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 

Starting Model: experimental
View more details

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
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