6VCB

Cryo-EM structure of the Glucagon-like peptide-1 receptor in complex with G protein, GLP-1 peptide and a positive allosteric modulator


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Structural insights into probe-dependent positive allosterism of the GLP-1 receptor.

Bueno, A.B.Sun, B.Willard, F.S.Feng, D.Ho, J.D.Wainscott, D.B.Showalter, A.D.Vieth, M.Chen, Q.Stutsman, C.Chau, B.Ficorilli, J.Agejas, F.J.Cumming, G.R.Jimenez, A.Rojo, I.Kobilka, T.S.Kobilka, B.K.Sloop, K.W.

(2020) Nat Chem Biol 16: 1105-1110

  • DOI: 10.1038/s41589-020-0589-7
  • Primary Citation of Related Structures:  
    6VCB

  • PubMed Abstract: 
  • Drugs that promote the association of protein complexes are an emerging therapeutic strategy. We report discovery of a G protein-coupled receptor (GPCR) ligand that stabilizes an active state conformation by cooperatively binding both the receptor and orthosteric ligand, thereby acting as a 'molecular glue' ...

    Drugs that promote the association of protein complexes are an emerging therapeutic strategy. We report discovery of a G protein-coupled receptor (GPCR) ligand that stabilizes an active state conformation by cooperatively binding both the receptor and orthosteric ligand, thereby acting as a 'molecular glue'. LSN3160440 is a positive allosteric modulator of the GLP-1R optimized to increase the affinity and efficacy of GLP-1(9-36), a proteolytic product of GLP-1(7-36). The compound enhances insulin secretion in a glucose-, ligand- and GLP-1R-dependent manner. Cryo-electron microscopy determined the structure of the GLP-1R bound to LSN3160440 in complex with GLP-1 and heterotrimeric G s . The modulator binds high in the helical bundle at an interface between TM1 and TM2, allowing access to the peptide ligand. Pharmacological characterization showed strong probe dependence of LSN3160440 for GLP-1(9-36) versus oxyntomodulin that is driven by a single residue. Our findings expand protein-protein modulation drug discovery to uncompetitive, active state stabilizers for peptide hormone receptors.


    Organizational Affiliation

    Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA. sloop_kyle_w@lilly.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptorA [auth R]445Homo sapiensMutation(s): 1 
Gene Names: GLP1R
Membrane Entity: Yes 
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Find proteins for P43220 (Homo sapiens)
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PHAROS:  P43220
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glucagon-like peptide 1B [auth P]31Homo sapiensMutation(s): 0 
Gene Names: GCG
Membrane Entity: Yes 
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Find proteins for P01275 (Homo sapiens)
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PHAROS:  P01275
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortC [auth A]380Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1GSP
Membrane Entity: Yes 
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PHAROS:  P63092
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]350Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody 35F [auth N]160Lama glamaMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QW7
Query on QW7

Download Ideal Coordinates CCD File 
G [auth R]1-[(1R)-1-(2,6-dichloro-3-methoxyphenyl)ethyl]-6-{2-[(2R)-piperidin-2-yl]phenyl}-1H-benzimidazole
C27 H27 Cl2 N3 O
YFCMSHPEVDOMQA-VGOFRKELSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2020-09-30
    Changes: Database references