8GHV | pdb_00008ghv

Cannabinoid Receptor 1-G Protein Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8GHV

This is version 1.1 of the entry. See complete history

Literature

Structural basis for activation of CB1 by an endocannabinoid analog.

Krishna Kumar, K.Robertson, M.J.Thadhani, E.Wang, H.Suomivuori, C.M.Powers, A.S.Ji, L.Nikas, S.P.Dror, R.O.Inoue, A.Makriyannis, A.Skiniotis, G.Kobilka, B.

(2023) Nat Commun 14: 2672-2672

  • DOI: https://doi.org/10.1038/s41467-023-37864-4
  • Primary Citation Related Structures: 
    8GHV

  • PubMed Abstract: 

    Endocannabinoids (eCBs) are endogenous ligands of the cannabinoid receptor 1 (CB1), a G protein-coupled receptor that regulates a number of therapeutically relevant physiological responses. Hence, understanding the structural and functional consequences of eCB-CB1 interactions has important implications for designing effective drugs targeting this receptor. To characterize the molecular details of eCB interaction with CB1, we utilized AMG315, an analog of the eCB anandamide to determine the structure of the AMG315-bound CB1 signaling complex. Compared to previous structures, the ligand binding pocket shows some differences. Using docking, molecular dynamics simulations, and signaling assays we investigated the functional consequences of ligand interactions with the "toggle switch" residues F200 3.36 and W356 6.48 . Further, we show that ligand-TM2 interactions drive changes to residues on the intracellular side of TM2 and are a determinant of efficacy in activating G protein. These intracellular TM2 rearrangements are unique to CB1 and are exploited by a CB1-specific allosteric modulator.


  • Organizational Affiliation
    • Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA.

Macromolecule Content 

  • Total Structure Weight: 169.79 kDa 
  • Atom Count: 8,237 
  • Modeled Residue Count: 1,125 
  • Deposited Residue Count: 1,523 
  • Unique protein chains: 5

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
Membrane Entity: Yes 
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-1344Homo 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
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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 
Entity Groups
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UniProt GroupP59768
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cannabinoid receptor 1495Homo sapiensMutation(s): 0 
Gene Names: CNR1CNR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
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 GroupP21554
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16E [auth S]259Mus musculusMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZI5
(Subject of Investigation/LOI)

Query on ZI5



Download:Ideal Coordinates CCD File
F [auth D](5Z,8Z,11Z,13S,14Z)-N-[(2R)-1-hydroxypropan-2-yl]-13-methylicosa-5,8,11,14-tetraenamide
C24 H41 N O2
PDGRTYPSRMWVBI-MVYUADCHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ZI5 BindingDB:  8GHV Ki: min: 7.8, max: 8.9 (nM) from 2 assay(s)
EC50: 0.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM127359

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Structure summary