3C59

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucagon-like peptide 1 receptor
A
122Homo sapiensGene Names: GLP1R
Find proteins for P43220 (Homo sapiens)
Go to Gene View: GLP1R
Go to UniProtKB:  P43220
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exendin-4
B
31Heloderma suspectumN/A
Find proteins for P26349 (Heloderma suspectum)
Go to UniProtKB:  P26349
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
10M
Query on 10M

Download SDF File 
Download CCD File 
A
decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside
(2R,3R,4S,5S,6R)-2-((2R,3S,4R,5R,6S)-6-Decylsulfanyl-4,5-dihydroxy-2-hydroxymethyl-tetrahydro-pyran-3-yloxy)-6-hydroxymethyl-tetrahydro-pyran-3,4,5-triol, n-Decyl-beta-D-thiomaltoside
C22 H42 O10 S
YZNNXXWNKQOETJ-HYLFJBCQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.850α = 90.00
b = 75.850β = 90.00
c = 87.550γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
XDSdata scaling
autoSHARPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-01-31 
  • 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
    Type: Advisory, Version format compliance