ligands. Previously we reported K channel cryo-EM structures in the presence and absence of pharmacological inhibitors and ATP, focusing on the mechanisms by which inhibitors act as pharmacological chaperones of K channels (Martin et al., 2019). Here we analyzed the same cryo-EM datasets with a focus on channel conformational dynamics to elucidate structural correlates pertinent to ligand interactions and channel gating. We found pharmacological inhibitors and ATP enrich a channel conformation in which the Kir6.2 cytoplasmic domain is closely associated with the transmembrane domain, while depleting one where the Kir6.2 cytoplasmic domain is extended away into the cytoplasm. This conformational change remodels a network of intra- and inter-subunit interactions as well as the ATP and PIP binding pockets. The structures resolved key contacts between the distal N-terminus of Kir6.2 and SUR1's ABC module involving residues implicated in channel function and showed a SUR1 residue, K134, participates in PIP binding. Molecular dynamics simulations revealed two Kir6.2 residues, K39 and R54, that mediate both ATP and PIP binding, suggesting a mechanism for competitive gating by ATP and PIP.
External links	J Mol Biol / PubMed:35964676 / PubMed Central
Methods	EM (single particle)
Resolution	3.41 - 7.4 Å
Structure data	26193 7tys EMDB-26193, PDB-7tys: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with Kir6.2-CTD in the up conformation Method: EM (single particle) / Resolution: 3.41 Å 26194 7tyt EMDB-26194, PDB-7tyt: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with Kir6.2-CTD in the down conformation Method: EM (single particle) / Resolution: 3.6 Å 26299 7u1e EMDB-26299, PDB-7u1e: CryoEM structure of the pancreatic ATP-sensitive potassium channel bound to ATP with Kir6.2-CTD in the down conformation Method: EM (single particle) / Resolution: 4.52 Å 26303 7u1q EMDB-26303, PDB-7u1q: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with SUR1-in conformation Method: EM (single particle) / Resolution: 3.9 Å 26304 7u1s EMDB-26304, PDB-7u1s: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with SUR1-out conformation Method: EM (single particle) / Resolution: 3.8 Å 26307 7u24 EMDB-26307, PDB-7u24: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and glibenclamide with Kir6.2-CTD in the up conformation Method: EM (single particle) / Resolution: 3.58 Å 26308 7u6y EMDB-26308: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and glibenclamide with Kir6.2-CTD in the down conformation PDB-7u6y: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel in the presence of glibenclamide and ATP with Kir6.2-CTD in the down conformation Method: EM (single particle) / Resolution: 6.8 Å 26309 7u7m EMDB-26309: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and in the presence of carbamazepine with Kir6.2-CTD in the up conformation PDB-7u7m: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel in the presence of carbamazepine and ATP with Kir6.2-CTD in the up conformation Method: EM (single particle) / Resolution: 5.2 Å 26312 7uaa EMDB-26312: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP with Kir6.2-CTD in the up conformation PDB-7uaa: CryoEM structure of the pancreatic ATP-sensitive potassium channel in the ATP-bound state with Kir6.2-CTD in the up conformation Method: EM (single particle) / Resolution: 5.7 Å 26320 7uqr EMDB-26320, PDB-7uqr: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel in the apo form with Kir6.2-CTD in the down conformation Method: EM (single particle) 26321 7u2x EMDB-26321, PDB-7u2x: Cryo-EM structure of the pancreatic ATP-sensitive potassium channel in the presence of carbamazepine and ATP with Kir6.2-CTD in the down conformation Method: EM (single particle) / Resolution: 4.1 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-K: Unknown entry ChemComp-POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipidYM / POPC ChemComp-P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / Phosphatidylserine ChemComp-65I: (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate ChemComp-BJX: Repaglinide / medicationYM / Repaglinide ChemComp-PTY: PHOSPHATIDYLETHANOLAMINE / phospholipidYM / Phosphatidylethanolamine ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine ChemComp-GBM: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / medication*YM / Glibenclamide
Source	cricetus cricetus (black-bellied hamster) rattus norvegicus (Norway rat)
Keywords	MEMBRANE PROTEIN / KATP channel / SUR1 / Kir6.2 / repaglinide / RPG / sulfonylurea receptor / potassium transport / glibenclamide / GBC / GBM / metabolic sensor