6ORV

Non-peptide agonist (TT-OAD2) bound to the Glucagon-Like peptide-1 (GLP-1) Receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Activation of the GLP-1 receptor by a non-peptidic agonist.

Zhao, P.Liang, Y.L.Belousoff, M.J.Deganutti, G.Fletcher, M.M.Willard, F.S.Bell, M.G.Christe, M.E.Sloop, K.W.Inoue, A.Truong, T.T.Clydesdale, L.Furness, S.G.B.Christopoulos, A.Wang, M.W.Miller, L.J.Reynolds, C.A.Danev, R.Sexton, P.M.Wootten, D.

(2020) Nature 577: 432-436

  • DOI: 10.1038/s41586-019-1902-z
  • Primary Citation of Related Structures:  
    6ORV

  • PubMed Abstract: 
  • Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, including diabetes and obesity 1 . Structures of active receptors reveal peptide agonists engage deep within the receptor core, leading to an outward movement of extracellular loop 3 and the tops of transmembrane helices 6 and 7, an inward movement of transmembrane helix 1, reorganization of extracellular loop 2 and outward movement of the intracellular side of transmembrane helix 6, resulting in G-protein interaction and activation 2-6 ...

    Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, including diabetes and obesity 1 . Structures of active receptors reveal peptide agonists engage deep within the receptor core, leading to an outward movement of extracellular loop 3 and the tops of transmembrane helices 6 and 7, an inward movement of transmembrane helix 1, reorganization of extracellular loop 2 and outward movement of the intracellular side of transmembrane helix 6, resulting in G-protein interaction and activation 2-6 . Here we solved the structure of a non-peptide agonist, TT-OAD2, bound to the glucagon-like peptide-1 (GLP-1) receptor. Our structure identified an unpredicted non-peptide agonist-binding pocket in which reorganization of extracellular loop 3 and transmembrane helices 6 and 7 manifests independently of direct ligand interaction within the deep transmembrane domain pocket. TT-OAD2 exhibits biased agonism, and kinetics of G-protein activation and signalling that are distinct from peptide agonists. Within the structure, TT-OAD2 protrudes beyond the receptor core to interact with the lipid or detergent, providing an explanation for the distinct activation kinetics that may contribute to the clinical efficacy of this compound series. This work alters our understanding of the events that drive the activation of class B receptors.


    Organizational Affiliation

    School of Pharmacy, Fudan University, Shanghai, China. denise.wootten@monash.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short AP394Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1GSP
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class B1
Protein: 
GLP-1 receptor in complex with TT-OAD2 non-peptide agonist
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
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PHAROS:  P63092
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 BP350Homo sapiensMutation(s): 0 
Gene Names: GNB1
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
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PHAROS:  P62873
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 GP71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class B1
Protein: 
GLP-1 receptor in complex with TT-OAD2 non-peptide agonist
Find proteins for P59768 (Homo sapiens)
Explore P59768 
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PHAROS:  P59768
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody 35 NP138Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptor RP491Homo sapiensMutation(s): 0 
Gene Names: GLP1R
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class B1
Protein: 
GLP-1 receptor in complex with TT-OAD2 non-peptide agonist
Find proteins for P43220 (Homo sapiens)
Explore P43220 
Go to UniProtKB:  P43220
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PHAROS:  P43220
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N2V
Query on N2V

Download Ideal Coordinates CCD File 
RP
N-{(3S,8S)-3-{4-[(3,4-dichlorophenyl)methoxy]phenyl}-7-[(1S)-1-phenylpropyl]-2,3,6,7,8,9-hexahydro[1,4]dioxino[2,3-g]isoquinoline-8-carbonyl}-4-(2,3-dimethylpyridin-4-yl)-L-phenylalanine
C50 H47 Cl2 N3 O6
DEDPYBWOUXWMOX-ZTAAISNPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1061044
National Health and Medical Research Council (NHMRC, Australia)Australia1065410
National Health and Medical Research Council (NHMRC, Australia)Australia1120919
National Health and Medical Research Council (NHMRC, Australia)Australia1126857
National Health and Medical Research Council (NHMRC, Australia)Australia1055134

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Database references