8V8K | pdb_00008v8k

Crystal Structure of Nanobody NbE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.331 (Depositor), 0.323 (DCC) 
  • R-Value Work: 
    0.286 (Depositor), 0.283 (DCC) 
  • R-Value Observed: 
    0.291 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of mu-opioid receptor targeting by a nanobody antagonist.

Yu, J.Kumar, A.Zhang, X.Martin, C.Van Holsbeeck, K.Raia, P.Koehl, A.Laeremans, T.Steyaert, J.Manglik, A.Ballet, S.Boland, A.Stoeber, M.

(2024) Nat Commun 15: 8687-8687

  • DOI: https://doi.org/10.1038/s41467-024-52947-6
  • Primary Citation of Related Structures:  
    8QOT, 8V8K

  • PubMed Abstract: 

    The μ-opioid receptor (μOR), a prototypical G protein-coupled receptor (GPCR), is the target of opioid analgesics such as morphine and fentanyl. Due to the severe side effects of current opioid drugs, there is considerable interest in developing novel modulators of μOR function. Most GPCR ligands today are small molecules, however biologics, including antibodies and nanobodies, represent alternative therapeutics with clear advantages such as affinity and target selectivity. Here, we describe the nanobody NbE, which selectively binds to the μOR and acts as an antagonist. We functionally characterize NbE as an extracellular and genetically encoded μOR ligand and uncover the molecular basis for μOR antagonism by determining the cryo-EM structure of the NbE-μOR complex. NbE displays a unique ligand binding mode and achieves μOR selectivity by interactions with the orthosteric pocket and extracellular receptor loops. Based on a β-hairpin loop formed by NbE that deeply protrudes into the μOR, we design linear and cyclic peptide analogs that recapitulate NbE's antagonism. The work illustrates the potential of nanobodies to uniquely engage with GPCRs and describes lower molecular weight μOR ligands that can serve as a basis for therapeutic developments.


  • Organizational Affiliation
    • Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody NbE
A, B, C
123Lama glamaMutation(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: 2.85 Å
  • R-Value Free:  0.331 (Depositor), 0.323 (DCC) 
  • R-Value Work:  0.286 (Depositor), 0.283 (DCC) 
  • R-Value Observed: 0.291 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.559α = 90
b = 76.559β = 90
c = 298.596γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR61DA051531

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Derived calculations
  • Version 1.2: 2024-10-23
    Changes: Database references, Structure summary