5ZKC

Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with NMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41589-018-0152-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human muscarinic receptor M <sub>2 </sub> 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 des ...

    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

    Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan.,RIKEN, SPring-8 Center, Hyogo, Japan.,Graduate School of Science and Molecular Chirality Research Center, Chiba University, Inage, Chiba, Japan.,Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,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.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Japan Science and Technology Agency (JST) and Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2
A
421Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 1 
Gene Names: cybC, CHRM2
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P08172 (Homo sapiens)
Go to Gene View: CHRM2
Go to UniProtKB:  P08172
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3C0
Query on 3C0

Download SDF File 
Download CCD File 
A
N-methyl scopolamine
(1R,2R,4S,5S,7s)-7-{[(2S)-3-hydroxy-2-phenylpropanoyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane
C18 H24 N O4
LZCOQTDXKCNBEE-IKIFYQGPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.430α = 90.00
b = 58.960β = 98.82
c = 88.970γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanThe Research Acceleration Program
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanThe Platform Project for Supporting Drug Discovery and Life Science Research
Japan Society for the Promotion of ScienceJapanInternational Collaboration in Chemistry
Japan Agency for Medical Research and Development (AMED)JapanThe Platform Project for Supporting Drug Discovery and Life Science Research
Japan Society for the Promotion of ScienceJapan15K08268, 15H06862
National Institutes of Health/National Human Genome Research InstituteUnited StatesNIH R01-GM097261

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-11-28
    Type: Data collection, Database references