4ZZC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.1 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proton-gated ion channel
A, B, C, D, E
317Gloeobacter violaceus PCC 7421Mutation(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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLC
Query on PLC

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G [auth A]
H [auth A]
HA [auth C]
IA [auth C]
IB [auth E]
G [auth A],
H [auth A],
HA [auth C],
IA [auth C],
IB [auth E],
JB [auth E],
U [auth B],
V [auth B],
VA [auth D],
WA [auth D]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
LMT
Query on LMT

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AB [auth D]
L [auth A]
M [auth A]
NA [auth C]
NB [auth E]
AB [auth D],
L [auth A],
M [auth A],
NA [auth C],
NB [auth E],
Z [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
XE
Query on XE

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AA [auth B]
BA [auth B]
BB [auth D]
CA [auth B]
CB [auth D]
AA [auth B],
BA [auth B],
BB [auth D],
CA [auth B],
CB [auth D],
DA [auth B],
DB [auth D],
EA [auth B],
EB [auth D],
FA [auth B],
FB [auth D],
GB [auth D],
N [auth A],
O [auth A],
OA [auth C],
OB [auth E],
P [auth A],
PA [auth C],
PB [auth E],
Q [auth A],
QA [auth C],
QB [auth E],
R [auth A],
RA [auth C],
RB [auth E],
S [auth A],
SA [auth C],
SB [auth E],
TA [auth C],
TB [auth E]
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
ACT
Query on ACT

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F [auth A]
GA [auth C]
HB [auth E]
K [auth A]
MA [auth C]
F [auth A],
GA [auth C],
HB [auth E],
K [auth A],
MA [auth C],
MB [auth E],
T [auth B],
UA [auth D],
Y [auth B],
ZA [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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I [auth A],
JA [auth C],
KB [auth E],
W [auth B],
XA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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J [auth A]
KA [auth C]
LA [auth C]
LB [auth E]
X [auth B]
J [auth A],
KA [auth C],
LA [auth C],
LB [auth E],
X [auth B],
YA [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180α = 90
b = 132.82β = 101.88
c = 159.15γ = 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