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 8DZP | pdb_00008dzp

momSalB bound Kappa Opioid Receptor in complex with Gi1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8DZP

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 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.

Macromolecule Content 

  • Total Structure Weight: 147.66 kDa 
  • Atom Count: 8,657 
  • Modeled Residue Count: 1,120 
  • Deposited Residue Count: 1,324 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kappa-type opioid receptor308Homo sapiensMutation(s): 1 
Gene Names: OPRK1, OPRK
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
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
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UniProt GroupP63096
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1340Homo 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 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
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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 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
Find similar proteins by:|  3D Structure
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
U99
(Subject of Investigation/LOI)

Query on U99



Download:Ideal Coordinates CCD File
F [auth A]methyl (2S,4aR,6aR,7R,9S,10aS,10bR)-2-(furan-3-yl)-9-(methoxymethoxy)-6a,10b-dimethyl-4,10-dioxododecahydro-2H-naphtho[2,1-c]pyran-7-carboxylate
C23 H30 O8
KFVUSZPWUZBAPF-AGQYDFLVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
U99 BindingDB:  8DZP Ki: min: 0.6, max: 1.9 (nM) from 2 assay(s)
EC50: 0.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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, Structure summary
  • Version 1.2: 2023-05-24
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.4: 2025-05-21
    Changes: Data collection