9BA0 | pdb_00009ba0

Structural mechanism of CB1R binding to peripheral and biased inverse agonists

• PDB DOI: https://doi.org/10.2210/pdb9BA0/pdb
• EM Map EMD-44394: EMDB EMDataResource

• Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Pyrococcus abyssi GE5, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-03 Released: 2024-11-20 
• Deposition Author(s): Kumari, P., Dvoracsko, S., Enos, M.D., Ramesh, K., Lim, D., Hassan, S.A., Kunos, G., Cinar, R., Iyer, M.R., Rosenbaum, D.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.13 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural mechanism of CB 1 R binding to peripheral and biased inverse agonists.

Kumari, P., Dvoracsko, S., Enos, M.D., Ramesh, K., Lim, D., Hassan, S.A., Kunos, G., Cinar, R., Iyer, M.R., Rosenbaum, D.M.

(2024) Nat Commun 15: 10694-10694

• PubMed: 39695122 
• DOI: https://doi.org/10.1038/s41467-024-54206-0
• Primary Citation Related Structures: 
  9B9Y, 9B9Z, 9BA0


• PubMed Abstract: 
  

  The cannabinoid receptor 1 (CB ₁ R) regulates synaptic transmission in the central nervous system, but also has important roles in the peripheral organs controlling cellular metabolism. While earlier generations of brain penetrant CB ₁ R antagonists advanced to the clinic for their effective treatment of obesity, such molecules were ultimately shown to exhibit negative effects on central reward pathways that thwarted their further therapeutic development. The peripherally restricted CB ₁ R inverse agonists MRI-1867 and MRI-1891 represent a new generation of compounds that retain the metabolic benefits of CB ₁ R inhibitors while sparing the negative psychiatric effects. To understand the mechanism of binding and inhibition of CB ₁ R by peripherally restricted antagonists, we developed a nanobody/fusion protein strategy for high-resolution cryo-EM structure determination of the GPCR inactive state, and used this method to determine structures of CB ₁ R bound to either MRI-1867 or MRI-1891. These structures reveal how these compounds retain high affinity and specificity for CB ₁ R's hydrophobic orthosteric site despite incorporating polar functionalities that lead to peripheral restriction. Further, the structure of the MRI-1891 complex along with accompanying molecular dynamics simulations shows how differential engagement with transmembrane helices and the proximal N-terminus can propagate through the receptor to contribute to biased inhibition of β-arrestin signaling.

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Organizational Affiliation: 
• Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India.
Section on Medicinal Chemistry, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, USA.
Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, USA.
Section on Fibrotic Disorders, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, USA.
Laboratory of Biomolecular Structure and Pharmacology, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary.
Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Section on Medicinal Chemistry, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, USA. [e-mail].
Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 75.38 kDa 
• Atom Count: 4,742 
• Modeled Residue Count: 601 
• Deposited Residue Count: 663 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cannabinoid receptor 1,Glycogen synthase	A [auth R]	535	Homo sapiens, Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: CNR1, CNR, PAB2292
UniProt & NIH Common Fund Data Resources
Find proteins for P21554 (Homo sapiens) Explore P21554  Go to UniProtKB:  P21554
PHAROS:  P21554 GTEx:  ENSG00000118432
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2J8  Go to UniProtKB:  Q9V2J8
UniProt Groups	Q9V2J8P21554

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CNb36	B [auth N]	128	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AKN	C [auth R]	N-(N-{(E)-[(4S)-3-(4-chlorophenyl)-4-phenyl-4,5-dihydro-1H-pyrazol-1-yl][4-(trifluoromethyl)benzene-1-sulfonamido]methylidene}carbamimidoyl)acetamide C26 H22 Cl F3 N6 O3 S GYJPQNPVIJXXTA-JOCHJYFZSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.13 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Kumari, P., Dvoracsko, S., Enos, M.D., Ramesh, K., Lim, D., Hassan, S.A., Kunos, G., Cinar, R., Iyer, M.R., Rosenbaum, D.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116387

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-01-01
  Changes: Data collection, Database references
• Version 1.3: 2025-05-28
  Changes: Data collection