3IOL

Crystal structure of Glucagon-Like Peptide-1 in complex with the extracellular domain of the Glucagon-Like Peptide-1 Receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of glucagon-like peptide-1 in complex with the extracellular domain of the glucagon-like peptide-1 receptor

Underwood, C.R.Garibay, P.Knudsen, L.B.Hastrup, S.Peters, G.H.Rudolph, R.Reedtz-Runge, S.

(2010) J.Biol.Chem. 285: 723-730

  • DOI: 10.1074/jbc.M109.033829

  • PubMed Abstract: 
  • GLP-1 (glucagon-like peptide-1) is an incretin released from intestinal L-cells in response to food intake. Activation of the GLP-1 receptor potentiates the synthesis and release of insulin from pancreatic beta-cells in a glucose-dependent manner. Th ...

    GLP-1 (glucagon-like peptide-1) is an incretin released from intestinal L-cells in response to food intake. Activation of the GLP-1 receptor potentiates the synthesis and release of insulin from pancreatic beta-cells in a glucose-dependent manner. The GLP-1 receptor belongs to class B of the G-protein-coupled receptors, a subfamily characterized by a large N-terminal extracellular ligand binding domain. Exendin-4 and GLP-1 are 50% identical, and exendin-4 is a full agonist with similar affinity and potency for the GLP-1 receptor. We recently solved the crystal structure of the GLP-1 receptor extracellular domain in complex with the competitive antagonist exendin-4(9-39). Interestingly, the isolated extracellular domain binds exendin-4 with much higher affinity than the endogenous agonist GLP-1. Here, we have solved the crystal structure of the extracellular domain in complex with GLP-1 to 2.1 Aresolution. The structure shows that important hydrophobic ligand-receptor interactions are conserved in agonist- and antagonist-bound forms of the extracellular domain, but certain residues in the ligand-binding site adopt a GLP-1-specific conformation. GLP-1 is a kinked but continuous alpha-helix from Thr(13) to Val(33) when bound to the extracellular domain. We supplemented the crystal structure with site-directed mutagenesis to link the structural information of the isolated extracellular domain with the binding properties of the full-length receptor. The data support the existence of differences in the binding modes of GLP-1 and exendin-4 on the full-length GLP-1 receptor.


    Organizational Affiliation

    Department of GLP-1 and Obesity Biology, Novo Nordisk, 2760 Måløv, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucagon-like peptide 1 receptor
A
126Homo sapiensMutation(s): 0 
Gene Names: GLP1R
Find proteins for P43220 (Homo sapiens)
Go to Gene View: GLP1R
Go to UniProtKB:  P43220
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glucagon
B
31Homo sapiensMutation(s): 0 
Gene Names: GCG
Find proteins for P01275 (Homo sapiens)
Go to Gene View: GCG
Go to UniProtKB:  P01275
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 35.670α = 90.00
b = 42.670β = 90.00
c = 95.090γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-08-14 
  • Released Date: 2009-10-27 
  • Deposition Author(s): Reedtz-Runge, S.

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2018-05-23
    Type: Advisory, Data collection