6KPF | pdb_00006kpf

Cryo-EM structure of a class A GPCR with G protein complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6KPF

This is version 2.1 of the entry. See complete history

Literature

Activation and Signaling Mechanism Revealed by Cannabinoid Receptor-GiComplex Structures.

Hua, T.Li, X.Wu, L.Iliopoulos-Tsoutsouvas, C.Wang, Y.Wu, M.Shen, L.Johnston, C.A.Nikas, S.P.Song, F.Song, X.Yuan, S.Sun, Q.Wu, Y.Jiang, S.Grim, T.W.Benchama, O.Stahl, E.L.Zvonok, N.Zhao, S.Bohn, L.M.Makriyannis, A.Liu, Z.J.

(2020) Cell 180: 655

  • DOI: https://doi.org/10.1016/j.cell.2020.01.008
  • Primary Citation Related Structures: 
    6KPC, 6KPF, 6KPG

  • PubMed Abstract: 

    Human endocannabinoid systems modulate multiple physiological processes mainly through the activation of cannabinoid receptors CB1 and CB2. Their high sequence similarity, low agonist selectivity, and lack of activation and G protein-coupling knowledge have hindered the development of therapeutic applications. Importantly, missing structural information has significantly held back the development of promising CB2-selective agonist drugs for treating inflammatory and neuropathic pain without the psychoactivity of CB1. Here, we report the cryoelectron microscopy structures of synthetic cannabinoid-bound CB2 and CB1 in complex with G i , as well as agonist-bound CB2 crystal structure. Of important scientific and therapeutic benefit, our results reveal a diverse activation and signaling mechanism, the structural basis of CB2-selective agonists design, and the unexpected interaction of cholesterol with CB1, suggestive of its endogenous allosteric modulating role.


  • Organizational Affiliation
    • iHuman Institute, ShanghaiTech University, Shanghai 201210, China. Electronic address: huatian@shanghaitech.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 153.6 kDa 
  • Atom Count: 8,775 
  • Modeled Residue Count: 1,135 
  • Deposited Residue Count: 1,384 
  • Unique protein chains: 5

Macromolecules

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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
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UniProt GroupP63096
Sequence Annotations
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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-1340Homo 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
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cannabinoid receptor 2D [auth R]360Homo sapiensMutation(s): 0 
Gene Names: CNR2CB2ACB2B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P34972 (Homo sapiens)
Explore P34972 
Go to UniProtKB:  P34972
PHAROS:  P34972
GTEx:  ENSG00000188822 
Entity Groups
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UniProt GroupP34972
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16E [auth S]259Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E3R
(Subject of Investigation/LOI)

Query on E3R



Download:Ideal Coordinates CCD File
F [auth R]7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]- 7-methyloctanenitrile
C25 H37 N O3
FTYAKKNPQHUECV-MISYRCLQSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.03
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 2.0: 2022-04-27
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Derived calculations, Refinement description, Structure summary