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- PDB-5yw7: Structure of pancreatic ATP-sensitive potassium channel bound wit... -

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Basic information

Entry
Database: PDB / ID: 5yw7
TitleStructure of pancreatic ATP-sensitive potassium channel bound with glibenclamide and ATPgammaS (focused refinement on SUR1 ABC transporter module at 4.4A)
ComponentsATP-binding cassette sub-family C member 8 isoform X2
KeywordsMEMBRANE PROTEIN / KATP / channel / glibenclamide / sulfonylurea
Function / homology
Function and homology information


sulfonylurea receptor activity / inorganic cation transmembrane transport / ATPase-coupled cation transmembrane transporter activity / potassium ion transport / ATPase activity / integral component of membrane / ATP binding / plasma membrane
Sulphonylurea receptor / P-loop containing nucleoside triphosphate hydrolase / ABC transporter type 1, transmembrane domain superfamily / ATP-binding cassette subfamily C member 8 / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / ABC transporter, conserved site
ATP-binding cassette sub-family C member 8 isoform X2
Biological speciesMesocricetus auratus (golden hamster)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 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
DepositionNov 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 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
B: ATP-binding cassette sub-family C member 8 isoform X2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,3133
Polymers177,2961
Non-polymers1,0172
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area630 Å2
ΔGint-5 kcal/mol
Surface area53830 Å2

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Components

#1: Protein ATP-binding cassette sub-family C member 8 isoform X2 / SUR1


Mass: 177295.516 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-GBM / 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / Glibenclamide, Glyburide / Glibenclamide


Mass: 494.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28ClN3O5S / Comment: medication*YM
#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.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*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 / Source: RECOMBINANT
Source (natural)Organism: Mesocricetus auratus (golden hamster)
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

SoftwareName: PHENIX / Version: (1.12_2829: ???) / Classification: refinement
EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 348180 / Symmetry type: POINT

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