7V3Z | pdb_00007v3z

Structure of cannabinoid receptor type 1(CB1)

• PDB DOI: https://doi.org/10.2210/pdb7V3Z/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Nitratidesulfovibrio vulgaris str. Hildenborough
• Expression System: Mammalian expression vector Flag-EGFP-MCS-pcDNA3.1
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2021-08-12 Released: 2021-11-24 
• Deposition Author(s): Liu, Z.J., Shen, L., Hua, T., Yao, D.Q., Wu, L.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 
  0.276 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

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

• PubMed: 34596399 
• DOI: https://doi.org/10.1021/jacs.1c06847
• Primary Citation 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.

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China.
Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, Yunnan 650500, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China.
RIKEN, SPring-8 Center, Hyogo 679-5165, Japan.
Departments of Molecular Medicine and Neuroscience, Scripps Research, Jupiter, Florida 33458, United States.
Center for Drug Discovery, Department of Pharmaceutical Sciences, and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.82 kDa 
• Atom Count: 3,398 
• Modeled Residue Count: 431 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fusion protein of Cannabinoid receptor 1 and Flavodoxin	A	438	Homo sapiens, Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 6  Gene Names: CNR1, CNR, DVU_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
UniProt Groups	P21554P00323

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	D [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
CLR (Subject of Investigation/LOI)	C [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
9GF (Subject of Investigation/LOI)	B [auth A]	2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol C24 H40 O3 YNZFFALZMRAPHQ-SYYKKAFVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9GF	BindingDB:  7V3Z	Ki: min: 0.32, max: 13 (nM) from 24 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: 0.16, max: 100 (nM) from 41 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free:  0.276 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.81	α = 90
b = 75.35	β = 90
c = 138.95	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHENIX	model building
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Liu, Z.J., Shen, L., Hua, T., Yao, D.Q., Wu, L.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91953202, 21837005, 31670733,31870744

Revision History  

• 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