5U09

High-resolution crystal structure of the human CB1 cannabinoid receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-resolution crystal structure of the human CB1 cannabinoid receptor.

Shao, Z.Yin, J.Chapman, K.Grzemska, M.Clark, L.Wang, J.Rosenbaum, D.M.

(2016) Nature 

  • DOI: 10.1038/nature20613
  • Primary Citation of Related Structures:  
    5U09

  • PubMed Abstract: 
  • The human cannabinoid G-protein-coupled receptors (GPCRs) CB1 and CB2 mediate the functional responses to the endocannabinoids anandamide and 2-arachidonyl glycerol (2-AG) and to the widely consumed plant phytocannabinoid Δ 9 -tetrahydroca ...

    The human cannabinoid G-protein-coupled receptors (GPCRs) CB1 and CB2 mediate the functional responses to the endocannabinoids anandamide and 2-arachidonyl glycerol (2-AG) and to the widely consumed plant phytocannabinoid Δ 9 -tetrahydrocannabinol (THC). The cannabinoid receptors have been the targets of intensive drug discovery efforts, because modulation of these receptors has therapeutic potential to control pain, epilepsy, obesity, and other disorders. Although much progress in understanding the biophysical properties of GPCRs has recently been made, investigations of the molecular mechanisms of the cannabinoids and their receptors have lacked high-resolution structural data. Here we report the use of GPCR engineering and lipidic cubic phase crystallization to determine the structure of the human CB1 receptor bound to the inhibitor taranabant at 2.6-Å resolution. We found that the extracellular surface of CB1, including the highly conserved membrane-proximal N-terminal region, is distinct from those of other lipid-activated GPCRs, forming a critical part of the ligand-binding pocket. Docking studies further demonstrate how this same pocket may accommodate the cannabinoid agonist THC. Our CB1 structure provides an atomic framework for studying cannabinoid receptor function and will aid the design and optimization of therapeutic modulators of the endocannabinoid system.


    Organizational Affiliation

    Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cannabinoid receptor 1,GlgA glycogen synthaseA508Homo sapiensPyrococcus abyssi GE5Mutation(s): 1 
Gene Names: CNR1CNR
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
CB1 cannabinoid receptor with bound inhibitor taranabant
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2J8 
Go to UniProtKB:  Q9V2J8
Find proteins for P21554 (Homo sapiens)
Explore P21554 
Go to UniProtKB:  P21554
NIH Common Fund Data Resources
PHAROS  P21554
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7DY
Query on 7DY

Download CCD File 
A
N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide
C27 H25 Cl F3 N3 O2
QLYKJCMUNUWAGO-GAJHUEQPSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7DYIC50:  0.8600000143051147   nM  BindingDB
7DYIC50:  0.30000001192092896   nM  BindingDB
7DYIC50:  0.28999999165534973   nM  BindingDB
7DYKi:  0.30000001192092896   nM  BindingDB
7DYEC50:  2.4000000953674316   nM  BindingDB
7DYIC50:  0.7400000095367432   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.652α = 90
b = 80.381β = 91.72
c = 81.178γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description