Crystal structure of acetylcholine bound to a prokaryotic pentameric ligand-gated ion channel, ELIC

Experimental Data Snapshot

  • Resolution: 2.91 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine.

Pan, J.Chen, Q.Willenbring, D.Yoshida, K.Tillman, T.Kashlan, O.B.Cohen, A.Kong, X.P.Xu, Y.Tang, P.

(2012) Nat Commun 3: 714-714

  • DOI: https://doi.org/10.1038/ncomms1703
  • Primary Citation of Related Structures:  
    3RQU, 3RQW

  • PubMed Abstract: 

    ELIC, the pentameric ligand-gated ion channel from Erwinia chrysanthemi, is a prototype for Cys-loop receptors. Here we show that acetylcholine is a competitive antagonist for ELIC. We determine the acetylcholine-ELIC cocrystal structure to a 2.9-Å resolution and find that acetylcholine binding to an aromatic cage at the subunit interface induces a significant contraction of loop C and other structural rearrangements in the extracellular domain. The side chain of the pore-lining residue F247 reorients and the pore size consequently enlarges, but the channel remains closed. We attribute the inability of acetylcholine to activate ELIC primarily to weak cation-π and electrostatic interactions in the pocket, because an acetylcholine derivative with a simple quaternary-to-tertiary ammonium substitution activates the channel. This study presents a compelling case for understanding the structural underpinning of the functional relationship between agonism and competitive antagonism in the Cys-loop receptors, providing a new framework for developing novel therapeutic drugs.

  • Organizational Affiliation

    Department of Anesthesiology, 2057 Biomedical Science Tower 3, 3501 Fifth Avenue, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
322Dickeya dadantii 3937Mutation(s): 0 
Gene Names: Dda3937_00520
Membrane Entity: Yes 
Find proteins for E0SJQ4 (Dickeya dadantii (strain 3937))
Explore E0SJQ4 
Go to UniProtKB:  E0SJQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0SJQ4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MES

Download Ideal Coordinates CCD File 
CA [auth E]
CB [auth J]
GA [auth F]
L [auth A]
MA [auth G]
CA [auth E],
CB [auth J],
GA [auth F],
L [auth A],
MA [auth G],
P [auth B],
VA [auth I],
X [auth D],
Y [auth D]
C6 H13 N O4 S
Query on ACH

Download Ideal Coordinates CCD File 
BA [auth E]
BB [auth J]
FA [auth F]
K [auth A]
LA [auth G]
BA [auth E],
BB [auth J],
FA [auth F],
K [auth A],
LA [auth G],
O [auth B],
RA [auth H],
T [auth C],
UA [auth I],
W [auth D]
C7 H16 N O2
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth I]
DA [auth E]
DB [auth J]
EA [auth E]
AA [auth D],
AB [auth I],
DA [auth E],
DB [auth J],
EA [auth E],
HA [auth F],
IA [auth F],
JA [auth F],
KA [auth F],
M [auth A],
N [auth A],
NA [auth G],
OA [auth G],
PA [auth G],
Q [auth B],
QA [auth G],
R [auth B],
S [auth B],
SA [auth H],
TA [auth H],
U [auth C],
V [auth C],
WA [auth I],
XA [auth I],
YA [auth I],
Z [auth D],
ZA [auth I]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
ACH PDBBind:  3RQW Kd: 2.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.91 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.763α = 90
b = 266.068β = 107.82
c = 111.162γ = 90
Software Package:
Software NamePurpose
SSRLdata collection
PHENIXmodel building
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2012-03-14
    Changes: Database references, Other, Structure summary
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description