3C5T

Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal Structure of the Ligand-bound Glucagon-like Peptide-1 Receptor Extracellular Domain

Runge, S., Thogersen, H., Madsen, K., Lau, J., Rudolph, R.

(2008) J Biol Chem 283: 11340-11347

  • DOI: 10.1074/jbc.M708740200
  • Primary Citation of Related Structures:  
    3C59, 3C5T

  • PubMed Abstract: 

    • The glucagon-like peptide-1 receptor (GLP-1R) belongs to Family B1 of the seven-transmembrane G protein-coupled receptors, and its natural agonist ligand is the peptide hormone glucagon-like peptide-1 (GLP-1). GLP-1 is involved in glucose homeostasis ...

    The glucagon-like peptide-1 receptor (GLP-1R) belongs to Family B1 of the seven-transmembrane G protein-coupled receptors, and its natural agonist ligand is the peptide hormone glucagon-like peptide-1 (GLP-1). GLP-1 is involved in glucose homeostasis, and activation of GLP-1R in the plasma membrane of pancreatic beta-cells potentiates glucose-dependent insulin secretion. The N-terminal extracellular domain (nGLP-1R) is an important ligand binding domain that binds GLP-1 and the homologous peptide Exendin-4 with differential affinity. Exendin-4 has a C-terminal extension of nine amino acid residues known as the "Trp cage", which is absent in GLP-1. The Trp cage was believed to interact with nGLP-1R and thereby explain the superior affinity of Exendin-4. However, the molecular details that govern ligand binding and specificity of nGLP-1R remain undefined. Here we report the crystal structure of human nGLP-1R in complex with the antagonist Exendin-4(9-39) solved by the multiwavelength anomalous dispersion method to 2.2A resolution. The structure reveals that Exendin-4(9-39) is an amphipathic alpha-helix forming both hydrophobic and hydrophilic interactions with nGLP-1R. The Trp cage of Exendin-4 is not involved in binding to nGLP-1R. The hydrophobic binding site of nGLP-1R is defined by discontinuous segments including primarily a well defined alpha-helix in the N terminus of nGLP-1R and a loop between two antiparallel beta-strands. The structure provides for the first time detailed molecular insight into ligand binding of the human GLP-1 receptor, an established target for treatment of type 2 diabetes.

    Organizational Affiliation: 

    Department of Structure and Biophysical Chemistry, Novo Nordisk, 2760 Måløv, Denmark. sffr@novonordisk.com



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptorA122Homo sapiensMutation(s): 0 
Gene Names: Glucagon-like peptide-1 receptor(GLP1R), GLP1R
Find proteins for P43220 (Homo sapiens)
Explore P43220 
Go to UniProtKB:  P43220
NIH Common Fund Data Resources
PHAROS  P43220
GTEx  ENSG00000112164
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exendin-4B31N/AMutation(s): 0 
Find proteins for P26349 (Heloderma suspectum)
Explore P26349 
Go to UniProtKB:  P26349
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
10M
Query on 10M
Download Ideal Coordinates CCD File 
A
decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside
C22 H42 O10 S
YZNNXXWNKQOETJ-HYLFJBCQSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.91α = 90
b = 75.91β = 90
c = 87.77γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-02-01 
  • Released Date: 2008-02-19 
    • Deposition Author(s): Runge, S.

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-05-23
    Changes: Data collection