9J1P | pdb_00009j1p

Cryo-EM structure of the g1:Ox-bound human GLP-1R-Gs complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Disulfide-Directed Multicyclic Peptides with N-Terminally Extendable alpha-Helices for Recognition and Activation of G Protein-Coupled Receptors.

Fan, S.Li, J.Zhuang, J.Zhou, Q.Mai, Y.Lin, B.Wang, M.W.Wu, C.

(2025) J Am Chem Soc 147: 4821-4832

  • DOI: https://doi.org/10.1021/jacs.4c12808
  • Primary Citation of Related Structures:  
    9J1P, 9J5F, 9J5H

  • PubMed Abstract: 

    Many peptide hormones adopt long α-helical structures upon interacting with their cognate receptors but often exhibit flexible conformations when unbound. Strategies that can stabilize long α-helices without disrupting their binding to receptors are still lacking, which hinders progress in their biological applications and drug development. Here, we present an approach that combines rational design with library screening to create and identify a unique disulfide-directed multicyclic peptide (DDMP) scaffold, which could effectively stabilize N-terminally extendable α-helices while displaying exceptional efficiency in disulfide pairing and oxidative folding. This DDMP scaffold was then utilized for stabilizing the α-helical structure of glucagon-like peptide-1 (GLP-1), resulting in a potent GLP-1 receptor (GLP-1R) agonist with a significantly improved α-helicity and proteolytic stability. By incorporating external α-helices into the DDMP scaffold, we can effectively preserve the native N-terminal α-helical structures while allowing for extensive evolution of the C-terminal disulfide-rich domain for enhancing target binding, as demonstrated by the generation of the DDMP-stabilized GLP-1 (g1:Ox). The cryo-electron microscopy structure of the g1:Ox-GLP-1R in complex with heterotrimeric G s reveals the molecular basis for the potent binding between g1:Ox and GLP-1R. Specifically, the DDMP moiety establishes additional interactions with the extracellular domain of GLP-1R, which are absent in the case of GLP-1. Thus, this work offers a novel and effective approach for engineering therapeutic peptides and other peptide α-helices, ensuring that both the N- and C-terminal regions remain essential for target recognition and activation.


  • Organizational Affiliation
    • The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas361Homo sapiensMutation(s): 0 
Gene Names: GNAI1GNAS
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
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PHAROS:  P63092
GTEx:  ENSG00000087460 
Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups  
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UniProt GroupsP63096P63092
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1345Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
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UniProt GroupP54311
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]70Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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UniProt GroupP63212
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody-35D [auth N]140Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
g1:OxE [auth P]49synthetic constructMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptorF [auth R]440Homo sapiensMutation(s): 0 
Gene Names: GLP1R
Membrane Entity: Yes 
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Find proteins for P43220 (Homo sapiens)
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Go to UniProtKB:  P43220
PHAROS:  P43220
GTEx:  ENSG00000112164 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91853112
National Natural Science Foundation of China (NSFC)China22174119
National Natural Science Foundation of China (NSFC)China82273961
National Natural Science Foundation of China (NSFC)China82073904
National Natural Science Foundation of China (NSFC)China81872915
National Natural Science Foundation of China (NSFC)China21521004
Other government20720210001
Other government20720220005IQ
Other governmentIRT_17R66
Other government2021ZD0203400
Other governmentZDKJ2021028

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection