5YC8 | pdb_00005yc8

Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with NMS (Hg-derivative)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.270 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural insights into the subtype-selective antagonist binding to the M2muscarinic receptor

Suno, R.Lee, S.Maeda, S.Yasuda, S.Yamashita, K.Hirata, K.Horita, S.Tawaramoto, M.S.Tsujimoto, H.Murata, T.Kinoshita, M.Yamamoto, M.Kobilka, B.K.Vaidehi, N.Iwata, S.Kobayashi, T.

(2018) Nat Chem Biol 14: 1150-1158

  • DOI: https://doi.org/10.1038/s41589-018-0152-y
  • Primary Citation Related Structures: 
    5YC8, 5ZK3, 5ZK8, 5ZKB, 5ZKC

  • PubMed Abstract: 

    Human muscarinic receptor M 2 is one of the five subtypes of muscarinic receptors belonging to the family of G-protein-coupled receptors. Muscarinic receptors are targets for multiple neurodegenerative diseases. The challenge has been designing subtype-selective ligands against one of the five muscarinic receptors. We report high-resolution structures of a thermostabilized mutant M 2 receptor bound to a subtype-selective antagonist AF-DX 384 and a nonselective antagonist NMS. The thermostabilizing mutation S110R in M 2 was predicted using a theoretical strategy previously developed in our group. Comparison of the crystal structures and pharmacological properties of the M 2 receptor shows that the Arg in the S110R mutant mimics the stabilizing role of the sodium cation, which is known to allosterically stabilize inactive state(s) of class A GPCRs. Molecular dynamics simulations reveal that tightening of the ligand-residue contacts in M 2 receptors compared to M 3 receptors leads to subtype selectivity of AF-DX 384.


  • Organizational Affiliation
    • Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. r.suno@mfour.med.kyoto-u.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 48.21 kDa 
  • Atom Count: 3,090 
  • Modeled Residue Count: 384 
  • Deposited Residue Count: 421 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Muscarinic acetylcholine receptor M2,Redesigned apo-cytochrome b562,Muscarinic acetylcholine receptor M2421Homo sapiensMutation(s): 1 
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 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP08172P0ABE7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.270 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.52α = 90
b = 59β = 98.89
c = 89.22γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary