3P50

Structure of propofol bound to a pentameric ligand-gated ion channel, GLIC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel

Nury, H.Van Renterghem, C.Weng, Y.Tran, A.Baaden, M.Dufresne, V.Changeux, J.P.Sonner, J.M.Delarue, M.Corringer, P.J.

(2011) Nature 469: 428-431

  • DOI: 10.1038/nature09647
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • General anaesthetics have enjoyed long and widespread use but their molecular mechanism of action remains poorly understood. There is good evidence that their principal targets are pentameric ligand-gated ion channels (pLGICs) such as inhibitory GABA ...

    General anaesthetics have enjoyed long and widespread use but their molecular mechanism of action remains poorly understood. There is good evidence that their principal targets are pentameric ligand-gated ion channels (pLGICs) such as inhibitory GABA(A) (γ-aminobutyric acid) receptors and excitatory nicotinic acetylcholine receptors, which are respectively potentiated and inhibited by general anaesthetics. The bacterial homologue from Gloeobacter violaceus (GLIC), whose X-ray structure was recently solved, is also sensitive to clinical concentrations of general anaesthetics. Here we describe the crystal structures of the complexes propofol/GLIC and desflurane/GLIC. These reveal a common general-anaesthetic binding site, which pre-exists in the apo-structure in the upper part of the transmembrane domain of each protomer. Both molecules establish van der Waals interactions with the protein; propofol binds at the entrance of the cavity whereas the smaller, more flexible, desflurane binds deeper inside. Mutations of some amino acids lining the binding site profoundly alter the ionic response of GLIC to protons, and affect its general-anaesthetic pharmacology. Molecular dynamics simulations, performed on the wild type (WT) and two GLIC mutants, highlight differences in mobility of propofol in its binding site and help to explain these effects. These data provide a novel structural framework for the design of general anaesthetics and of allosteric modulators of brain pLGICs.


    Organizational Affiliation

    Institut Pasteur, Groupe Récepteurs-Canaux, F-75015 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glr4197 protein
A, B, C, D, E
318Gloeobacter 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLC
Query on PLC

Download SDF File 
Download CCD File 
A, B, C, D, E
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
 Ligand Interaction
LMT
Query on LMT

Download SDF File 
Download CCD File 
A, B, D, E
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
PFL
Query on PFL

Download SDF File 
Download CCD File 
A, B, C, D, E
2,6-BIS(1-METHYLETHYL)PHENOL
2,6-DIISOPROPYLPHENOL; PROPOFOL
C12 H18 O
OLBCVFGFOZPWHH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PFLIC50: 24000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 181.130α = 90.00
b = 132.780β = 102.32
c = 159.970γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4model building
BUSTERrefinement
CCP4phasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-04-11
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description