6JB1

Structure of pancreatic ATP-sensitive potassium channel bound with repaglinide and ATPgammaS at 3.3A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Structural Basis for the Binding of Repaglinide to the Pancreatic KATPChannel.

Ding, D.Wang, M.Wu, J.X.Kang, Y.Chen, L.

(2019) Cell Rep 27: 1848-1857.e4

  • DOI: 10.1016/j.celrep.2019.04.050
  • Primary Citation of Related Structures:  

  • PubMed 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 channel (K <sub>ATP </sub>). However, the mechanisms by ...

    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 ATP ). However, the mechanisms by which RPG binds to the K ATP channel are poorly understood. Here, we describe two cryo-EM structures: the pancreatic K ATP 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.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: chenlei2016@pku.edu.cn.,State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China.,State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-sensitive inward rectifier potassium channel 11
A, C, E, G
390Mus musculusMutation(s): 0 
Gene Names: Kcnj11
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
SUR1/Kir6.2 pancreatic ATP-sensitive K+ channel
Find proteins for Q61743 (Mus musculus)
Go to UniProtKB:  Q61743
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-binding cassette sub-family C member 8 isoform X2
B, D, F, H
1582Mesocricetus auratusMutation(s): 0 
Gene Names: Abcc8
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
SUR1/Kir6.2 pancreatic ATP-sensitive K+ channel
Find proteins for A0A1U7R319 (Mesocricetus auratus)
Go to UniProtKB:  A0A1U7R319
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP

Download SDF File 
Download CCD File 
B, D, F, H
Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-RYVHXNAXSA-N
 Ligand Interaction
BJX
Query on BJX

Download SDF File 
Download CCD File 
B, D, F, H
Repaglinide
2-ethoxy-4-[2-({(1S)-3-methyl-1-[2-(piperidin-1-yl)phenyl]butyl}amino)-2-oxoethyl]benzoic acid
C27 H36 N2 O4
FAEKWTJYAYMJKF-QHCPKHFHSA-N
 Ligand Interaction
PTY
Query on PTY

Download SDF File 
Download CCD File 
B, D, F, H
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
POV
Query on POV

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
POPC
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
AGS
Query on AGS

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0502004
National Natural Science Foundation of ChinaChina31622021
National Natural Science Foundation of ChinaChina31821091
National Natural Science Foundation of ChinaChina31870833

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release