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 1.3 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
  • Primary Citation of Related Structures:  
    6BAA

  • PubMed Abstract: 
  • 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 remai ...

    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 and Molecular Biology, Oregon Health and Science University, Portland, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-sensitive inward rectifier potassium channel 11 ABCD390Rattus 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)
Explore P70673 
Go to UniProtKB:  P70673
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-binding cassette sub-family C member 8 EFGH1582Cricetus cricetusMutation(s): 0 
Gene Names: ABCC8SUR
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)
Explore Q09427 
Go to UniProtKB:  Q09427
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download Ideal Coordinates CCD File 
E, F, G, H
5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
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



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States--

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references
  • Version 1.2: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence