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- PDB-5ykg: Structure of pancreatic ATP-sensitive potassium channel bound wit... -

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Basic information

Entry
Database: PDB / ID: 5ykg
TitleStructure of pancreatic ATP-sensitive potassium channel bound with glibenclamide and ATPgammaS (Class2 at 4.57A)
Components
  • ATP-binding cassette sub-family C member 8 isoform X2
  • ATP-sensitive inward rectifier potassium channel 11
KeywordsMEMBRANE PROTEIN / KATP / channel / glibenclamide / sulfonylurea
Function / homology
Function and homology information


inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inorganic cation transmembrane transport / ATPase-coupled cation transmembrane transporter activity / inward rectifier potassium channel activity / positive regulation of cation channel activity / ankyrin binding / nervous system process ...inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inorganic cation transmembrane transport / ATPase-coupled cation transmembrane transporter activity / inward rectifier potassium channel activity / positive regulation of cation channel activity / ankyrin binding / nervous system process / potassium ion import across plasma membrane / response to ATP / axolemma / intercalated disc / response to testosterone / potassium ion binding / potassium ion transmembrane transport / voltage-gated potassium channel activity / regulation of ion transmembrane transport / negative regulation of insulin secretion / regulation of insulin secretion / regulation of membrane potential / heat shock protein binding / T-tubule / acrosomal vesicle / response to ischemia / potassium ion transport / cellular response to glucose stimulus / sarcolemma / positive regulation of protein localization to plasma membrane / nuclear envelope / cellular response to nicotine / glucose metabolic process / cellular response to tumor necrosis factor / myelin sheath / ion channel binding / response to estradiol / protein C-terminus binding / endosome / ATPase activity / intracellular membrane-bounded organelle / neuronal cell body / response to drug / endoplasmic reticulum / mitochondrion / integral component of membrane / ATP binding / plasma membrane / cytosol
ABC transporter transmembrane region / P-loop containing nucleoside triphosphate hydrolase / Potassium channel, inwardly rectifying, Kir6.2 / ABC transporter type 1, transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / ATP-binding cassette subfamily C member 8 / Immunoglobulin E-set / Potassium channel, inwardly rectifying, Kir / AAA+ ATPase domain / ABC transporter, conserved site ...ABC transporter transmembrane region / P-loop containing nucleoside triphosphate hydrolase / Potassium channel, inwardly rectifying, Kir6.2 / ABC transporter type 1, transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / ATP-binding cassette subfamily C member 8 / Immunoglobulin E-set / Potassium channel, inwardly rectifying, Kir / AAA+ ATPase domain / ABC transporter, conserved site / ABC transporter type 1, transmembrane domain superfamily / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel transmembrane domain / Inward rectifier potassium channel C-terminal domain / ABC transporter / Sulphonylurea receptor / ABC transporter-like
ATP-binding cassette sub-family C member 8 isoform X2 / ATP-sensitive inward rectifier potassium channel 11
Biological speciesMus musculus (house mouse)
Mesocricetus auratus (golden hamster)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.57 Å
AuthorsChen, L. / Wu, J.X.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2016YFA0502004 China
National Natural Science Foundation of China31622021 China
National Natural Science Foundation of China31521062 China
China Postdoctoral Science Foundation2016M600856 China
China Postdoctoral Science Foundation2017T100014 China
CitationJournal: Protein Cell / Year: 2018
Title: Ligand binding and conformational changes of SUR1 subunit in pancreatic ATP-sensitive potassium channels.
Authors: Jing-Xiang Wu / Dian Ding / Mengmeng Wang / Yunlu Kang / Xin Zeng / Lei Chen /
Abstract: ATP-sensitive potassium channels (K) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of β-cells, pancreatic K channels control insulin release and regulate ...ATP-sensitive potassium channels (K) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of β-cells, pancreatic K channels control insulin release and regulate metabolism at the whole body level. They are implicated in many metabolic disorders and diseases and are therefore important drug targets. Here, we present three structures of pancreatic K channels solved by cryo-electron microscopy (cryo-EM), at resolutions ranging from 4.1 to 4.5 Å. These structures depict the binding site of the antidiabetic drug glibenclamide, indicate how Kir6.2 (inward-rectifying potassium channel 6.2) N-terminus participates in the coupling between the peripheral SUR1 (sulfonylurea receptor 1) subunit and the central Kir6.2 channel, reveal the binding mode of activating nucleotides, and suggest the mechanism of how Mg-ADP binding on nucleotide binding domains (NBDs) drives a conformational change of the SUR1 subunit.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: ATP-sensitive inward rectifier potassium channel 11
B: ATP-binding cassette sub-family C member 8 isoform X2
C: ATP-sensitive inward rectifier potassium channel 11
D: ATP-binding cassette sub-family C member 8 isoform X2
E: ATP-sensitive inward rectifier potassium channel 11
F: ATP-binding cassette sub-family C member 8 isoform X2
G: ATP-sensitive inward rectifier potassium channel 11
H: ATP-binding cassette sub-family C member 8 isoform X2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)889,80720
Polymers883,6458
Non-polymers6,16212
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31600 Å2
ΔGint-294 kcal/mol
Surface area321110 Å2

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Components

#1: Protein
ATP-sensitive inward rectifier potassium channel 11 / Inward rectifier K(+) channel Kir6.2 / Potassium channel / inwardly rectifying subfamily J member 11


Mass: 43615.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj11 / Production host: Homo sapiens (human) / References: UniProt: Q61743
#2: Protein
ATP-binding cassette sub-family C member 8 isoform X2 / SUR1


Mass: 177295.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Gene: Abcc8 / Production host: Homo sapiens (human) / References: UniProt: A0A1U7R319
#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-GBM / 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / Glibenclamide, Glyburide / Glibenclamide


Mass: 494.004 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H28ClN3O5S / Comment: medication*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: KATPATP-sensitive potassium channel / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 4.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40340 / Symmetry type: POINT

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