Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18198.23 
• Atom Count: 1088 
• Residue Count: 153 
• Unique protein chains: 2

3C5T

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

• DOI: 10.2210/pdb3C5T/pdb

• Classification: Signaling protein/Signaling protein
• Organism(s): Homo sapiens, Heloderma suspectum
• Expression System: Escherichia coli BL21(DE3)


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.238 
• R-Value Work: 0.203 

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

• PubMed: 18287102 
• DOI: 10.1074/jbc.M708740200
• Primary Citation of Related Structures:  
  3C59


• 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.

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Organizational Affiliation: 

Department of Structure and Biophysical Chemistry, Novo Nordisk, 2760 Måløv, Denmark. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucagon-like peptide 1 receptor	A	122	Homo sapiens	Mutation(s): 0  Gene Names: GLP1R
Find proteins for P43220 (Homo sapiens) Go to Gene View: GLP1R Go to UniProtKB:  P43220

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Exendin-4	B	31	Heloderma suspectum	Mutation(s): 0
Find proteins for P26349 (Heloderma suspectum) Go to UniProtKB:  P26349

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
10M	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.238 
• R-Value Work: 0.203 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 75.910	α = 90.00
b = 75.910	β = 90.00
c = 87.770	γ = 120.00

Software Package:

Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction
MOLREP	phasing
XSCALE	data scaling

Structure Validation

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
  Type: Advisory, Version format compliance
• Version 1.2: 2018-05-23
  Type: Data collection