8YKD | pdb_00008ykd

Cryo-EM structure of ADGRG2-Gs complex with NTF nanobody


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8YKD

This is version 1.2 of the entry. See complete history

Literature

Development of an allosteric adhesion GPCR nanobody with therapeutic potential.

Zheng, Y.Jiang, D.Lu, Y.Zhang, C.Huang, S.M.Lin, H.Zhang, D.Guo, S.Han, J.Chen, J.He, Y.Zhang, M.Gao, Y.Guo, Y.Wei, R.Xia, M.Qin, Y.Liu, Z.Yang, F.Ge, S.Yi, F.Yu, X.Lin, H.Xiao, P.Sun, J.P.Feng, S.

(2025) Nat Chem Biol 21: 1519-1530

  • DOI: https://doi.org/10.1038/s41589-025-01896-2
  • Primary Citation Related Structures: 
    8YKD

  • PubMed Abstract: 

    Allosteric modulation of receptor responses to endogenous agonists has therapeutic value, maintaining ligand profiles, reducing side effects and restoring mutant responses. Adhesion G-protein-coupled receptors (aGPCRs), with large N termini, are ideal for allosteric modulator development. We designed a nanobody strategy targeting ADGRG2 N-terminal fragments and got a specific nanobody Nb23-bi, which promoted dehydroepiandrosterone (DHEA)-induced ADGRG2 activation and reversed mutant-induced dysfunctions. By combining structural characterization, crosslinking mass spectrometry, mutational analysis and molecular dynamics simulations, we clarified the allosteric mechanism of how the Nb23-bi modulates conformational changes in the DHEA-binding pocket. Animal studies showed that Nb23-bi promoted the response of DHEA in alleviating testicular inflammation and reversing mutant defects. In summary, we developed an allosteric nanobody of ADGRG2 and gained insights into its functions in reversing disease-associated dysfunctions. Our study may serve as a template for developing allosteric modulators of other aGPCRs for biological and therapeutic purposes.


  • Organizational Affiliation
    • Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 233.15 kDa 
  • Atom Count: 9,410 
  • Modeled Residue Count: 1,225 
  • Deposited Residue Count: 2,108 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha361SpodopteraMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P63091 (Canis lupus familiaris)
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Entity Groups
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UniProt GroupP63091
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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-1358SpodopteraMutation(s): 0 
Gene Names: GNB1
UniProt
Find proteins for P62871 (Bos taurus)
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UniProt GroupP62871
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit gammaC [auth G]108SpodopteraMutation(s): 0 
Gene Names: mRhiFer1_005810
Membrane Entity: Yes 
UniProt
Find proteins for A0A7J7XNR4 (Rhinolophus ferrumequinum)
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UniProt GroupA0A7J7XNR4
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody-35D [auth N]128SpodopteraMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Adhesion G-protein coupled receptor G2E [auth R]903SpodopteraMutation(s): 2 
Gene Names: Adgrg2Gpr64Me6
Membrane Entity: Yes 
UniProt
Find proteins for Q8CJ12 (Mus musculus)
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UniProt GroupQ8CJ12
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ScFv-16F [auth S]250SpodopteraMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AND
(Subject of Investigation/LOI)

Query on AND



Download:Ideal Coordinates CCD File
G [auth R]3-BETA-HYDROXY-5-ANDROSTEN-17-ONE
C19 H28 O2
FMGSKLZLMKYGDP-USOAJAOKSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



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: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Data collection, Database references
  • Version 1.2: 2025-10-08
    Changes: Data collection, Database references