7V3Z | pdb_00007v3z

Structure of cannabinoid receptor type 1(CB1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 
    0.276 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FMNClick on this verticalbar to view detailsBest fitted CLRClick on this verticalbar to view detailsBest fitted 9GFClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

A Genetically Encoded F-19 NMR Probe Reveals the Allosteric Modulation Mechanism of Cannabinoid Receptor 1.

Wang, X.Liu, D.Shen, L.Li, F.Li, Y.Yang, L.Xu, T.Tao, H.Yao, D.Wu, L.Hirata, K.Bohn, L.M.Makriyannis, A.Liu, X.Hua, T.Liu, Z.J.Wang, J.

(2021) J Am Chem Soc 143: 16320-16325

  • DOI: https://doi.org/10.1021/jacs.1c06847
  • Primary Citation of Related Structures:  
    7V3Z

  • PubMed Abstract: 

    Due to the lack of genetically encoded probes for fluorine-19 nuclear magnetic resonance spectroscopy ( 19 F NMR), its utility for probing eukaryotic membrane protein dynamics is limited. Here we report an efficient method for the genetic incorporation of an unnatural amino acid (UAA), 3'-trifluoromenthyl-phenylalanine (mtfF), into cannabinoid receptor 1 (CB1) in the Baculovirus Expression System. The probe can be inserted at any environmentally sensitive site, while causing minimal structural perturbation to the target protein. Using 19 F NMR and X-ray crystallography methods, we discovered that the allosteric modulator Org27569 and agonists synergistically stabilize a previously unrecognized pre-active state. An allosteric modulation model is proposed to explain Org27569's distinct behavior. We demonstrate that our site-specific 19 F NMR labeling method is a powerful tool in decoding the mechanism of GPCR allosteric modulation. This new method should be broadly applicable for uncovering conformational states for many important eukaryotic membrane proteins.


  • Organizational Affiliation

    iHuman Institute, ShanghaiTech University, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
fusion protein of Cannabinoid receptor 1 and Flavodoxin438Homo sapiensNitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 6 
Gene Names: CNR1CNRDVU_2680
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00323 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00323P21554
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
9GF BindingDB:  7V3Z Ki: min: 0.32, max: 13 (nM) from 25 assay(s)
Kd: min: 0.5, max: 3.3 (nM) from 10 assay(s)
IC50: min: 0.13, max: 28 (nM) from 9 assay(s)
EC50: min: 0.14, max: 100 (nM) from 43 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free:  0.276 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.81α = 90
b = 75.35β = 90
c = 138.95γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXmodel building
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FMNClick on this verticalbar to view detailsBest fitted CLRClick on this verticalbar to view detailsBest fitted 9GFClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91953202, 21837005, 31670733,31870744

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary