5L4H | pdb_00005l4h

X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with 5-(2-BROMO-ETHYL)-5-ETHYL-PYRIMIDINE-2,4,6-TRIONE (brominated barbiturate)

• PDB DOI: https://doi.org/10.2210/pdb5L4H/pdb

• Classification: MEMBRANE PROTEIN, TRANSPORT PROTEIN
• Organism(s): Gloeobacter violaceus PCC 7421
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2016-05-25 Released: 2016-12-21 
• Deposition Author(s): Fourati, Z., Ruza, R.R., Delarue, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

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

• PubMed: 27986812 
• 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.

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Organizational Affiliation: 
• From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France.
the Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom.
the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France.
the Department of Computer Science, University of California, Davis, California 95616.
the Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom. Electronic address: [e-mail].
From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 182.08 kDa 
• Atom Count: 12,731 
• Modeled Residue Count: 1,555 
• Deposited Residue Count: 1,585 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton-gated ion channel	A, B, C, D, E	317	Gloeobacter violaceus PCC 7421	Mutation(s): 0  Gene Names: glvI, glr4197 Membrane Entity: Yes
UniProt
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NDN8  Go to UniProtKB:  Q7NDN8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMT	I [auth D]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
6JW	L [auth E]	5-(2-bromoethyl)-5-ethyl-1,3-diazinane-2,4,6-trione C8 H11 Br N2 O3 LJVTYPFTOBMROG-UHFFFAOYSA-N
CL	F [auth A], G [auth B], H [auth C], J [auth D], K [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.235 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.145	α = 90
b = 127.942	β = 101.03
c = 159.7	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Fourati, Z., Ruza, R.R., Delarue, M.

Revision History  

• 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: 2024-10-16
  Changes: Data collection, Database references, Structure summary