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

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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


Ion homeostasis / Regulation of insulin secretion / ABC-family proteins mediated transport / ATP sensitive Potassium channels / inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inward rectifier potassium channel activity / positive regulation of cation channel activity ...Ion homeostasis / Regulation of insulin secretion / ABC-family proteins mediated transport / ATP sensitive Potassium channels / inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inward rectifier potassium channel activity / positive regulation of cation channel activity / potassium ion import across plasma membrane / cellular response to nicotine / response to ATP / ankyrin binding / axolemma / nervous system process / potassium ion transmembrane transport / intercalated disc / potassium ion binding / ATPase-coupled transmembrane transporter activity / response to testosterone / T-tubule / voltage-gated potassium channel activity / negative regulation of insulin secretion / regulation of membrane potential / regulation of insulin secretion / acrosomal vesicle / response to ischemia / heat shock protein binding / potassium ion transport / cellular response to glucose stimulus / sarcolemma / positive regulation of protein localization to plasma membrane / nuclear envelope / glucose metabolic process / cellular response to tumor necrosis factor / myelin sheath / ion channel binding / response to estradiol / protein C-terminus binding / endosome / response to drug / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum / mitochondrion / integral component of membrane / ATP binding / plasma membrane / cytosol
Sulphonylurea receptor / ABC transporter / Potassium channel, inwardly rectifying, Kir6.2 / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Immunoglobulin E-set / Potassium channel, inwardly rectifying, Kir / ABC transporter, conserved site ...Sulphonylurea receptor / ABC transporter / Potassium channel, inwardly rectifying, Kir6.2 / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Immunoglobulin E-set / Potassium channel, inwardly rectifying, Kir / ABC transporter, conserved site / P-loop containing nucleoside triphosphate hydrolase / ABC transporter type 1, transmembrane domain superfamily / Potassium channel, inwardly rectifying, transmembrane domain / ATP-binding cassette subfamily C member 8 / Inward rectifier potassium channel, C-terminal / ATP-binding cassette, ABC transporter-type domain profile. / Inward rectifier potassium channel C-terminal domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporters family signature. / ABC transporter transmembrane region / Inward rectifier potassium channel transmembrane domain
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 supportChina , 4件
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0502004China
National Natural Science Foundation of China31622021China
National Natural Science Foundation of China31821091China
National Natural Science Foundation of China31870833China
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
DateDeposition: Jan 25, 2019 / Release: May 22, 2019
RevisionDateData content typeProviderType
1.0May 22, 2019Structure modelrepositoryInitial release

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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/peptide , 2 types, 8 molecules ACEGBDFH

#1: Protein/peptide
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/peptide
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


Mass: 760.076 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C42H82NO8P / POPC
#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


Mass: 1229.312 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C56H92O29 / Digitonin / 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


Mass: 452.586 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H36N2O4 / Repaglinide
#7: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H80NO8P / Phosphatidylethanolamine

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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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