Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Macromolecule Content

• Total Structure Weight: 18.60 kDa 
• Atom Count: 1130 
• Residue Count: 126 
• Unique protein chains: 2

3IOL

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

• DOI: 10.2210/pdb3IOL/pdb

• Classification: SIGNALING PROTEIN/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.226 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

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

• PubMed: 19861722 
• DOI: 10.1074/jbc.M109.033829
• Structures With Same Primary Citation


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucagon-like peptide 1 receptor	A	126	Homo sapiens	Mutation(s): 0  Gene Names: GLP1R
Find proteins for P43220 (Homo sapiens) Go to UniProtKB:  P43220
NIH Common Fund Data Resources
PHAROS  P43220 GTEx  ENSG00000112164

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Glucagon	B	31	Homo sapiens	Mutation(s): 0  Gene Names: GCG
Find proteins for P01275 (Homo sapiens) Go to UniProtKB:  P01275
NIH Common Fund Data Resources
PHAROS  P01275 GTEx  ENSG00000115263

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
10M	A	decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside C22 H42 O10 S YZNNXXWNKQOETJ-HYLFJBCQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.226 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.67	α = 90
b = 42.67	β = 90
c = 95.09	γ = 90

Software Package:

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

Structure Validation

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