5XEZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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This is version 2.0 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:  
    5XEZ, 5XF1

  • 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 containing both the extracellular domain and transmembrane domain in an inactive conformation ...

    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

    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, B574Homo sapiensEscherichia virus T4Mutation(s): 2 
Gene Names: GCGRET4Tp126
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
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody, mAb1, heavy chainC, E [auth H]231Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody, mAb1, light chainD, F [auth L]214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E], H [auth F], I [auth G], J [auth I], K [auth J]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
97V (Subject of Investigation/LOI)
Query on 97V

Download Ideal Coordinates CCD File 
M [auth A], P [auth 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 (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
L [auth A], N [auth B], O [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.61α = 90
b = 245.33β = 90.01
c = 96.15γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references
  • Version 1.2: 2017-06-14
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary