3C59

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


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: https://doi.org/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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptor122Homo sapiensMutation(s): 0 
Gene Names: Glucagon-like peptide-1 receptor(GLP1R)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P43220 (Homo sapiens)
Explore P43220 
Go to UniProtKB:  P43220
PHAROS:  P43220
GTEx:  ENSG00000112164 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43220
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exendin-431N/AMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P26349 (Heloderma suspectum)
Explore P26349 
Go to UniProtKB:  P26349
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26349
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
10M
Query on 10M

Download Ideal Coordinates CCD File 
C [auth A]decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside
C22 H42 O10 S
YZNNXXWNKQOETJ-HYLFJBCQSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.85α = 90
b = 75.85β = 90
c = 87.55γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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