6PT0

Cryo-EM structure of human cannabinoid receptor 2-Gi protein in complex with agonist WIN 55,212-2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Cryo-EM Structure of the Human Cannabinoid Receptor CB2-GiSignaling Complex.

Xing, C.Zhuang, Y.Xu, T.H.Feng, Z.Zhou, X.E.Chen, M.Wang, L.Meng, X.Xue, Y.Wang, J.Liu, H.McGuire, T.F.Zhao, G.Melcher, K.Zhang, C.Xu, H.E.Xie, X.Q.

(2020) Cell --: --

  • DOI: 10.1016/j.cell.2020.01.007

  • PubMed Abstract: 
  • Drugs selectively targeting CB2 hold promise for treating neurodegenerative disorders, inflammation, and pain while avoiding psychotropic side effects mediated by CB1. The mechanisms underlying CB2 activation and signaling are poorly understood but c ...

    Drugs selectively targeting CB2 hold promise for treating neurodegenerative disorders, inflammation, and pain while avoiding psychotropic side effects mediated by CB1. The mechanisms underlying CB2 activation and signaling are poorly understood but critical for drug design. Here we report the cryo-EM structure of the human CB2-G i signaling complex bound to the agonist WIN 55,212-2. The 3D structure reveals the binding mode of WIN 55,212-2 and structural determinants for distinguishing CB2 agonists from antagonists, which are supported by a pair of rationally designed agonist and antagonist. Further structural analyses with computational docking results uncover the differences between CB2 and CB1 in receptor activation, ligand recognition, and G i coupling. These findings are expected to facilitate rational structure-based discovery of drugs targeting the cannabinoid system.


    Organizational Affiliation

    Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA.,Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA. Electronic address: chengzh@pitt.edu.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. Electronic address: eric.xu@simm.ac.cn.,Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI 49503, USA.,Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Pharmacy and Therapeutics, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute and Departments of Computational Biology and of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute and Departments of Computational Biology and of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA. Electronic address: xix15@pitt.edu.,Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cannabinoid receptor 2
R
369Homo sapiensMutation(s): 0 
Gene Names: CNR2 (CB2A, CB2B)
Find proteins for P34972 (Homo sapiens)
Go to Gene View: CNR2
Go to UniProtKB:  P34972
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(i) subunit alpha-1
A
354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
Find proteins for P63096 (Homo sapiens)
Go to Gene View: GNAI1
Go to UniProtKB:  P63096
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B
354Homo sapiensMutation(s): 0 
Gene Names: GNB1
Find proteins for P62873 (Homo sapiens)
Go to Gene View: GNB1
Go to UniProtKB:  P62873
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
C
68Homo sapiensMutation(s): 0 
Gene Names: GNG2
Find proteins for P59768 (Homo sapiens)
Go to Gene View: GNG2
Go to UniProtKB:  P59768
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
scFv16
E
259N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WI5
Query on WI5

Download SDF File 
Download CCD File 
R
{(3R)-5-methyl-3-[(morpholin-4-yl)methyl]-2,3-dihydro[1,4]oxazino[2,3,4-hi]indol-6-yl}(naphthalen-1-yl)methanone
C27 H26 N2 O3
HQVHOQAKMCMIIM-HXUWFJFHSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
R
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
R
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesP30 DA035778A1
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR01 DA025612
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States1R35GM128641
Ministry of Science and Technology (MoST, China)ChinaXDB08020303
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM127710
Jay and Betty Van Andel FoundationUnited States--

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release