5XEZ

Structure of the Full-length glucagon class B G protein-coupled receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the full-length glucagon class B G-protein-coupled receptor.

Zhang, H.Qiao, A.Yang, D.Yang, L.Dai, A.de Graaf, C.Reedtz-Runge, S.Dharmarajan, V.Zhang, H.Han, G.W.Grant, T.D.Sierra, R.G.Weierstall, U.Nelson, G.Liu, W.Wu, Y.Ma, L.Cai, X.Lin, G.Wu, X.Geng, Z.Dong, Y.Song, G.Griffin, P.R.Lau, J.Cherezov, V.Yang, H.Hanson, M.A.Stevens, R.C.Zhao, Q.Jiang, H.Wang, M.W.Wu, B.

(2017) Nature 546: 259-264

  • DOI: 10.1038/nature22363
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human glucagon receptor, GCGR, belongs to the class B G-protein-coupled receptor family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR contain ...

    The human glucagon receptor, GCGR, belongs to the class B G-protein-coupled receptor family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR containing both the extracellular domain and transmembrane domain in an inactive conformation. The two domains are connected by a 12-residue segment termed the stalk, which adopts a β-strand conformation, instead of forming an α-helix as observed in the previously solved structure of the GCGR transmembrane domain. The first extracellular loop exhibits a β-hairpin conformation and interacts with the stalk to form a compact β-sheet structure. Hydrogen-deuterium exchange, disulfide crosslinking and molecular dynamics studies suggest that the stalk and the first extracellular loop have critical roles in modulating peptide ligand binding and receptor activation. These insights into the full-length GCGR structure deepen our understanding of the signalling mechanisms of class B G-protein-coupled receptors.


    Organizational Affiliation

    Novo Nordisk Research Centre China, No. 20 Life Science Park Road, Changping District, Beijing 102206, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.,GPCR Consortium, San Marcos, California 92078, USA.,Hauptman-Woodward Institute, SUNY at Buffalo, 700 Ellicott Street, Buffalo, New York 14203, USA.,Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands.,Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, USA.,Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.,School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai 201210, China.,Novo Nordisk A/S, Novo Nordisk Park, Måløv 2760, Denmark.,Department of Chemistry, Bridge Institute, University of Southern California, 3430 S. Vermont Avenue, Los Angeles, California 90089, USA.,iHuman Institute, ShanghaiTech University, 393 Hua Xia Zhong Road, Shanghai 201210, China.,Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.,School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China.,The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Pudong, Shanghai 201203, China.,Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.,Biodesign Center for Applied Structural Discovery, Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucagon receptor,Endolysin,Glucagon receptor
A, B
574Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 2 
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
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody, mAb1, heavy chain
C, H
231N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antibody, mAb1, light chain
D, L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
97V
Query on 97V

Download SDF File 
Download CCD File 
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
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.610α = 90.00
b = 245.330β = 90.01
c = 96.150γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
PHASERphasing
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references
  • Version 1.2: 2017-06-14
    Type: Database references