9U7L | pdb_00009u7l

G protein-coupled receptor complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9U7L

This is version 1.0 of the entry. See complete history

Literature

Structural basis for positive allosteric regulation of CB2 receptor.

Wang, X.Cai, Y.Yang, X.Wu, S.Xian, J.Wang, J.Lei, D.Li, W.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-72923-6
  • Primary Citation Related Structures: 
    9U7L

  • PubMed Abstract: 

    The synthetic positive allosteric modulator (PAM) of cannabinoid receptor CB2, Ec21a, exhibits better subtype selectivity and receptor specificity over orthosteric ligands, which holds promise for treating neuropathic pain and seizure without causing psychotropic side effects mediated by CB1. The poor understanding of allosteric binding site and regulatory mechanism of Ec21a hinders further development of CB2 allosteric modulators. Here, we resolve the cryo-EM structure of CB2 in complex with PAM Ec21a and agonist CP55940, revealing a sandwich-like pattern of ECL2-Ec21a-CP55940, in which Ec21a binds above CP55940 acting as a "plug" and sterically hinders the dissociation of the CP55940. Through structural analysis and cell functional experiments, we find that Ec21a significantly enhances the activation efficiency of CP55940 via increasing and prolonging the interaction between CP55940 and CB2. Furthermore, by assessing the allosteric effects of Ec21a in combination with various agonists, we expand the potential range of ligand pairings and provide a structural framework for the design of bitopic ligands. Our findings address a gap in the understanding of the CB2 allosteric site and offer valuable guidance for the rational design of CB2 allosteric and bitopic ligands.


  • Organizational Affiliation
    • Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, China. xuehuiw_01@163.com.

Macromolecule Content 

  • Total Structure Weight: 126.01 kDa 
  • Atom Count: 6,960 
  • Modeled Residue Count: 906 
  • Deposited Residue Count: 1,123 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1338Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cannabinoid receptor 2D [auth R]360Homo sapiensMutation(s): 0 
Gene Names: CNR2CB2ACB2B
UniProt & NIH Common Fund Data Resources
Find proteins for P34972 (Homo sapiens)
Explore P34972 
Go to UniProtKB:  P34972
PHAROS:  P34972
GTEx:  ENSG00000188822 
Entity Groups
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UniProt GroupP34972
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EOL(
Subject of Investigation/LOI)

Query on A1EOL



Download:Ideal Coordinates CCD File
F [auth R]~{N}-[5-bromanyl-1-[(4-fluorophenyl)methyl]-4-methyl-2-oxidanylidene-pyridin-3-yl]cycloheptanecarboxamide
C21 H24 Br F N2 O2
NSGDYZCDUPSTQT-UHFFFAOYSA-N
9GF
(Subject of Investigation/LOI)

Query on 9GF



Download:Ideal Coordinates CCD File
E [auth R]2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol
C24 H40 O3
YNZFFALZMRAPHQ-SYYKKAFVSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158
RECONSTRUCTIONcryoSPARC4.6

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release