VOOZH about

URL: https://www.rcsb.org/structure/8EF5

⇱ RCSB PDB - 8EF5: Fentanyl-bound mu-opioid receptor-Gi complex


πŸ‘ RCSB PDB
251,806
Structures from the PDB archive
1,068,577
Computed Structure Models (CSM)

 8EF5 | pdb_00008ef5

Fentanyl-bound mu-opioid receptor-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Γ…
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

This is version 1.3 of the entry. See complete history


Literature

Molecular recognition of morphine and fentanyl by the human mu-opioid receptor.

Zhuang, Y.Wang, Y.He, B.He, X.Zhou, X.E.Guo, S.Rao, Q.Yang, J.Liu, J.Zhou, Q.Wang, X.Liu, M.Liu, W.Jiang, X.Yang, D.Jiang, H.Shen, J.Melcher, K.Chen, H.Jiang, Y.Cheng, X.Wang, M.W.Xie, X.Xu, H.E.

(2022) Cell 185: 4361-4375.e19

  • PubMed36368306 Search on PubMed
  • DOI: https://doi.org/10.1016/j.cell.2022.09.041
  • Primary Citation Related Structures: 
    8EF5, 8EF6, 8EFB, 8EFL, 8EFO, 8EFQ

  • PubMed Abstract: 

    Morphine and fentanyl are among the most used opioid drugs that confer analgesia and unwanted side effects through both G protein and arrestin signaling pathways of ΞΌ-opioid receptor (ΞΌOR). Here, we report structures of the human ΞΌOR-G protein complexes bound to morphine and fentanyl, which uncover key differences in how they bind the receptor. We also report structures of ΞΌOR bound to TRV130, PZM21, and SR17018, which reveal preferential interactions of these agonists with TM3 side of the ligand-binding pocket rather than TM6/7 side. In contrast, morphine and fentanyl form dual interactions with both TM3 and TM6/7 regions. Mutations at the TM6/7 interface abolish arrestin recruitment of ΞΌOR promoted by morphine and fentanyl. Ligands designed to reduce TM6/7 interactions display preferential G protein signaling. Our results provide crucial insights into fentanyl recognition and signaling of ΞΌOR, which may facilitate rational design of next-generation analgesics.


  • Organizational Affiliation
    • The CAS Key Laboratory of Receptor Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. Electronic address: zhuangyouwen@simm.ac.cn.
    • The CAS Key Laboratory of Receptor Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China.
    • University of Chinese Academy of Sciences, Beijing 100049, China; The State Key Laboratory of Drug Research, The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
    • Department of Structural Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
    • University of Chinese Academy of Sciences, Beijing 100049, China; The State Key Laboratory of Drug Research, The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China.
    • School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
    • The CAS Key Laboratory of Receptor Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
    • School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China.
    • Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
    • The CAS Key Laboratory of Receptor Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; The State Key Laboratory of Drug Research, The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
    • The CAS Key Laboratory of Receptor Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
    • Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China; Shanghai Yuansi Standard Science and Technology Co., Ltd, Shanghai 200080, China.
    • The CAS Key Laboratory of Receptor Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; The State Key Laboratory of Drug Research, The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China. Electronic address: mwwang@simm.ac.cn.
    • The CAS Key Laboratory of Receptor Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; The State Key Laboratory of Drug Research, The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China. Electronic address: xxie@simm.ac.cn.
    • The CAS Key Laboratory of Receptor Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: eric.xu@simm.ac.cn.

Macromolecule Content 

  • Total Structure Weight: 240.57 kDa 
  • Atom Count: 11,705 
  • Modeled Residue Count: 1,441 
  • Deposited Residue Count: 2,111 
  • Unique protein chains: 5

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mu-type opioid receptorA [auth R],
F [auth M]
367Homo sapiensMutation(s): 0 
Gene Names: OPRM1MOR1
Membrane Entity: Yes 
πŸ‘ Image
UniProt & NIH Common Fund Data Resources
Find proteins for P35372 (Homo sapiens)
Explore P35372 
Go to UniProtKB:  P35372
PHAROS:  P35372
GTEx:  ENSG00000112038 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35372
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A],
G [auth F]
354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
πŸ‘ Image
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]353Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
πŸ‘ Image
UniProt
Find proteins for P54311 (Rattus norvegicus)
Explore P54311 
Go to UniProtKB:  P54311
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54311
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth C]68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
πŸ‘ Image
UniProt
Find proteins for P63212 (Bos taurus)
Explore P63212 
Go to UniProtKB:  P63212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63212
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16248synthetic constructMutation(s): 0 
πŸ‘ Image
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
I [auth R]
J [auth R]
K [auth R]
L [auth R]
M [auth R]
I [auth R],
J [auth R],
K [auth R],
L [auth R],
M [auth R],
O [auth M],
P [auth M],
Q [auth M],
R [auth M],
S [auth M]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
πŸ‘ Image
7V7 (Subject of Investigation/LOI)
Query on 7V7

Download Ideal Coordinates CCD File 
H [auth R],
N [auth M]
N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide
C22 H28 N2 O
PJMPHNIQZUBGLI-UHFFFAOYSA-N
πŸ‘ Image
Binding Affinity Annotations 
IDSourceBinding Affinity
7V7 BindingDB:  8EF5 Ki: min: 0.05, max: 8.5 (nM) from 21 assay(s)
IC50: min: 1.1, max: 3400 (nM) from 13 assay(s)
EC50: min: 0.51, max: 53 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Γ…
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report

πŸ‘ Image


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFA0507002
Chinese Academy of SciencesChinaXDB08020303
Chinese Academy of SciencesChinaE1G707R078

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-05-14
    Changes: Data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.