Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 72.23 kDa 
• Atom Count: 4710 
• Residue Count: 586 
• 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, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.232 
• R-Value Observed: 0.233 

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 
• DOI: 10.1038/nature25153
• Primary Citation of Related Structures:  
  5YQZ


• 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.

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Organizational Affiliation: 

CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucagon receptor,Endolysin,Glucagon receptor	R	575	Homo sapiens, Escherichia virus T4	Mutation(s): 3  Gene Names: GCGR EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class B	Protein:  Class B GPCR glucagon receptor, full length in complex with glucagon analog NNC1702
Find proteins for P47871 (Homo sapiens) Explore P47871  Go to UniProtKB:  P47871
NIH Common Fund Data Resources
PHAROS  P47871 GTEx  ENSG00000215644
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucagon analogue	P	28	Homo sapiens	Mutation(s): 0  Gene Names: GCG
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class B	Protein:  Class B GPCR glucagon receptor, full length in complex with glucagon analog NNC1702
Find proteins for P01275 (Homo sapiens) Explore P01275  Go to UniProtKB:  P01275
NIH Common Fund Data Resources
PHAROS  P01275 GTEx  ENSG00000115263

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	A, B	2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	R	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
PO4	R	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.232 
• R-Value Observed: 0.233 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.12	α = 90
b = 108.79	β = 90
c = 216.25	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-11-08 
• Released Date: 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.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31422017
National Science Foundation (China)	China	81525024

Revision History 

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary