4ZZB | pdb_00004zzb

The GLIC pentameric Ligand-Gated Ion Channel Locally-closed form complexed to xenon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.216 (Depositor) 
  • R-Value Observed: 
    0.217 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZZB

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel.

Sauguet, L.Fourati, Z.Prange, T.Delarue, M.Colloc'h, N.

(2016) PLoS One 11: e0149795-e0149795

  • DOI: https://doi.org/10.1371/journal.pone.0149795
  • Primary Citation Related Structures: 
    4ZZB, 4ZZC

  • PubMed Abstract: 

    GLIC receptor is a bacterial pentameric ligand-gated ion channel whose action is inhibited by xenon. Xenon has been used in clinical practice as a potent gaseous anaesthetic for decades, but the molecular mechanism of interactions with its integral membrane receptor targets remains poorly understood. Here we characterize by X-ray crystallography the xenon-binding sites within both the open and "locally-closed" (inactive) conformations of GLIC. Major binding sites of xenon, which differ between the two conformations, were identified in three distinct regions that all belong to the trans-membrane domain of GLIC: 1) in an intra-subunit cavity, 2) at the interface between adjacent subunits, and 3) in the pore. The pore site is unique to the locally-closed form where the binding of xenon effectively seals the channel. A putative mechanism of the inhibition of GLIC by xenon is proposed, which might be extended to other pentameric cationic ligand-gated ion channels.


  • Organizational Affiliation
    • Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 185.11 kDa 
  • Atom Count: 12,659 
  • 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
317Gloeobacter violaceus PCC 8105Mutation(s): 3 
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
LMT

Query on LMT



Download:Ideal Coordinates CCD File
F [auth A]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
XE

Query on XE



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
HA [auth D]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
HA [auth D],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
OA [auth E],
PA [auth E],
QA [auth E],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
GA [auth D]
I [auth A]
NA [auth E]
R [auth B]
W [auth C]
GA [auth D],
I [auth A],
NA [auth E],
R [auth B],
W [auth C],
Z [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
EA [auth D],
G [auth A],
LA [auth E],
P [auth B],
X [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
FA [auth D],
H [auth A],
MA [auth E],
Q [auth B],
Y [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.216 (Depositor) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.966α = 90
b = 130.528β = 100.33
c = 157.526γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2018-11-21
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary