6BAA

Cryo-EM structure of the pancreatic beta-cell KATP channel bound to ATP and glibenclamide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Anti-diabetic drug binding site in a mammalian KATPchannel revealed by Cryo-EM.

Martin, G.M.Kandasamy, B.DiMaio, F.Yoshioka, C.Shyng, S.L.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.31054

  • PubMed Abstract: 
  • Sulfonylureas are anti-diabetic medications that act by inhibiting pancreatic K <sub>ATP </sub> channels composed of SUR1 and Kir6.2. The mechanism by which these drugs interact with and inhibit the channel has been extensively investigated, yet it r ...

    Sulfonylureas are anti-diabetic medications that act by inhibiting pancreatic K ATP channels composed of SUR1 and Kir6.2. The mechanism by which these drugs interact with and inhibit the channel has been extensively investigated, yet it remains unclear where the drug binding pocket resides. Here, we present a cryo-EM structure of a hamster SUR1/rat Kir6.2 channel bound to a high-affinity sulfonylurea drug glibenclamide and ATP at 3.63 Å resolution, which reveals unprecedented details of the ATP and glibenclamide binding sites. Importantly, the structure shows for the first time that glibenclamide is lodged in the transmembrane bundle of the SUR1-ABC core connected to the first nucleotide binding domain near the inner leaflet of the lipid bilayer. Mutation of residues predicted to interact with glibenclamide in our model led to reduced sensitivity to glibenclamide. Our structure provides novel mechanistic insights of how sulfonylureas and ATP interact with the K ATP channel complex to inhibit channel activity.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, United States.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-sensitive inward rectifier potassium channel 11
A, B, C, D
390Rattus norvegicusMutation(s): 0 
Gene Names: Kcnj11
Membrane protein
mpstruc
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 P70673 (Rattus norvegicus)
Go to UniProtKB:  P70673
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-binding cassette sub-family C member 8
E, F, G, H
1582Cricetus cricetusMutation(s): 0 
Gene Names: ABCC8 (SUR)
Membrane protein
mpstruc
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 Q09427 (Cricetus cricetus)
Go to Gene View: ABCC8
Go to UniProtKB:  Q09427
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
GBM
Query on GBM

Download SDF File 
Download CCD File 
E, F, G, H
5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
Glibenclamide, Glyburide
C23 H28 Cl N3 O5 S
ZNNLBTZKUZBEKO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.63 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
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited States--

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-02-28
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Data collection, Database references