Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.32 kDa 
• Atom Count: 6707 
• Residue Count: 846 
• 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, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• 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: 3.00 Å
• R-Value Free: 0.256 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

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, 5VEX


• 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: 

School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucagon-like peptide 1 receptor, Endolysin chimera	A, B	455	Homo sapiens, Escherichia virus T4	Mutation(s): 14  Gene Names: GLP1R EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class B	Protein:  GLP-1 receptor in complex with PF-06372222
Find proteins for P43220 (Homo sapiens) Explore P43220  Go to UniProtKB:  P43220
NIH Common Fund Data Resources
PHAROS  P43220 GTEx  ENSG00000112164
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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: 3.00 Å
• R-Value Free: 0.256 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.81	α = 91.55
b = 67.51	β = 89.88
c = 83.66	γ = 107.56

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2017-06-14
  Changes: Database references