5LID

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channel
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
307Dickeya chrysanthemiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
Explore P0C7B7 
Go to UniProtKB:  P0C7B7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XY
Query on 6XY

Download Ideal Coordinates CCD File 
AA [auth I] , BA [auth I] , CA [auth J] , DA [auth J] , K [auth A] , L [auth A] , M [auth B] , N [auth B] , 
AA [auth I],  BA [auth I],  CA [auth J],  DA [auth J],  K [auth A],  L [auth A],  M [auth B],  N [auth B],  O [auth C],  P [auth C],  Q [auth D],  R [auth D],  S [auth E],  T [auth E],  U [auth F],  V [auth F],  W [auth G],  X [auth G],  Y [auth H],  Z [auth H]
bromopromazine
C17 H19 Br N2 S
MEYGNYCKJKFOTR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.72α = 90
b = 267.91β = 106.7
c = 111.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




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
  • Version 1.2: 2019-10-16
    Changes: Data collection