5LID | pdb_00005lid

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 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1073/pnas.1603101113
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 361.1 kDa 
  • Atom Count: 25,070 
  • Modeled Residue Count: 3,070 
  • Deposited Residue Count: 3,070 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channel
A, B, C, D, E
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C7B7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / 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]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free:  0.257 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
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
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references