7YIT

Molecular mechanism of biased signaling at the kappa opioid receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.290 

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Literature

Molecular mechanism of biased signaling at the kappa opioid receptor.

El Daibani, A.Paggi, J.M.Kim, K.Laloudakis, Y.D.Popov, P.Bernhard, S.M.Krumm, B.E.Olsen, R.H.J.Diberto, J.Carroll, F.I.Katritch, V.Wunsch, B.Dror, R.O.Che, T.

(2023) Nat Commun 14: 1338-1338

  • DOI: https://doi.org/10.1038/s41467-023-37041-7
  • Primary Citation of Related Structures:  
    7YIT

  • PubMed Abstract: 

    The κ-opioid receptor (KOR) has emerged as an attractive drug target for pain management without addiction, and biased signaling through particular pathways of KOR may be key to maintaining this benefit while minimizing side-effect liabilities. As for most G protein-coupled receptors (GPCRs), however, the molecular mechanisms of ligand-specific signaling at KOR have remained unclear. To better understand the molecular determinants of KOR signaling bias, we apply structure determination, atomic-level molecular dynamics (MD) simulations, and functional assays. We determine a crystal structure of KOR bound to the G protein-biased agonist nalfurafine, the first approved KOR-targeting drug. We also identify an arrestin-biased KOR agonist, WMS-X600. Using MD simulations of KOR bound to nalfurafine, WMS-X600, and a balanced agonist U50,488, we identify three active-state receptor conformations, including one that appears to favor arrestin signaling over G protein signaling and another that appears to favor G protein signaling over arrestin signaling. These results, combined with mutagenesis validation, provide a molecular explanation of how agonists achieve biased signaling at KOR.


  • Organizational Affiliation

    Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kappa-type opioid receptor305Homo sapiensMutation(s): 2 
Gene Names: OPRK1OPRK
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens)
Explore P41145 
Go to UniProtKB:  P41145
PHAROS:  P41145
GTEx:  ENSG00000082556 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41145
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody39B [auth D]123Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562C [auth E]109Escherichia coliMutation(s): 4 
Gene Names: cybC
Membrane Entity: Yes 
UniProt
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABE7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IVB (Subject of Investigation/LOI)
Query on IVB

Download Ideal Coordinates CCD File 
D [auth A]nalfurafine
C28 H32 N2 O5
XGZZHZMWIXFATA-UEZBDDGYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.290 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.75α = 90
b = 76.53β = 90
c = 154.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
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 Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM143061

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Derived calculations, Structure summary