8F7W

Gi bound kappa-opioid receptor in complex with dynorphin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of the entire human opioid receptor family.

Wang, Y.Zhuang, Y.DiBerto, J.F.Zhou, X.E.Schmitz, G.P.Yuan, Q.Jain, M.K.Liu, W.Melcher, K.Jiang, Y.Roth, B.L.Xu, H.E.

(2023) Cell 186: 413-427.e17

  • DOI: https://doi.org/10.1016/j.cell.2022.12.026
  • Primary Citation of Related Structures:  
    8F7Q, 8F7R, 8F7S, 8F7W, 8F7X

  • PubMed Abstract: 

    Opioids are effective analgesics, but their use is beset by serious side effects, including addiction and respiratory depression, which contribute to the ongoing opioid crisis. The human opioid system contains four opioid receptors (μOR, δOR, κOR, and NOPR) and a set of related endogenous opioid peptides (EOPs), which show distinct selectivity toward their respective opioid receptors (ORs). Despite being key to the development of safer analgesics, the mechanisms of molecular recognition and selectivity of EOPs to ORs remain unclear. Here, we systematically characterize the binding of EOPs to ORs and present five structures of EOP-OR-G i complexes, including β-endorphin- and endomorphin-bound μOR, deltorphin-bound δOR, dynorphin-bound κOR, and nociceptin-bound NOPR. These structures, supported by biochemical results, uncover the specific recognition and selectivity of opioid peptides and the conserved mechanism of opioid receptor activation. These results provide a structural framework to facilitate rational design of safer opioid drugs for pain relief.


  • Organizational Affiliation

    The CAS Key Laboratory of Receptor Research and the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kappa-type opioid receptorA [auth R]378Homo sapiensMutation(s): 0 
Gene Names: OPRK1OPRK
Membrane Entity: Yes 
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Find proteins for P41145 (Homo sapiens)
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PHAROS:  P41145
GTEx:  ENSG00000082556 
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UniProt GroupP41145
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DynorphinB [auth P]8Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P01213 (Homo sapiens)
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PHAROS:  P01213
GTEx:  ENSG00000101327 
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UniProt GroupP01213
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1C [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]353Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth C]68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16F [auth E]248synthetic constructMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFA0507002
National Natural Science Foundation of China (NSFC)China82121005
Chinese Academy of SciencesChinaXDB08020303

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2023-02-01
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary