3EAM

An open-pore structure of a bacterial pentameric ligand-gated ion channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation.

Bocquet, N.Nury, H.Baaden, M.Le Poupon, C.Changeux, J.P.Delarue, M.Corringer, P.J.

(2009) Nature 457: 111-114

  • DOI: 10.1038/nature07462

  • PubMed Abstract: 
  • Pentameric ligand-gated ion channels from the Cys-loop family mediate fast chemo-electrical transduction, but the mechanisms of ion permeation and gating of these membrane proteins remain elusive. Here we present the X-ray structure at 2.9 A resoluti ...

    Pentameric ligand-gated ion channels from the Cys-loop family mediate fast chemo-electrical transduction, but the mechanisms of ion permeation and gating of these membrane proteins remain elusive. Here we present the X-ray structure at 2.9 A resolution of the bacterial Gloeobacter violaceus pentameric ligand-gated ion channel homologue (GLIC) at pH 4.6 in an apparently open conformation. This cationic channel is known to be permanently activated by protons. The structure is arranged as a funnel-shaped transmembrane pore widely open on the outer side and lined by hydrophobic residues. On the inner side, a 5 A constriction matches with rings of hydrophilic residues that are likely to contribute to the ionic selectivity. Structural comparison with ELIC, a bacterial homologue from Erwinia chrysanthemi solved in a presumed closed conformation, shows a wider pore where the narrow hydrophobic constriction found in ELIC is removed. Comparative analysis of GLIC and ELIC reveals, in concert, a rotation of each extracellular beta-sandwich domain as a rigid body, interface rearrangements, and a reorganization of the transmembrane domain, involving a tilt of the M2 and M3 alpha-helices away from the pore axis. These data are consistent with a model of pore opening based on both quaternary twist and tertiary deformation.


    Organizational Affiliation

    Pasteur Institute, G5 Group of Channel-Receptor, CNRS URA 2182.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glr4197 protein
A, B, C, D, E
317Gloeobacter violaceus (strain PCC 7421)Mutation(s): 0 
Gene Names: glvI
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Cys-Loop Receptor Family
Protein: 
Prokaryotic pentameric ligand-gated ion channel (GLIC)
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain PCC 7421))
Go to UniProtKB:  Q7NDN8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download SDF File 
Download CCD File 
A, B, C, D, E
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
LMT
Query on LMT

Download SDF File 
Download CCD File 
A, B, C, E
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 183.320α = 90.00
b = 133.640β = 102.94
c = 160.180γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance