5LG3

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with chlorpromazine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine.

Nys, M.Wijckmans, E.Farinha, A.Yoluk, O.Andersson, M.Brams, M.Spurny, R.Peigneur, S.Tytgat, J.Lindahl, E.Ulens, C.

(2016) Proc Natl Acad Sci U S A 113: E6696-E6703

  • DOI: 10.1073/pnas.1603101113
  • Primary Citation of Related Structures:  
    5LG3, 5LID

  • PubMed Abstract: 
  • Pentameric ligand-gated ion channels or Cys-loop receptors are responsible for fast inhibitory or excitatory synaptic transmission. The antipsychotic compound chlorpromazine is a widely used tool to probe the ion channel pore of the nicotinic acetylcholine receptor, which is a prototypical Cys-loop receptor ...

    Pentameric ligand-gated ion channels or Cys-loop receptors are responsible for fast inhibitory or excitatory synaptic transmission. The antipsychotic compound chlorpromazine is a widely used tool to probe the ion channel pore of the nicotinic acetylcholine receptor, which is a prototypical Cys-loop receptor. In this study, we determine the molecular determinants of chlorpromazine binding in the Erwinia ligand-gated ion channel (ELIC). We report the X-ray crystal structures of ELIC in complex with chlorpromazine or its brominated derivative bromopromazine. Unexpectedly, we do not find a chlorpromazine molecule in the channel pore of ELIC, but behind the β8-β9 loop in the extracellular ligand-binding domain. The β8-β9 loop is localized downstream from the neurotransmitter binding site and plays an important role in coupling of ligand binding to channel opening. In combination with electrophysiological recordings from ELIC cysteine mutants and a thiol-reactive derivative of chlorpromazine, we demonstrate that chlorpromazine binding at the β8-β9 loop is responsible for receptor inhibition. We further use molecular-dynamics simulations to support the X-ray data and mutagenesis experiments. Together, these data unveil an allosteric binding site in the extracellular ligand-binding domain of ELIC. Our results extend on previous observations and further substantiate our understanding of a multisite model for allosteric modulation of Cys-loop receptors.


    Organizational Affiliation

    Laboratory of Structural Neurobiology, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium; chris.ulens@kuleuven.be.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-aminobutyric-acid receptor subunit beta-1
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
307Dickeya dadantii 3937Mutation(s): 0 
Gene Names: Dda3937_00520
Membrane Entity: Yes 
UniProt
Find proteins for E0SJQ4 (Dickeya dadantii (strain 3937))
Explore E0SJQ4 
Go to UniProtKB:  E0SJQ4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z80 (Subject of Investigation/LOI)
Query on Z80

Download Ideal Coordinates CCD File 
K [auth A] , L [auth B] , M [auth C] , N [auth D] , O [auth E] , P [auth F] , Q [auth G] , R [auth H] , 
K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J]
3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine
C17 H19 Cl N2 S
ZPEIMTDSQAKGNT-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Z80 BindingDB:  5LG3 IC50: 1.58e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.2α = 90
b = 266.65β = 107.71
c = 111.04γ = 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: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references