9U4Y | pdb_00009u4y

cryo-EM structure of Xenopus laevis GnRHR bound with mammal GnRH


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 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

Cryo-EM structures of GnRHR: Foundations for next-generation therapeutics.

Shen, S.He, X.Liu, H.Hu, W.Xu, H.E.Duan, J.

(2025) Proc Natl Acad Sci U S A 122: e2500112122-e2500112122

  • DOI: https://doi.org/10.1073/pnas.2500112122
  • Primary Citation of Related Structures:  
    9U4W, 9U4Y

  • PubMed Abstract: 

    Gonadotropin-releasing hormone receptor (GnRHR) is critical for reproductive health and a key therapeutic target for endocrine disorders and hormone-responsive cancers. Using high-resolution cryoelectron microscopy, we determined the structures of Sus scrofa and Xenopus laevis GnRHRs bound to mammal GnRH, uncovering conserved and species-specific mechanisms of receptor activation and G protein coupling. The conserved "U"-shaped GnRH conformation mediates high-affinity binding through key interactions with residues such as K 3.32 , Y 6.51 , and Y 6.52 . Species-specific variations in extracellular loops and receptor-ligand contacts fine-tune receptor function, while ligand binding induces structural rearrangements, including N terminus displacement and TM6 rotation, critical for signaling. Structure-activity relationship analysis demonstrates how D-amino acid substitutions in GnRH analogs enhance stability and receptor affinity. Distinct binding modes of agonists and antagonists elucidate mechanisms of ligand-dependent activation and inactivation. These insights lay the groundwork for designing next-generation GnRHR therapeutics with enhanced specificity and efficacy for conditions like endometriosis, prostate cancer, and infertility.


  • Organizational Affiliation
    • State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1A [auth B]344Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2B [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gonadoliberin-111synthetic constructMutation(s): 1 
UniProt
Find proteins for Q28588 (Ovis aries)
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UniProt GroupQ28588
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alpha-1D [auth A]246Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16E [auth S]285Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2 adrenergic receptor,Gonadotropin-releasing hormone receptorF [auth R]504AtelesXenopus laevis
This entity is chimeric
Mutation(s): 0 
Gene Names: ADRB2ADRB2RB2ARgnrhr.LgnrhrGNRHR1gnrhr2-Axgnrhr
Membrane Entity: Yes 
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Find proteins for P07550 (Homo sapiens)
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PHAROS:  P07550
GTEx:  ENSG00000169252 
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UniProt GroupP07550
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
C
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection, Database references