Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 484.49 kDa 
• Atom Count: 34660 
• Modelled Residue Count: 4040 
• Deposited Residue Count: 4200 
• Unique protein chains: 1

3U8N

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3950 (1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane)

• DOI: 10.2210/pdb3U8N/pdb

• Classification: Acetylcholine-binding protein/agonist
• Organism(s): Lymnaea stagnalis
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-10-17 Released: 2011-12-14 
• Deposition Author(s): Rohde, L.A.H., Ahring, P.K., Jensen, M.L., Nielsen, E.O., Peters, D., Helgstrand, C., Krintel, C., Harpsoe, K., Gajhede, M., Kastrup, J.S., Balle, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.230 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Literature

Intersubunit bridge formation governs agonist efficacy at nicotinic acetylcholine alpha 4 beta 2 receptors: unique role of halogen bonding revealed.

Rohde, L.A., Ahring, P.K., Jensen, M.L., Nielsen, E., Peters, D., Helgstrand, C., Krintel, C., Harpse, K., Gajhede, M., Kastrup, J.S., Balle, T.

(2012) J Biol Chem 287: 4248-4259

• PubMed: 22170047 
• DOI: 10.1074/jbc.M111.292243
• Primary Citation of Related Structures:  
  3U8N, 3U8J, 3U8K, 3U8L, 3U8M


• PubMed Abstract: 
  

The α4β2 subtype of the nicotinic acetylcholine receptor has been pursued as a drug target for treatment of psychiatric and neurodegenerative disorders and smoking cessation aids for decades. Still, a thorough understanding of structure-function relationships of α4β2 agonists is lacking. Using binding experiments, electrophysiology and x-ray crystallography we have investigated a consecutive series of five prototypical pyridine-containing agonists derived from 1-(pyridin-3-yl)-1,4-diazepane. A correlation between binding affinities at α4β2 and the acetylcholine-binding protein from Lymnaea stagnalis (Ls-AChBP) confirms Ls-AChBP as structural surrogate for α4β2 receptors. Crystal structures of five agonists with efficacies at α4β2 from 21-76% were determined in complex with Ls-AChBP. No variation in closure of loop C is observed despite large efficacy variations. Instead, the efficacy of a compound appears tightly coupled to its ability to form a strong intersubunit bridge linking the primary and complementary binding interfaces. For the tested agonists, a specific halogen bond was observed to play a large role in establishing such strong intersubunit anchoring.

---

Organizational Affiliation: 

Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Copenhagen 2100, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine-binding protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	210	Lymnaea stagnalis	Mutation(s): 0
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154  Go to UniProtKB:  P58154

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
09S	AA [auth E],  BA [auth F],  DA [auth G],  EA [auth H],  GA [auth I],  HA [auth J],  IA [auth K],  JA [auth L],  KA [auth M],  LA [auth N],  NA [auth O],  OA [auth P],  RA [auth Q],  SA [auth R],  TA [auth S],  U [auth A],  VA [auth T],  W [auth B],  Y [auth C],  Z [auth D]	1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane C12 H18 Br N3 O UGNNTIXQGYYUAP-UHFFFAOYSA-N
NAG	CA [auth G], WA [auth T], X [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	FA [auth H], MA [auth N], PA [auth P], QA [auth P], UA [auth S], V [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
09S	Ki :  0.06700000166893005   nM  PDBBind
09S	Ki:  0.07000000029802322   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.230 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 239.12	α = 90
b = 73.11	β = 97.45
c = 271.84	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-17 
• Released Date: 2011-12-14 
Deposition Author(s): Rohde, L.A.H., Ahring, P.K., Jensen, M.L., Nielsen, E.O., Peters, D., Helgstrand, C., Krintel, C., Harpsoe, K., Gajhede, M., Kastrup, J.S., Balle, T.

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2013-09-18
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Data collection, Structure summary
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary