8DZR

GR89,696 bound Kappa Opioid Receptor in complex with gustducin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Ligand and G-protein selectivity in the kappa-opioid receptor.

Han, J.Zhang, J.Nazarova, A.L.Bernhard, S.M.Krumm, B.E.Zhao, L.Lam, J.H.Rangari, V.A.Majumdar, S.Nichols, D.E.Katritch, V.Yuan, P.Fay, J.F.Che, T.

(2023) Nature 617: 417-425

  • DOI: https://doi.org/10.1038/s41586-023-06030-7
  • Primary Citation of Related Structures:  
    8DZP, 8DZQ, 8DZR, 8DZS

  • PubMed Abstract: 

    The κ-opioid receptor (KOR) represents a highly desirable therapeutic target for treating not only pain but also addiction and affective disorders 1 . However, the development of KOR analgesics has been hindered by the associated hallucinogenic side effects 2 . The initiation of KOR signalling requires the G i/o -family proteins including the conventional (G i1 , G i2 , G i3 , G oA and G oB ) and nonconventional (G z and G g ) subtypes. How hallucinogens exert their actions through KOR and how KOR determines G-protein subtype selectivity are not well understood. Here we determined the active-state structures of KOR in a complex with multiple G-protein heterotrimers-G i1 , G oA , G z and G g -using cryo-electron microscopy. The KOR-G-protein complexes are bound to hallucinogenic salvinorins or highly selective KOR agonists. Comparisons of these structures reveal molecular determinants critical for KOR-G-protein interactions as well as key elements governing G i/o -family subtype selectivity and KOR ligand selectivity. Furthermore, the four G-protein subtypes display an intrinsically different binding affinity and allosteric activity on agonist binding at KOR. These results provide insights into the actions of opioids and G-protein-coupling specificity at KOR and establish a foundation to examine the therapeutic potential of pathway-selective agonists of KOR.


  • Organizational Affiliation

    Department of Anesthesiology, Washington University in St Louis, St Louis, MO, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kappa-type opioid receptor287Homo sapiensMutation(s): 1 
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 
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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
G alpha gustducin protein354Homo sapiensMutation(s): 0 
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Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1339Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ScFv16 protein251Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U9I (Subject of Investigation/LOI)
Query on U9I

Download Ideal Coordinates CCD File 
F [auth A]methyl (3R)-4-[(3,4-dichlorophenyl)acetyl]-3-[(pyrrolidin-1-yl)methyl]piperazine-1-carboxylate
C19 H25 Cl2 N3 O3
HJUAKZYKCANOOZ-OAHLLOKOSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
U9I BindingDB:  8DZR Ki: min: 0.36, max: 360 (nM) from 6 assay(s)
IC50: min: 0.02, max: 0.04 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesGM143061

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 1.2: 2023-05-24
    Changes: Database references
  • Version 1.3: 2023-05-31
    Changes: Structure summary
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary