5L47 | pdb_00005l47

X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with cyanoselenobarbital (seleniated barbiturate)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.230 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State.

Fourati, Z.Ruza, R.R.Laverty, D.Drege, E.Delarue-Cochin, S.Joseph, D.Koehl, P.Smart, T.Delarue, M.

(2017) J Biological Chem 292: 1550-1558

  • DOI: https://doi.org/10.1074/jbc.M116.766964
  • Primary Citation Related Structures: 
    5L47, 5L4E, 5L4H

  • PubMed Abstract: 

    Barbiturates induce anesthesia by modulating the activity of anionic and cationic pentameric ligand-gated ion channels (pLGICs). Despite more than a century of use in clinical practice, the prototypic binding site for this class of drugs within pLGICs is yet to be described. In this study, we present the first X-ray structures of barbiturates bound to GLIC, a cationic prokaryotic pLGIC with excellent structural homology to other relevant channels sensitive to general anesthetics and, as shown here, to barbiturates, at clinically relevant concentrations. Several derivatives of barbiturates containing anomalous scatterers were synthesized, and these derivatives helped us unambiguously identify a unique barbiturate binding site within the central ion channel pore in a closed conformation. In addition, docking calculations around the observed binding site for all three states of the receptor, including a model of the desensitized state, showed that barbiturates preferentially stabilize the closed state. The identification of this pore binding site sheds light on the mechanism of barbiturate inhibition of cationic pLGICs and allows the rationalization of several structural and functional features previously observed for barbiturates.


  • Organizational Affiliation
    • From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France.

Macromolecule Content 

  • Total Structure Weight: 182.15 kDa 
  • Atom Count: 12,764 
  • Modeled Residue Count: 1,555 
  • Deposited Residue Count: 1,585 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proton-gated ion channel
A, B, C, D, E
317GloeobacterMutation(s): 0 
Gene Names: glvIglr4197
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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6JA

Query on 6JA



Download:Ideal Coordinates CCD File
J [auth B]2-[5-ethyl-2,4,6-tris(oxidanylidene)-1,3-diazinan-5-yl]ethyl selenocyanate
C9 H11 N3 O3 Se
LFTCFIKEJOPJTJ-UHFFFAOYSA-N
D12

Query on D12



Download:Ideal Coordinates CCD File
O [auth D]DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
M [auth C],
Q [auth D],
T [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
L [auth C],
P [auth D],
S [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A],
N [auth C],
R [auth D],
U [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.230 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.158α = 90
b = 128.124β = 102.72
c = 162.193γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance13BSV8002002

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2017-02-15
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary