6KPC

Crystal structure of an agonist bound GPCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Activation and Signaling Mechanism Revealed by Cannabinoid Receptor-GiComplex Structures.

Hua, T.Li, X.Wu, L.Iliopoulos-Tsoutsouvas, C.Wang, Y.Wu, M.Shen, L.Johnston, C.A.Nikas, S.P.Song, F.Song, X.Yuan, S.Sun, Q.Wu, Y.Jiang, S.Grim, T.W.Benchama, O.Stahl, E.L.Zvonok, N.Zhao, S.Bohn, L.M.Makriyannis, A.Liu, Z.J.

(2020) Cell 180: 655

  • DOI: https://doi.org/10.1016/j.cell.2020.01.008
  • Primary Citation of Related Structures:  
    6KPC, 6KPF, 6KPG

  • PubMed Abstract: 

    Human endocannabinoid systems modulate multiple physiological processes mainly through the activation of cannabinoid receptors CB1 and CB2. Their high sequence similarity, low agonist selectivity, and lack of activation and G protein-coupling knowledge have hindered the development of therapeutic applications. Importantly, missing structural information has significantly held back the development of promising CB2-selective agonist drugs for treating inflammatory and neuropathic pain without the psychoactivity of CB1. Here, we report the cryoelectron microscopy structures of synthetic cannabinoid-bound CB2 and CB1 in complex with G i , as well as agonist-bound CB2 crystal structure. Of important scientific and therapeutic benefit, our results reveal a diverse activation and signaling mechanism, the structural basis of CB2-selective agonists design, and the unexpected interaction of cholesterol with CB1, suggestive of its endogenous allosteric modulating role.


  • Organizational Affiliation

    iHuman Institute, ShanghaiTech University, Shanghai 201210, China. Electronic address: huatian@shanghaitech.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cannabinoid receptor 2,Endolysin500Homo sapiensEnterobacteria phage RB59Mutation(s): 8 
Gene Names: CNR2CB2ACB2BeRB59_126
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P34972 (Homo sapiens)
Explore P34972 
Go to UniProtKB:  P34972
PHAROS:  P34972
GTEx:  ENSG00000188822 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P34972
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E3R (Subject of Investigation/LOI)
Query on E3R

Download Ideal Coordinates CCD File 
B [auth A]7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]- 7-methyloctanenitrile
C25 H37 N O3
FTYAKKNPQHUECV-MISYRCLQSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.96α = 90
b = 140.22β = 90
c = 156.26γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 2.0: 2022-04-27
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Derived calculations, Refinement description, Structure summary