Structure of the glucagon receptor in complex with a glucagon analogue.

Zhang, H.; Qiao, A.; Yang, L.; Van Eps, N.; Frederiksen, K.S.; Yang, D.; Dai, A.; Cai, X.; Zhang, H.; Yi, C.; Cao, C.; He, L.; Yang, H.; Lau, J.; Ernst, O.P.; Hanson, M.A.; Stevens, R.C.; Wang, M.W.; Reedtz-Runge, S.; Jiang, H.; Zhao, Q.; Wu, B.

doi:10.2210/pdb5yqz/pdb

Macromolecule Content

Total Structure Weight: 72263.78
Atom Count: 4710
Residue Count: 603
Unique protein chains: 2

5YQZ

Structure of the glucagon receptor in complex with a glucagon analogue

DOI: 10.2210/pdb5YQZ/pdb

Classification: SIGNALING PROTEIN/HYDROLASE
Organism(s): Homo sapiens, Enterobacteria phage T4
Expression System: Spodoptera frugiperda
Mutation(s): 3

Deposited: 2017-11-08 Released: 2018-01-17
Deposition Author(s): Zhang, H., Qiao, A., Yang, L., VAN EPS, N., Frederiksen, K., Yang, D., Dai, A., Cai, X., Zhang, H., Yi, C., Can, C., He, L., Yang, H., Lau, J., Ernst, O., Hanson, M., Stevens, R., Wang, M., Seedtz-Runge, S., Jiang, H., Zhao, Q., Wu, B.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3 Å
R-Value Free: 0.261
R-Value Work: 0.232

wwPDB Validation3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of the glucagon receptor in complex with a glucagon analogue.

Zhang, H., Qiao, A., Yang, L., Van Eps, N., Frederiksen, K.S., Yang, D., Dai, A., Cai, X., Zhang, H., Yi, C., Cao, C., He, L., Yang, H., Lau, J., Ernst, O.P., Hanson, M.A., Stevens, R.C., Wang, M.W., Reedtz-Runge, S., Jiang, H., Zhao, Q., Wu, B.

(2018) Nature 553: 106-110

PubMed: 29300013 Search on PubMed
DOI: 10.1038/nature25153

PubMed Abstract:

Class B G-protein-coupled receptors (GPCRs), which consist of an extracellular domain (ECD) and a transmembrane domain (TMD), respond to secretin peptides to play a key part in hormonal homeostasis, and are important therapeutic targets for a variety of diseases. Previous work has suggested that peptide ligands bind to class B GPCRs according to a two-domain binding model, in which the C-terminal region of the peptide targets the ECD and the N-terminal region of the peptide binds to the TMD binding pocket. Recently, three structures of class B GPCRs in complex with peptide ligands have been solved. These structures provide essential insights into peptide ligand recognition by class B GPCRs. However, owing to resolution limitations, the specific molecular interactions for peptide binding to class B GPCRs remain ambiguous. Moreover, these previously solved structures have different ECD conformations relative to the TMD, which introduces questions regarding inter-domain conformational flexibility and the changes required for receptor activation. Here we report the 3.0 Å-resolution crystal structure of the full-length human glucagon receptor (GCGR) in complex with a glucagon analogue and partial agonist, NNC1702. This structure provides molecular details of the interactions between GCGR and the peptide ligand. It reveals a marked change in the relative orientation between the ECD and TMD of GCGR compared to the previously solved structure of the inactive GCGR-NNC0640-mAb1 complex. Notably, the stalk region and the first extracellular loop undergo major conformational changes in secondary structure during peptide binding, forming key interactions with the peptide. We further propose a dual-binding-site trigger model for GCGR activation-which requires conformational changes of the stalk, first extracellular loop and TMD-that extends our understanding of the previously established two-domain peptide-binding model of class B GPCRs.

Organizational Affiliation:

CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucagon receptor,Endolysin,Glucagon receptor	R	575	Homo sapiens, Enterobacteria phage T4 This entity is chimeric	Mutation(s): 3 Gene Names: GCGR, E EC: 3.2.1.17
Membrane protein mpstruct	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: G Protein-Coupled Receptors (GPCRs)	Protein: Class B GPCR glucagon receptor
Find proteins for P47871 (Homo sapiens) Go to Gene View: GCGR Go to UniProtKB: P47871
Protein Feature View Full Protein Feature View for P47871
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB: P00720
Protein Feature View Full Protein Feature View for P00720

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Glucagon analogue	P	28	Homo sapiens	Mutation(s): 0 Gene Names: GCG
Membrane protein mpstruct	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: G Protein-Coupled Receptors (GPCRs)	Protein: Class B GPCR glucagon receptor
Find proteins for P01275 (Homo sapiens) Go to Gene View: GCG Go to UniProtKB: P01275
Protein Feature View Full Protein Feature View for P01275

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
OLC Query on OLC Download SDF File Download CCD File	R	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 1-Oleoyl-R-glycerol C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Ligand Interaction
PO4 Query on PO4 Download SDF File Download CCD File	R	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
NAG Query on NAG Download SDF File Download CCD File	R	N-ACETYL-D-GLUCOSAMINE C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction