7LCI

PF 06882961 bound to the glucagon-like peptide-1 receptor (GLP-1R):Gs complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

Evolving cryo-EM structural approaches for GPCR drug discovery.

Zhang, X.Johnson, R.M.Drulyte, I.Yu, L.Kotecha, A.Danev, R.Wootten, D.Sexton, P.M.Belousoff, M.J.

(2021) Structure 29: 963

  • DOI: 10.1016/j.str.2021.04.008
  • Primary Citation of Related Structures:  
    7LCI, 7LCJ, 7LCK

  • PubMed Abstract: 
  • G protein-coupled receptors (GPCRs) are the largest class of cell surface drug targets. Advances in stabilization of GPCR:transducer complexes, together with improvements in cryoelectron microscopy (cryo-EM) have recently been applied to structure-assisted drug design for GPCR agonists ...

    G protein-coupled receptors (GPCRs) are the largest class of cell surface drug targets. Advances in stabilization of GPCR:transducer complexes, together with improvements in cryoelectron microscopy (cryo-EM) have recently been applied to structure-assisted drug design for GPCR agonists. Nonetheless, limitations in the commercial application of these approaches, including the use of nanobody 35 (Nb35) to aid complex stabilization and the high cost of 300 kV imaging, have restricted broad application of cryo-EM in drug discovery. Here, using the PF 06882961-bound GLP-1R as exemplar, we validated the formation of stable complexes with a modified Gs protein in the absence of Nb35. In parallel, we compare 200 versus 300 kV image acquisition using a Falcon 4 or K3 direct electron detector. Moreover, the 200 kV Glacios-Falcon 4 yielded a 3.2 Å map with clear density for bound drug and multiple structurally ordered waters. Our work paves the way for broader commercial application of cryo-EM for GPCR drug discovery.


    Organizational Affiliation

    Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia. Electronic address: matthew.belousoff@monash.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptorA [auth R]491Homo sapiensMutation(s): 0 
Gene Names: GLP1R
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P43220 (Homo sapiens)
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Go to UniProtKB:  P43220
PHAROS:  P43220
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortB [auth A]394Homo sapiensMutation(s): 1 
Gene Names: GNASGNAS1GSP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
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PHAROS:  P63092
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]340Homo 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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]58Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
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PHAROS:  P59768
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UK4 (Subject of Investigation/LOI)
Query on UK4

Download Ideal Coordinates CCD File 
E [auth R]2-[(4-{6-[(4-cyano-2-fluorophenyl)methoxy]pyridin-2-yl}piperidin-1-yl)methyl]-1-{[(2S)-oxetan-2-yl]methyl}-1H-benzimidazole-6-carboxylic acid
C31 H30 F N5 O4
HYBAKUMPISVZQP-DEOSSOPVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaIC200100052
National Health and Medical Research Council (NHMRC, Australia)Australia1126857
National Health and Medical Research Council (NHMRC, Australia)Australia1184726
National Health and Medical Research Council (NHMRC, Australia)Australia1150083
Japan Science and TechnologyJapan18069571

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2021-09-15
    Changes: Database references