Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.77 kDa 
• Atom Count: 3058 
• Residue Count: 381 
• Unique protein chains: 1

5ZKB

Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with AF-DX 384

• DOI: 10.2210/pdb5ZKB/pdb

• Classification: MEMBRANE PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-03-23 Released: 2018-11-21 
• Deposition Author(s): Suno, R., Maeda, S., Yasuda, S., Yamashita, K., Hirata, K., Horita, S., Tawaramoto, M.S., Tsujimoto, H., Murata, T., Kinoshita, M., Yamamoto, M., Kobilka, B.K., Iwata, S., Kobayashi, T.
• Funding Organization(s): Japan Science and Technology, Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science, Japan Agency for Medical Research and Development (AMED), National Institutes of Health/National Human Genome Research Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.280 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

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

• PubMed: 30420692 
• DOI: 10.1038/s41589-018-0152-y
• Primary Citation of Related Structures:  
  5YC8, 5ZKC, 5ZKB, 5ZK8, 5ZK3


• 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.

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Organizational Affiliation: 

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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2	A	421	Homo sapiens	Mutation(s): 1  Gene Names: CHRM2
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P08172 (Homo sapiens) Explore P08172  Go to UniProtKB:  P08172
NIH Common Fund Data Resources
PHAROS  P08172 GTEx  ENSG00000181072

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
82F	A	N-[2-[(2S)-2-[(dipropylamino)methyl]piperidin-1-yl]ethyl]-6-oxidanylidene-5H-pyrido[2,3-b][1,4]benzodiazepine-11-carboxamide C27 H38 N6 O2 MZDYABXXPZNUCT-NRFANRHFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.280 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.01	α = 90
b = 60.09	β = 92.66
c = 48.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-03-23 
• Released Date: 2018-11-21 
Deposition Author(s): Suno, R., Maeda, S., Yasuda, S., Yamashita, K., Hirata, K., Horita, S., Tawaramoto, M.S., Tsujimoto, H., Murata, T., Kinoshita, M., Yamamoto, M., Kobilka, B.K., Iwata, S., Kobayashi, T.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	The Research Acceleration Program
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	The Platform Project for Supporting Drug Discovery and Life Science Research
Japan Society for the Promotion of Science	Japan	International Collaboration in Chemistry
Japan Agency for Medical Research and Development (AMED)	Japan	The Platform Project for Supporting Drug Discovery and Life Science Research
Japan Society for the Promotion of Science	Japan	15K08268, 15H06862
National Institutes of Health/National Human Genome Research Institute	United States	NIH R01-GM097261

Revision History 

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