4HFI

The GLIC pentameric Ligand-Gated Ion Channel at 2.4 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.

Sauguet, L.Poitevin, F.Murail, S.Van Renterghem, C.Moraga-Cid, G.Malherbe, L.Thompson, A.W.Koehl, P.Corringer, P.J.Baaden, M.Delarue, M.

(2013) EMBO J 32: 728-741

  • DOI: 10.1038/emboj.2013.17
  • Primary Citation of Related Structures:  
    4HFI, 4IL4, 4ILA, 4ILB, 4ILC, 4IL9

  • PubMed Abstract: 
  • To understand the molecular mechanism of ion permeation in pentameric ligand-gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a prokaryotic pLGIC, at 2.4 Å. Anomalous diffraction data were used to place bound anions and cations ...

    To understand the molecular mechanism of ion permeation in pentameric ligand-gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a prokaryotic pLGIC, at 2.4 Å. Anomalous diffraction data were used to place bound anions and cations. This reveals ordered water molecules at the level of two rings of hydroxylated residues (named Ser6' and Thr2') that contribute to the ion selectivity filter. Two water pentagons are observed, a self-stabilized ice-like water pentagon and a second wider water pentagon, with one sodium ion between them. Single-channel electrophysiology shows that the side-chain hydroxyl of Ser6' is crucial for ion translocation. Simulations and electrostatics calculations complemented the description of hydration in the pore and suggest that the water pentagons observed in the crystal are important for the ion to cross hydrophobic constriction barriers. Simulations that pull a cation through the pore reveal that residue Ser6' actively contributes to ion translocation by reorienting its side chain when the ion is going through the pore. Generalization of these findings to the pLGIC family is proposed.


    Organizational Affiliation

    Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, CNRS UMR3528, Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proton-gated ion channelA, B, C, D, E317Gloeobacter violaceus PCC 7421Mutation(s): 0 
Gene Names: glvIglr4197
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NDN8 
Go to UniProtKB:  Q7NDN8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLC
Query on PLC

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , G [auth A] , H [auth A] , I [auth A] , IA [auth D] , JA [auth D] , 
AA [auth C],  BA [auth C],  CA [auth C],  G [auth A],  H [auth A],  I [auth A],  IA [auth D],  JA [auth D],  KA [auth D],  QA [auth E],  RA [auth E],  S [auth B],  SA [auth E],  T [auth B],  U [auth B]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
 Ligand Interaction
LMT
Query on LMT

Download Ideal Coordinates CCD File 
GA [auth C], OA [auth D], P [auth A], Q [auth A], WA [auth E], Y [auth B]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A] , FA [auth C] , HA [auth D] , NA [auth D] , O [auth A] , PA [auth E] , R [auth B] , VA [auth E] , 
F [auth A],  FA [auth C],  HA [auth D],  NA [auth D],  O [auth A],  PA [auth E],  R [auth B],  VA [auth E],  X [auth B],  Z [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth C], J [auth A], K [auth A], L [auth A], LA [auth D], TA [auth E], V [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
EA [auth C], M [auth A], MA [auth D], N [auth A], UA [auth E], W [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.89α = 90
b = 133.2β = 102.74
c = 160.2γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Database references