3P50

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/nature09647
  • Primary Citation of Related Structures:  
    3P4W, 3P50

  • 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(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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glr4197 protein
A, B, C, D, E
318Gloeobacter violaceusMutation(s): 0 
Gene Names: glr4197
Membrane Entity: Yes 
UniProt
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NDN8 
Go to UniProtKB:  Q7NDN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NDN8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLC
Query on PLC

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
M [auth B]
N [auth B]
P [auth C]
I [auth A],
J [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
U [auth D],
V [auth D],
Y [auth E],
Z [auth E]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
LMT
Query on LMT

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
K [auth B]
R [auth D]
S [auth D]
F [auth A],
G [auth A],
K [auth B],
R [auth D],
S [auth D],
W [auth E]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PFL
Query on PFL

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
O [auth C],
T [auth D],
X [auth E]
2,6-BIS(1-METHYLETHYL)PHENOL
C12 H18 O
OLBCVFGFOZPWHH-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PFL PDBBind:  3P50 IC50: 2.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.13α = 90
b = 132.78β = 102.32
c = 159.97γ = 90
Software Package:
Software NamePurpose
CCP4model building
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-11
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description