X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) F16'S pore mutant (F247S) with alternate M4 conformation.

Experimental Data Snapshot

  • Resolution: 3.45 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


A lipid site shapes the agonist response of a pentameric ligand-gated ion channel.

Henault, C.M.Govaerts, C.Spurny, R.Brams, M.Estrada-Mondragon, A.Lynch, J.Bertrand, D.Pardon, E.Evans, G.L.Woods, K.Elberson, B.W.Cuello, L.G.Brannigan, G.Nury, H.Steyaert, J.Baenziger, J.E.Ulens, C.

(2019) Nat Chem Biol 15: 1156-1164

  • DOI: https://doi.org/10.1038/s41589-019-0369-4
  • Primary Citation of Related Structures:  
    6HJX, 6HJY, 6HK0

  • PubMed Abstract: 

    Phospholipids are key components of cellular membranes and are emerging as important functional regulators of different membrane proteins, including pentameric ligand-gated ion channels (pLGICs). Here, we take advantage of the prokaryote channel ELIC (Erwinia ligand-gated ion channel) as a model to understand the determinants of phospholipid interactions in this family of receptors. A high-resolution structure of ELIC in a lipid-bound state reveals a phospholipid site at the lower half of pore-forming transmembrane helices M1 and M4 and at a nearby site for neurosteroids, cholesterol or general anesthetics. This site is shaped by an M4-helix kink and a Trp-Arg-Pro triad that is highly conserved in eukaryote GABA A/C and glycine receptors. A combined approach reveals that M4 is intrinsically flexible and that M4 deletions or disruptions of the lipid-binding site accelerate desensitization in ELIC, suggesting that lipid interactions shape the agonist response. Our data offer a structural context for understanding lipid modulation in pLGICs.

  • Organizational Affiliation

    VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.

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 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.45 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.8α = 90
b = 264.697β = 108.8
c = 111.185γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references