Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.02 kDa 
• Atom Count: 3410 
• Modelled Residue Count: 431 
• Deposited Residue Count: 438 
• Unique protein chains: 1

5XR8

Crystal structure of the human CB1 in complex with agonist AM841

• PDB DOI: 10.2210/pdb5XR8/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Desulfovibrio vulgaris str. Hildenborough
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2017-06-07 Released: 2017-07-12 
• Deposition Author(s): Hua, T., Vemuri, K., Nikas, P.S., Laprairie, R.B., Wu, Y., Qu, L., Pu, M., Korde, A., Shan, J., 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.274 
• R-Value Work: 0.255 
• R-Value Observed: 0.256 

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

• PubMed: 28678776 
• DOI: 10.1038/nature23272
• Primary Citation of Related Structures:  
  5XR8, 5XRA


• PubMed Abstract: 
  

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.

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Organizational Affiliation: 

School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cannabinoid receptor 1,Flavodoxin,Cannabinoid receptor 1	A	438	Homo sapiens, Desulfovibrio vulgaris str. Hildenborough	Mutation(s): 5  Gene Names: CNR1, CNR, DVU_2680 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00323 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P00323  Go to UniProtKB:  P00323
Find proteins for P21554 (Homo sapiens) Explore P21554  Go to UniProtKB:  P21554
PHAROS:  P21554 GTEx:  ENSG00000118432
UniProt Groups	P21554P00323

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
8D0	C [auth A]	(6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol C26 H39 N O3 S JCIYJYHFBBXSBF-HMXCVIKNSA-N
CLR	D [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.274 
• R-Value Work: 0.255 
• R-Value Observed: 0.256 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.83	α = 90
b = 73.61	β = 90
c = 139.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-06-07 
• Released Date: 2017-07-12 
Deposition Author(s): Hua, T., Vemuri, K., Nikas, P.S., Laprairie, R.B., Wu, Y., Qu, L., Pu, M., Korde, A., Shan, J., 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.

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-07-19
  Changes: Database references
• Version 1.2: 2017-08-09
  Changes: Database references
• Version 1.3: 2017-08-16
  Changes: Data collection
• Version 1.4: 2017-10-18
  Changes: Author supporting evidence
• Version 1.5: 2017-11-08
  Changes: Source and taxonomy
• Version 2.0: 2020-01-22
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary