4ALX

Crystal Structure of Ls-AChBP complexed with the potent nAChR antagonist DHbE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Lymnaea Stagnalis Achbp Complexed with the Potent Nachr Antagonist Dh-Betab-E Suggests a Unique Mode of Antagonism

Shahsavar, A.Kastrup, J.S.Nielsen, E.O.Kristensen, J.L.Gajhede, M.Balle, T.

(2012) PLoS One 7: 40757

  • DOI: https://doi.org/10.1371/journal.pone.0040757
  • Primary Citation of Related Structures:  
    4ALX

  • PubMed Abstract: 

    Nicotinic acetylcholine receptors (nAChRs) are pentameric ligand-gated ion channels that belong to the Cys-loop receptor superfamily. These receptors are allosteric proteins that exist in different conformational states, including resting (closed), activated (open), and desensitized (closed) states. The acetylcholine binding protein (AChBP) is a structural homologue of the extracellular ligand-binding domain of nAChRs. In previous studies, the degree of the C-loop radial extension of AChBP has been assigned to different conformational states of nAChRs. It has been suggested that a closed C-loop is preferred for the active conformation of nAChRs in complex with agonists whereas an open C-loop reflects an antagonist-bound (closed) state. In this work, we have determined the crystal structure of AChBP from the water snail Lymnaea stagnalis (Ls) in complex with dihydro-β-erythroidine (DHβE), which is a potent competitive antagonist of nAChRs. The structure reveals that binding of DHβE to AChBP imposes closure of the C-loop as agonists, but also a shift perpendicular to previously observed C-loop movements. These observations suggest that DHβE may antagonize the receptor via a different mechanism compared to prototypical antagonists and toxins.


  • Organizational Affiliation

    Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACETYLCHOLINE BINDING PROTEIN
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
229Lymnaea stagnalisMutation(s): 0 
UniProt
Find proteins for P58154 (Lymnaea stagnalis)
Explore P58154 
Go to UniProtKB:  P58154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58154
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IZN
Query on IZN

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth I]
DA [auth J]
K [auth A]
M [auth B]
AA [auth H],
CA [auth I],
DA [auth J],
K [auth A],
M [auth B],
P [auth C],
Q [auth D],
T [auth E],
U [auth F],
Y [auth G]
(4bS,6S)-6-methoxy-1,4,6,7,9,10,12,13-octahydro-3H,5H-pyrano[4',3':3,4]pyrido[2,1-i]indol-3-one
C16 H21 N O3
ALSKYCOJJPXPFS-BBRMVZONSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
BA [auth H]
EA [auth J]
L [auth A]
N [auth B]
V [auth F]
BA [auth H],
EA [auth J],
L [auth A],
N [auth B],
V [auth F],
Z [auth G]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
FA [auth J]
O [auth B]
R [auth D]
S [auth D]
W [auth F]
FA [auth J],
O [auth B],
R [auth D],
S [auth D],
W [auth F],
X [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
IZN Binding MOAD:  4ALX Ki: 52 (nM) from 1 assay(s)
PDBBind:  4ALX Ki: 52 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.249α = 90
b = 121.308β = 90
c = 152.074γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata 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: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection