2WNL

CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH ANABASEINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history


Literature

Structural determinants for interaction of partial agonists with acetylcholine binding protein and neuronal alpha7 nicotinic acetylcholine receptor.

Hibbs, R.E.Sulzenbacher, G.Shi, J.Talley, T.T.Conrod, S.Kem, W.R.Taylor, P.Marchot, P.Bourne, Y.

(2009) EMBO J 28: 3040-3051

  • DOI: https://doi.org/10.1038/emboj.2009.227
  • Primary Citation of Related Structures:  
    2WN9, 2WNC, 2WNJ, 2WNL

  • PubMed Abstract: 

    The pentameric acetylcholine-binding protein (AChBP) is a soluble surrogate of the ligand binding domain of nicotinic acetylcholine receptors. Agonists bind within a nest of aromatic side chains contributed by loops C and F on opposing faces of each subunit interface. Crystal structures of Aplysia AChBP bound with the agonist anabaseine, two partial agonists selectively activating the alpha7 receptor, 3-(2,4-dimethoxybenzylidene)-anabaseine and its 4-hydroxy metabolite, and an indole-containing partial agonist, tropisetron, were solved at 2.7-1.75 A resolution. All structures identify the Trp 147 carbonyl oxygen as the hydrogen bond acceptor for the agonist-protonated nitrogen. In the partial agonist complexes, the benzylidene and indole substituent positions, dictated by tight interactions with loop F, preclude loop C from adopting the closed conformation seen for full agonists. Fluctuation in loop C position and duality in ligand binding orientations suggest molecular bases for partial agonism at full-length receptors. This study, while pointing to loop F as a major determinant of receptor subtype selectivity, also identifies a new template region for designing alpha7-selective partial agonists to treat cognitive deficits in mental and neurodegenerative disorders.


  • Organizational Affiliation

    Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SOLUBLE ACETYLCHOLINE RECEPTOR
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
227Aplysia californicaMutation(s): 0 
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WSF8
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
R [auth E],
U [auth F],
W [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
N [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
AN5
Query on AN5

Download Ideal Coordinates CCD File 
L [auth A],
P [auth D],
T [auth F],
Y [auth I]
5-amino-1-pyridin-3-ylpentan-1-one
C10 H14 N2 O
GSEJHUSUJYZWBW-UHFFFAOYSA-N
AN4
Query on AN4

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B],
Q [auth E],
V [auth G],
Z [auth J]
3,4,5,6-tetrahydro-2,3'-bipyridine
C10 H12 N2
AUBPMADJYNSPOA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
O [auth C],
S [auth E],
X [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AN5 PDBBind:  2WNL Kd: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.251α = 90
b = 125.768β = 95.4
c = 257.001γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-11-21
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 2.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 2.3: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary