6B73

Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor.

Che, T.Majumdar, S.Zaidi, S.A.Ondachi, P.McCorvy, J.D.Wang, S.Mosier, P.D.Uprety, R.Vardy, E.Krumm, B.E.Han, G.W.Lee, M.Y.Pardon, E.Steyaert, J.Huang, X.P.Strachan, R.T.Tribo, A.R.Pasternak, G.W.Carroll, F.I.Stevens, R.C.Cherezov, V.Katritch, V.Wacker, D.Roth, B.L.

(2018) Cell 172: 55-67.e15

  • DOI: https://doi.org/10.1016/j.cell.2017.12.011
  • Primary Citation of Related Structures:  
    6B73

  • PubMed Abstract: 

    The κ-opioid receptor (KOP) mediates the actions of opioids with hallucinogenic, dysphoric, and analgesic activities. The design of KOP analgesics devoid of hallucinatory and dysphoric effects has been hindered by an incomplete structural and mechanistic understanding of KOP agonist actions. Here, we provide a crystal structure of human KOP in complex with the potent epoxymorphinan opioid agonist MP1104 and an active-state-stabilizing nanobody. Comparisons between inactive- and active-state opioid receptor structures reveal substantial conformational changes in the binding pocket and intracellular and extracellular regions. Extensive structural analysis and experimental validation illuminate key residues that propagate larger-scale structural rearrangements and transducer binding that, collectively, elucidate the structural determinants of KOP pharmacology, function, and biased signaling. These molecular insights promise to accelerate the structure-guided design of safer and more effective κ-opioid receptor therapeutics.


  • Organizational Affiliation

    Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562, kappa-type opioid receptor
A, B
418Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 4 
Gene Names: cybCOPRK1OPRK
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 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP41145P0ABE7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody
C, D
134Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.31α = 90
b = 150.75β = 105.66
c = 100.28γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-3000data reduction
HKL-3000data 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 Mental Health (NIH/NIMH)United StatesRO1MH61887, U19MH82441

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary