7WV9

Allosteric modulator ZCZ011 binding to CP55940-bound cannabinoid receptor 1 in complex with Gi protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular mechanism of allosteric modulation for the cannabinoid receptor CB1.

Yang, X.Wang, X.Xu, Z.Wu, C.Zhou, Y.Wang, Y.Lin, G.Li, K.Wu, M.Xia, A.Liu, J.Cheng, L.Zou, J.Yan, W.Shao, Z.Yang, S.

(2022) Nat Chem Biol 18: 831-840

  • DOI: https://doi.org/10.1038/s41589-022-01038-y
  • Primary Citation of Related Structures:  
    7FEE, 7WV9

  • PubMed Abstract: 

    Given the promising clinical value of allosteric modulators of G protein-coupled-receptors (GPCRs), mechanistic understanding of how these modulators alter GPCR function is of significance. Here, we report the crystallographic and cryo-electron microscopy structures of the cannabinoid receptor CB1 bound to the positive allosteric modulator (PAM) ZCZ011. These structures show that ZCZ011 binds to an extrahelical site in the transmembrane 2 (TM2)-TM3-TM4 surface. Through (un)biased molecular dynamics simulations and mutagenesis experiments, we show that TM2 rearrangement is critical for the propagation of allosteric signals. ZCZ011 exerts a PAM effect by promoting TM2 rearrangement in favor of receptor activation and increasing the population of receptors that adopt an active conformation. In contrast, ORG27569, a negative allosteric modulator (NAM) of CB1, also binds to the TM2-TM3-TM4 surface and exerts a NAM effect by impeding the TM2 rearrangement. Our findings fill a gap in the understanding of CB1 allosteric regulation and could guide the rational design of CB1 allosteric modulators.


  • Organizational Affiliation

    State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-2355Homo sapiensMutation(s): 4 
Gene Names: GNAI2GNAI2B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P04899 (Homo sapiens)
Explore P04899 
Go to UniProtKB:  P04899
PHAROS:  P04899
GTEx:  ENSG00000114353 
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UniProt GroupP04899
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1359Homo 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 
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UniProt GroupP62873
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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
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cannabinoid receptor 1D [auth R]472Homo sapiensMutation(s): 0 
Gene Names: CNR1CNR
Membrane Entity: Yes 
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Find proteins for P21554 (Homo sapiens)
Explore P21554 
Go to UniProtKB:  P21554
PHAROS:  P21554
GTEx:  ENSG00000118432 
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UniProt GroupP21554
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ScFv16E [auth S]266Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9GF (Subject of Investigation/LOI)
Query on 9GF

Download Ideal Coordinates CCD File 
F [auth R]2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol
C24 H40 O3
YNZFFALZMRAPHQ-SYYKKAFVSA-N
7IC (Subject of Investigation/LOI)
Query on 7IC

Download Ideal Coordinates CCD File 
G [auth R]6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole
C21 H18 N2 O2 S
RJSPNRDBWHHFMH-KRWDZBQOSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Structure summary
  • Version 1.2: 2022-08-10
    Changes: Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Structure summary