9EK0 | pdb_00009ek0

Human M5 muscarinic acetylcholine receptor complex with mini-Gq and iperoxo


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 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 reveals an extrahelical allosteric binding site at the M 5 mAChR.

Burger, W.A.C.Mobbs, J.I.Rana, B.Wang, J.Joshi, K.Gentry, P.R.Yeasmin, M.Venugopal, H.Bender, A.M.Lindsley, C.W.Miao, Y.Christopoulos, A.Valant, C.Thal, D.M.

(2025) Nat Commun 16: 7046-7046

  • DOI: https://doi.org/10.1038/s41467-025-62212-z
  • Primary Citation of Related Structures:  
    9EJZ, 9EK0

  • PubMed Abstract: 

    The M 5 muscarinic acetylcholine receptor (M 5 mAChR) represents a promising therapeutic target for neurological disorders. However, the high conservation of its orthosteric binding site poses significant challenges for drug development. While selective positive allosteric modulators (PAMs) offer a potential solution, a structural understanding of the M 5 mAChR and its allosteric binding sites remains limited. Here, we present a 2.8 Å cryo-electron microscopy structure of the M 5 mAChR complexed with heterotrimeric G q protein and the agonist iperoxo, completing the active-state structural characterization of the mAChR family. To identify the binding site of M 5 -selective PAMs, we implement an integrated approach combining mutagenesis, pharmacological assays, structural biology, and molecular dynamics simulations. Our mutagenesis studies reveal that selective M 5 PAMs bind outside previously characterized M 5 mAChR allosteric sites. Subsequently, we obtain a 2.1 Å structure of M 5 mAChR co-bound with acetylcholine and the selective PAM VU6007678, revealing an allosteric pocket at the extrahelical interface between transmembrane domains 3 and 4 that is confirmed through mutagenesis and simulations. These findings demonstrate the diverse mechanisms of allosteric regulation in mAChRs and highlight the value of integrating pharmacological and structural approaches to identify allosteric binding sites.


  • Organizational Affiliation
    • Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Muscarinic acetylcholine receptor M5A [auth R]343Homo sapiensMutation(s): 0 
Gene Names: CHRM5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08912 (Homo sapiens)
Explore P08912 
Go to UniProtKB:  P08912
PHAROS:  P08912
GTEx:  ENSG00000184984 
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UniProt GroupP08912
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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-1350Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
Explore P54311 
Go to UniProtKB:  P54311
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UniProt GroupP54311
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein Gq alpha subunit chimeraC [auth A]245Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]68Homo 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 
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UniProt GroupP59768
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IXO (Subject of Investigation/LOI)
Query on IXO

Download Ideal Coordinates CCD File 
E [auth R]4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium
C10 H17 N2 O2
WXXOCGISBCTWPW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5127

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1196951
Australian Research Council (ARC)AustraliaLP180100560

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release