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
  • Primary Citation of Related Structures:  
    6PT0

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cannabinoid receptor 2R369Homo sapiensMutation(s): 0 
Gene Names: CNR2CB2ACB2B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
CB2-Gi cannabinoid receptor complex
Find proteins for P34972 (Homo sapiens)
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Go to UniProtKB:  P34972
NIH Common Fund Data Resources
PHAROS  P34972
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1A354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
CB2-Gi cannabinoid receptor complex
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
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PHAROS  P63096
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
scFv16E259synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B354Homo sapiensMutation(s): 0 
Gene Names: GNB1
Find proteins for P62873 (Homo sapiens)
Explore P62873 
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PHAROS  P62873
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C68Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
CB2-Gi cannabinoid receptor complex
Find proteins for P59768 (Homo sapiens)
Explore P59768 
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PHAROS  P59768
Protein Feature View
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  • Reference Sequence
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

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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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WI5Ki:  5   nM  BindingDB
WI5Ki:  4   nM  BindingDB
WI5Ki:  70   nM  BindingDB
WI5EC50:  89.5999984741211   nM  BindingDB
WI5EC50:  124.5   nM  BindingDB
WI5Ki:  0.44999998807907104   nM  BindingDB
WI5Ki:  3   nM  BindingDB
WI5EC50:  0.4699999988079071   nM  BindingDB
WI5Ki:  4.53000020980835   nM  BindingDB
WI5EC50:  25   nM  BindingDB
WI5EC50:  1.5   nM  BindingDB
WI5Ki:  1.2000000476837158   nM  BindingDB
WI5IC50:  1.100000023841858   nM  BindingDB
WI5Ki:  1.600000023841858   nM  BindingDB
WI5Ki:  3.0999999046325684   nM  BindingDB
WI5EC50:  16   nM  BindingDB
WI5Ki:  0.2800000011920929   nM  BindingDB
WI5EC50:  15   nM  BindingDB
WI5EC50:  14   nM  BindingDB
WI5Ki:  2.200000047683716   nM  BindingDB
WI5IC50:  15.699999809265137   nM  BindingDB
WI5Ki:  2.0999999046325684   nM  BindingDB
WI5Ki:  20   nM  BindingDB
WI5Ki:  0.28999999165534973   nM  BindingDB
WI5Ki:  3.700000047683716   nM  BindingDB
WI5Ki:  9.100000381469727   nM  BindingDB
WI5Ki:  1.190000057220459   nM  BindingDB
WI5Ki:  16   nM  BindingDB
WI5EC50:  2   nM  BindingDB
WI5EC50:  0.38999998569488525   nM  BindingDB
WI5Ki:  0.4099999964237213   nM  BindingDB
WI5Ki:  13   nM  BindingDB
WI5Ki:  0.30000001192092896   nM  BindingDB
WI5IC50:  3.4000000953674316   nM  BindingDB
WI5EC50:  86   nM  BindingDB
WI5Ki:  1.2999999523162842   nM  BindingDB
WI5Ki:  2   nM  BindingDB
WI5IC50:  8.899999618530273   nM  BindingDB
WI5EC50:  24.600000381469727   nM  BindingDB
WI5Ki:  3.9000000953674316   nM  BindingDB
WI5Ki:  4.599999904632568   nM  BindingDB
WI5Ki:  2.509999990463257   nM  BindingDB
WI5Ki:  0.8999999761581421   nM  BindingDB
WI5Ki:  24   nM  BindingDB
WI5Ki:  2.9000000953674316   nM  BindingDB
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