3ZKR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Multisite Binding of a General Anesthetic to the Prokaryotic Pentameric Erwinia Chrysanthemi Ligand-Gated Ion Channel (Elic).

Spurny, R.Billen, B.Howard, R.J.Brams, M.Debaveye, S.Price, K.L.Weston, D.A.Strelkov, S.V.Tytgat, J.Bertrand, S.Bertrand, D.Lummis, S.C.R.Ulens, C.

(2013) J Biol Chem 288: 8355

  • DOI: https://doi.org/10.1074/jbc.M112.424507
  • Primary Citation of Related Structures:  
    3ZKR

  • PubMed Abstract: 

    Pentameric ligand-gated ion channels (pLGICs), such as nicotinic acetylcholine, glycine, γ-aminobutyric acid GABA(A/C) receptors, and the Gloeobacter violaceus ligand-gated ion channel (GLIC), are receptors that contain multiple allosteric binding sites for a variety of therapeutics, including general anesthetics. Here, we report the x-ray crystal structure of the Erwinia chrysanthemi ligand-gated ion channel (ELIC) in complex with a derivative of chloroform, which reveals important features of anesthetic recognition, involving multiple binding at three different sites. One site is located in the channel pore and equates with a noncompetitive inhibitor site found in many pLGICs. A second transmembrane site is novel and is located in the lower part of the transmembrane domain, at an interface formed between adjacent subunits. A third site is also novel and is located in the extracellular domain in a hydrophobic pocket between the β7-β10 strands. Together, these results extend our understanding of pLGIC modulation and reveal several specific binding interactions that may contribute to modulator recognition, further substantiating a multisite model of allosteric modulation in this family of ion channels.


  • Organizational Affiliation

    Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PB 601, B-3000 Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MBR
Query on MBR

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth H]
CA [auth I]
DA [auth I]
EA [auth J]
AA [auth H],
BA [auth H],
CA [auth I],
DA [auth I],
EA [auth J],
FA [auth J],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth E],
U [auth E],
V [auth F],
W [auth F],
X [auth F],
Y [auth G],
Z [auth G]
TRIBROMOMETHANE
C H Br3
DIKBFYAXUHHXCS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.109α = 90
b = 266.248β = 109.78
c = 110.746γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-04-03
    Changes: Database references
  • Version 1.2: 2014-09-17
    Changes: Atomic model, Derived calculations, Non-polymer description, Other