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- PDB-6jb1: Structure of pancreatic ATP-sensitive potassium channel bound wit... -

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Basic information

Entry
Database: PDB / ID: 6jb1
TitleStructure of pancreatic ATP-sensitive potassium channel bound with repaglinide and ATPgammaS at 3.3A resolution
Components
  • ATP-binding cassette sub-family C member 8 isoform X2
  • ATP-sensitive inward rectifier potassium channel 11
KeywordsMEMBRANE PROTEIN / KATP / channel / repaglinide / Kir / ABC transporter / SUR / diabetes / insulin secretagogue
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 / response to ATP / potassium ion import across plasma membrane ...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 / response to ATP / potassium ion import across plasma membrane / ankyrin binding / axolemma / nervous system process / intercalated disc / potassium ion transmembrane transport / potassium ion binding / response to testosterone / voltage-gated potassium channel activity / regulation of ion transmembrane transport / negative regulation of insulin secretion / regulation of insulin secretion / response to ischemia / T-tubule / acrosomal vesicle / regulation of membrane potential / heat shock protein binding / 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 / response to drug / protein C-terminus binding / endosome / ATPase activity / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum / mitochondrion / cell / integral component of membrane / ATP binding / plasma membrane / cytosol
ABC transporter type 1, transmembrane domain / Potassium channel, inwardly rectifying, transmembrane domain / AAA+ ATPase domain / ABC transporter-like / Immunoglobulin E-set / Potassium channel, inwardly rectifying, Kir / Potassium channel, inwardly rectifying, Kir6.2 / ABC transporter, conserved site / P-loop containing nucleoside triphosphate hydrolase / Potassium channel, inwardly rectifying, Kir, cytoplasmic ...ABC transporter type 1, transmembrane domain / Potassium channel, inwardly rectifying, transmembrane domain / AAA+ ATPase domain / ABC transporter-like / Immunoglobulin E-set / Potassium channel, inwardly rectifying, Kir / Potassium channel, inwardly rectifying, Kir6.2 / ABC transporter, conserved site / P-loop containing nucleoside triphosphate hydrolase / Potassium channel, inwardly rectifying, Kir, cytoplasmic / ABC transporter type 1, transmembrane domain superfamily / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel transmembrane domain / Inward rectifier potassium channel C-terminal domain / ABC transporter / ABC transporter transmembrane region / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / G protein-activated inward rectifier potassium channel 1 / Helix Hairpins - #70 / Helix Hairpins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
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: 3.3 Å
AuthorsChen, L. / Ding, D. / Wang, M. / Wu, J.-X. / Kang, Y.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0502004 China
National Natural Science Foundation of China31622021 China
National Natural Science Foundation of China31821091 China
National Natural Science Foundation of China31870833 China
CitationJournal: Cell Rep / Year: 2019
Title: The Structural Basis for the Binding of Repaglinide to the Pancreatic K Channel.
Authors: Dian Ding / Mengmeng Wang / Jing-Xiang Wu / Yunlu Kang / Lei Chen /
Abstract: Repaglinide (RPG) is a short-acting insulin secretagogue widely prescribed for the treatment of type 2 diabetes. It boosts insulin secretion by inhibiting the pancreatic ATP-sensitive potassium ...Repaglinide (RPG) is a short-acting insulin secretagogue widely prescribed for the treatment of type 2 diabetes. It boosts insulin secretion by inhibiting the pancreatic ATP-sensitive potassium channel (K). However, the mechanisms by which RPG binds to the K channel are poorly understood. Here, we describe two cryo-EM structures: the pancreatic K channel in complex with inhibitory RPG and adenosine-5'-(γ-thio)-triphosphate (ATPγS) at 3.3 Å and a medium-resolution structure of a RPG-bound mini SUR1 protein in which the N terminus of the inward-rectifying potassium channel 6.1 (Kir6.1) is fused to the ABC transporter module of the sulfonylurea receptor 1 (SUR1). These structures reveal the binding site of RPG in the SUR1 subunit. Furthermore, the high-resolution structure reveals the complex architecture of the ATP binding site, which is formed by both Kir6.2 and SUR1 subunits, and the domain-domain interaction interfaces.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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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)933,66676
Polymers883,6458
Non-polymers50,02168
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#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

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Non-polymers , 5 types, 68 molecules

#3: Chemical...
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#4: 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
#5: Chemical
ChemComp-AJP / Digitonin / Digitonin


Mass: 1229.312 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C56H92O29 / Comment: detergent*YM
#6: Chemical
ChemComp-BJX / Repaglinide / 2-ethoxy-4-[2-({(1S)-3-methyl-1-[2-(piperidin-1-yl)phenyl]butyl}amino)-2-oxoethyl]benzoic acid / Repaglinide


Mass: 452.586 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H36N2O4 / Comment: medication*YM
#7: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*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
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277548 / Symmetry type: POINT

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