8V9W

X-ray crystal structure of JGFN4 complexed with fentanyl

  • Classification: ANTITOXIN
  • Organism(s): Camelidae
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-12-10 Released: 2024-08-07 
  • Deposition Author(s): Moller, N., Shi, K., Aihara, H.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Identification and biophysical characterization of a novel domain-swapped camelid antibody specific for fentanyl.

Gallant, J.P.Hicks, D.Shi, K.Moeller, N.H.Hoppe, B.Lake, E.W.Baehr, C.Pravetoni, M.Aihara, H.LeBeau, A.M.

(2024) J Biol Chem 300: 107502-107502

  • DOI: https://doi.org/10.1016/j.jbc.2024.107502
  • Primary Citation of Related Structures:  
    8V9W, 8V9X, 8V9Y, 8V9Z, 8VA0

  • PubMed Abstract: 

    Opioid use disorders (OUD) and overdoses are ever-evolving public health threats that continue to grow in incidence and prevalence in the United States and abroad. Current treatments consist of opioid receptor agonists and antagonists, which are safe and effective but still suffer from some limitations. Murine and humanized monoclonal antibodies (mAb) have emerged as an alternative and complementary strategy to reverse and prevent opioid-induced respiratory depression. To explore antibody applications beyond traditional heavy-light chain mAbs, we identified and biophysically characterized a novel single-domain antibody specific for fentanyl from a camelid variable-heavy-heavy (VHH) domain phage display library. Structural data suggested that VHH binding to fentanyl was facilitated by a unique domain-swapped dimerization mechanism, which accompanied a rearrangement of complementarity-determining region loops leading to the formation of a fentanyl-binding pocket. Structure-guided mutagenesis further identified an amino acid substitution that improved the affinity and relaxed the requirement for dimerization of the VHH in fentanyl binding. Our studies demonstrate VHH engagement of an opioid and inform on how to further engineer a VHH for enhanced stability and efficacy, laying the groundwork for exploring the in vivo applications of VHH-based biologics against OUD and overdose.


  • Organizational Affiliation

    Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
JGFN4
A, B, C, D
120CamelidaeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.431α = 90
b = 97.138β = 90
c = 57.578γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01-CA214279
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR37-AI064064

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release