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 7T8X | pdb_00007t8x

Cryo-EM structure of ACh-bound M2R-Go signaling complex in S1 state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7T8X

This is version 1.2 of the entry. See complete history. 

Literature

Structural and dynamic insights into supra-physiological activation and allosteric modulation of a muscarinic acetylcholine receptor.

Xu, J., Wang, Q., Hubner, H., Hu, Y., Niu, X., Wang, H., Maeda, S., Inoue, A., Tao, Y., Gmeiner, P., Du, Y., Jin, C., Kobilka, B.K.

(2023) Nat Commun 14: 376-376

  • DOI: https://doi.org/10.1038/s41467-022-35726-z
  • Primary Citation Related Structures: 
    7T8X, 7T90, 7T94, 7T96

  • PubMed Abstract: 

    The M2 muscarinic receptor (M2R) is a prototypical G-protein-coupled receptor (GPCR) that serves as a model system for understanding GPCR regulation by both orthosteric and allosteric ligands. Here, we investigate the mechanisms governing M2R signaling versatility using cryo-electron microscopy (cryo-EM) and NMR spectroscopy, focusing on the physiological agonist acetylcholine and a supra-physiological agonist iperoxo, as well as a positive allosteric modulator LY2119620. These studies reveal that acetylcholine stabilizes a more heterogeneous M2R-G-protein complex than iperoxo, where two conformers with distinctive G-protein orientations were determined. We find that LY2119620 increases the affinity for both agonists, but differentially modulates agonists efficacy in G-protein and β-arrestin pathways. Structural and spectroscopic analysis suggest that LY211620 stabilizes distinct intracellular conformational ensembles from agonist-bound M2R, which may enhance β-arrestin recruitment while impairing G-protein activation. These results highlight the role of conformational dynamics in the complex signaling behavior of GPCRs, and could facilitate design of better drugs.


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

Macromolecule Content 

  • Total Structure Weight: 152.91 kDa 
  • Atom Count: 8,555 
  • Modeled Residue Count: 1,126 
  • Deposited Residue Count: 1,379 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Muscarinic acetylcholine receptor M2,muscarinic acetylcholine receptor M2 chimera353Homo sapiensMutation(s): 0 
Gene Names: CHRM2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08172 (Homo sapiens)
Explore P08172 
Go to UniProtKB:  P08172
PHAROS:  P08172
GTEx:  ENSG00000181072 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08172
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(o) subunit alpha354Homo sapiensMutation(s): 4 
Gene Names: GNAO1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P09471 (Homo sapiens)
Explore P09471 
Go to UniProtKB:  P09471
PHAROS:  P09471
GTEx:  ENSG00000087258 
Entity Groups
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UniProt GroupP09471
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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(T) subunit beta-1345Homo 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: 4
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: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody fragment256Mus musculusMutation(s): 0 
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Reference Sequence

Small Molecules

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

Query on ACH



Download:Ideal Coordinates CCD File
F [auth A]ACETYLCHOLINE
C7 H16 N O2
OIPILFWXSMYKGL-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ACH BindingDB:  7T8X Ki: min: 158, max: 1.00e+4 (nM) from 9 assay(s)
IC50: min: 12, max: 2.40e+4 (nM) from 2 assay(s)
EC50: min: 7, max: 1905 (nM) from 9 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary