5XRA

Crystal structure of the human CB1 in complex with agonist AM11542


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structures of agonist-bound human cannabinoid receptor CB1

Hua, T.Vemuri, K.Nikas, S.P.Laprairie, R.B.Wu, Y.Qu, L.Pu, M.Korde, A.Jiang, S.Ho, J.H.Han, G.W.Ding, K.Li, X.Liu, H.Hanson, M.A.Zhao, S.Bohn, L.M.Makriyannis, A.Stevens, R.C.Liu, Z.J.

(2017) Nature 547: 468-471

  • DOI: 10.1038/nature23272
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The cannabinoid receptor 1 (CB <sub>1 </sub>) is the principal target of the psychoactive constituent of marijuana, the partial agonist Δ <sup>9 </sup>-tetrahydrocannabinol (Δ <sup>9 </sup>-THC). Here we report two agonist-bound crystal structures of ...

    The cannabinoid receptor 1 (CB 1 ) is the principal target of the psychoactive constituent of marijuana, the partial agonist Δ 9 -tetrahydrocannabinol (Δ 9 -THC). Here we report two agonist-bound crystal structures of human CB 1 in complex with a tetrahydrocannabinol (AM11542) and a hexahydrocannabinol (AM841) at 2.80 Å and 2.95 Å resolution, respectively. The two CB 1 -agonist complexes reveal important conformational changes in the overall structure, relative to the antagonist-bound state, including a 53% reduction in the volume of the ligand-binding pocket and an increase in the surface area of the G-protein-binding region. In addition, a 'twin toggle switch' of Phe200 3.36 and Trp356 6.48 (superscripts denote Ballesteros-Weinstein numbering) is experimentally observed and appears to be essential for receptor activation. The structures reveal important insights into the activation mechanism of CB 1 and provide a molecular basis for predicting the binding modes of Δ 9 -THC, and endogenous and synthetic cannabinoids. The plasticity of the binding pocket of CB 1 seems to be a common feature among certain class A G-protein-coupled receptors. These findings should inspire the design of chemically diverse ligands with distinct pharmacological properties.


    Organizational Affiliation

    GPCR Consortium, San Marcos, California 92078, USA.,Center for Drug Discovery, Department of Pharmaceutical Sciences; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, USA.,Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cannabinoid receptor 1,Flavodoxin,Cannabinoid receptor 1
A
438Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Homo sapiens
This entity is chimeric
Mutation(s): 5 
Gene Names: CNR1 (CNR)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
CB1 cannabinoid receptor complexed with stabilizing antagonist AM6538
Find proteins for P00323 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  P00323
Find proteins for P21554 (Homo sapiens)
Go to Gene View: CNR1
Go to UniProtKB:  P21554
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
FMN
Query on FMN

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A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
OLA
Query on OLA

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A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
8D3
Query on 8D3

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A
(6aR,10aR)-3-(8-bromanyl-2-methyl-octan-2-yl)-6,6,9-trimethyl-6a,7,10,10a-tetrahydrobenzo[c]chromen-1-ol
C25 H37 Br O2
SZDVFUZKFPGYEK-WOJBJXKFSA-N
 Ligand Interaction
CLR
Query on CLR

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A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.234 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 66.050α = 90.00
b = 75.870β = 90.00
c = 138.900γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Database references
  • Version 1.3: 2017-08-16
    Type: Data collection, Refinement description
  • Version 1.4: 2017-10-18
    Type: Author supporting evidence