8DJG

ADGRL3-lectin domain in complex with an activating synthetic antibody fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder.

Kordon, S.P.Dutka, P.Adamska, J.M.Bandekar, S.J.Leon, K.Erramilli, S.K.Adams, B.Li, J.Kossiakoff, A.A.Arac, D.

(2023) Nat Commun 14: 635-635

  • DOI: https://doi.org/10.1038/s41467-023-36312-7
  • Primary Citation of Related Structures:  
    8DJG

  • PubMed Abstract: 

    Adhesion G protein-coupled receptors (aGPCRs) are cell-surface proteins with large extracellular regions that bind to multiple ligands to regulate key biological functions including neurodevelopment and organogenesis. Modulating a single function of a specific aGPCR isoform while affecting no other function and no other receptor is not trivial. Here, we engineered an antibody, termed LK30, that binds to the extracellular region of the aGPCR ADGRL3, and specifically acts as an agonist for ADGRL3 but not for its isoform, ADGRL1. The LK30/ADGRL3 complex structure revealed that the LK30 binding site on ADGRL3 overlaps with the binding site for an ADGRL3 ligand - teneurin. In cellular-adhesion assays, LK30 specifically broke the trans-cellular interaction of ADGRL3 with teneurin, but not with another ADGRL3 ligand - FLRT3. Our work provides proof of concept for the modulation of isoform- and ligand-specific aGPCR functions using unique tools, and thus establishes a foundation for the development of fine-tuned aGPCR-targeted therapeutics.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
sAB Heavy Chain
A, C
233synthetic constructMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
sAB Light Chain
B, D
215synthetic constructMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Adhesion G protein-coupled receptor L3
E, F
109Homo sapiensMutation(s): 0 
Gene Names: ADGRL3KIAA0768LEC3LPHN3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HAR2 (Homo sapiens)
Explore Q9HAR2 
Go to UniProtKB:  Q9HAR2
PHAROS:  Q9HAR2
GTEx:  ENSG00000150471 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HAR2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.799α = 90
b = 97.849β = 90
c = 163.058γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM120322
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134035-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1F32GM142266-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description