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: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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 180: 645

  • DOI: 10.1016/j.cell.2020.01.007
  • Structures With Same Primary Citation

  • 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

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cannabinoid receptor 2
R
369Homo sapiensMutation(s): 0 
Gene Names: CNR2CB2ACB2B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
CB2-Gi cannabinoid receptor complex
Find proteins for P34972 (Homo sapiens)
Go to UniProtKB:  P34972
NIH Common Fund Data Resources
PHAROS  P34972

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(i) subunit alpha-1
A
354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
CB2-Gi cannabinoid receptor complex
Find proteins for P63096 (Homo sapiens)
Go to UniProtKB:  P63096
NIH Common Fund Data Resources
PHAROS  P63096

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  P62873
NIH Common Fund Data Resources
PHAROS  P62873

Find similar proteins by: Sequence  |  Structure

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
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
CB2-Gi cannabinoid receptor complex
Find proteins for P59768 (Homo sapiens)
Go to UniProtKB:  P59768
NIH Common Fund Data Resources
PHAROS  P59768

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
scFv16
E
259synthetic constructMutation(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 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
CLR
Query on CLR

Download CCD File 
R
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
PLM
Query on PLM

Download CCD File 
R
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 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
  • Version 1.1: 2020-03-04
    Changes: Database references