5YQZ

Structure of the glucagon receptor in complex with a glucagon analogue

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 

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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

  • 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 ...

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucagon receptor,Endolysin,Glucagon receptorA [auth R]575Homo sapiens, Escherichia virus T4Mutation(s): 3 
Gene Names: GCGR, E, T4Tp126
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P47871 (Homo sapiens)
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Go to UniProtKB:  P47871
PHAROS:  P47871
GTEx:  ENSG00000215644
Find proteins for P00720 (Enterobacteria phage T4)
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Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glucagon analogueB [auth P]28Homo sapiensMutation(s): 0 
Gene Names: GCG
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P01275 (Homo sapiens)
Explore P01275 
Go to UniProtKB:  P01275
PHAROS:  P01275
GTEx:  ENSG00000115263
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth A], D [auth B]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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 = 60.12α = 90
b = 108.79β = 90
c = 216.25γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata scaling
PHASERphasing

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)China31422017
National Science Foundation (China)China81525024

Revision History  (Full details and data files)

  • 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