Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: authors reported there is no experimental evidence

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106321.83 
• Atom Count: 6707 
• Residue Count: 910 
• Unique protein chains: 1

5VEX

Structure of the human GLP-1 receptor complex with NNC0640

• DOI: 10.2210/pdb5VEX/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Enterobacteria phage T4
• Expression System: Spodoptera frugiperda
• Mutation(s): 14 


• Deposited: 2017-04-05 Released: 2017-05-17 
• Deposition Author(s): Song, G., Yang, D., Wang, Y., Graaf, C.D., Zhou, Q., Jiang, S., Liu, K., Cai, X., Dai, A., Lin, G., Liu, D., Wu, F., Wu, Y., Zhao, S., Ye, L., Han, G.W., Lau, J., Wu, B., Hanson, M.A., Liu, Z.-J., Wang, M.-W., Stevens, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.256 
• R-Value Work: 0.233 

Literature

Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators.

Song, G., Yang, D., Wang, Y., de Graaf, C., Zhou, Q., Jiang, S., Liu, K., Cai, X., Dai, A., Lin, G., Liu, D., Wu, F., Wu, Y., Zhao, S., Ye, L., Han, G.W., Lau, J., Wu, B., Hanson, M.A., Liu, Z.J., Wang, M.W., Stevens, R.C.

(2017) Nature 546: 312-315

• PubMed: 28514449 
• DOI: 10.1038/nature22378
• Primary Citation of Related Structures:  
  5VEW


• PubMed Abstract: 
  

The glucagon-like peptide-1 receptor (GLP-1R) and the glucagon receptor (GCGR) are members of the secretin-like class B family of G-protein-coupled receptors (GPCRs) and have opposing physiological roles in insulin release and glucose homeostasis. The treatment of type 2 diabetes requires positive modulation of GLP-1R to inhibit glucagon secretion and stimulate insulin secretion in a glucose-dependent manner. Here we report crystal structures of the human GLP-1R transmembrane domain in complex with two different negative allosteric modulators, PF-06372222 and NNC0640, at 2.7 and 3.0 Å resolution, respectively. The structures reveal a common binding pocket for negative allosteric modulators, present in both GLP-1R and GCGR and located outside helices V-VII near the intracellular half of the receptor. The receptor is in an inactive conformation with compounds that restrict movement of the intracellular tip of helix VI, a movement that is generally associated with activation mechanisms in class A GPCRs. Molecular modelling and mutagenesis studies indicate that agonist positive allosteric modulators target the same general region, but in a distinct sub-pocket at the interface between helices V and VI, which may facilitate the formation of an intracellular binding site that enhances G-protein coupling.

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Organizational Affiliation: 

iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucagon-like peptide 1 receptor, Endolysin chimera	A, B	455	Homo sapiens, Enterobacteria phage T4 This entity is chimeric	Mutation(s): 14  Gene Names: GLP1R, E EC: 3.2.1.17
Membrane protein mpstruct	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs)	Protein:  GLP-1 receptor in complex with PF-06372222
Find proteins for P43220 (Homo sapiens) Go to Gene View: GLP1R Go to UniProtKB:  P43220
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB:  P00720

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
97V	A, B	4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl)phenyl]carbamoyl}amino]methyl}-N-(1H-tetrazol-5-yl)benzamide C29 H31 N7 O4 S PPTKULJUDJWTSA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.256 
• R-Value Work: 0.233 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 64.810	α = 91.55
b = 67.510	β = 89.88
c = 83.660	γ = 107.56

Software Package:

Software Name	Purpose
XDS	data reduction
BUSTER	refinement
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-04-05 
• Released Date: 2017-05-17 
• Deposition Author(s): Song, G., Yang, D., Wang, Y., Graaf, C.D., Zhou, Q., Jiang, S., Liu, K., Cai, X., Dai, A., Lin, G., Liu, D., Wu, F., Wu, Y., Zhao, S., Ye, L., Han, G.W., Lau, J., Wu, B., Hanson, M.A., Liu, Z.-J., Wang, M.-W., Stevens, R.C.

Revision History 

• Version 1.0: 2017-05-17
  Type: Initial release
• Version 1.1: 2017-05-31
  Type: Database references
• Version 1.2: 2017-06-14
  Type: Database references