4F8H

X-ray Structure of the Anesthetic Ketamine Bound to the GLIC Pentameric Ligand-gated Ion Channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Pentameric Ligand-Gated Ion Channel GLIC Bound with Anesthetic Ketamine.

Pan, J.Chen, Q.Willenbring, D.Mowrey, D.Kong, X.P.Cohen, A.Divito, C.B.Xu, Y.Tang, P.

(2012) Structure 20: 1463-1469

  • DOI: 10.1016/j.str.2012.08.009

  • PubMed Abstract: 
  • Pentameric ligand-gated ion channels (pLGICs) are targets of general anesthetics, but a structural understanding of anesthetic action on pLGICs remains elusive. GLIC, a prokaryotic pLGIC, can be inhibited by anesthetics, including ketamine. The ketam ...

    Pentameric ligand-gated ion channels (pLGICs) are targets of general anesthetics, but a structural understanding of anesthetic action on pLGICs remains elusive. GLIC, a prokaryotic pLGIC, can be inhibited by anesthetics, including ketamine. The ketamine concentration leading to half-maximal inhibition of GLIC (58 μM) is comparable to that on neuronal nicotinic acetylcholine receptors. A 2.99 Å resolution X-ray structure of GLIC bound with ketamine revealed ketamine binding to an intersubunit cavity that partially overlaps with the homologous antagonist-binding site in pLGICs. The functional relevance of the identified ketamine site was highlighted by profound changes in GLIC activation upon cysteine substitution of the cavity-lining residue N152. The relevance is also evidenced by changes in ketamine inhibition upon the subsequent chemical labeling of N152C. The results provide structural insight into the molecular recognition of ketamine and are valuable for understanding the actions of anesthetics and other allosteric modulators on pLGICs.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proton-gated ion channel
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 3 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
RKE
Query on RKE

Download SDF File 
Download CCD File 
A, B, C, D, E
(R)-ketamine
(2R)-2-(2-chlorophenyl)-2-(methylamino)cyclohexanone
C13 H16 Cl N O
YQEZLKZALYSWHR-CYBMUJFWSA-N
 Ligand Interaction
LMD
Query on LMD

Download SDF File 
Download CCD File 
A, B, C, D, E
tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
n-Tetradecyl-b-D-maltopyranosid
C26 H50 O11
UKPROSIGWJBJGA-IWODYCRQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RKEIC50: 58000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.069α = 90.00
b = 132.742β = 103.61
c = 162.077γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
SOLVEphasing
XDSdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-09-26
    Type: Database references
  • Version 1.2: 2018-06-13
    Type: Data collection