4IRE

Crystal structure of GLIC with mutations at the loop C region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Signal transduction pathways in the pentameric ligand-gated ion channels.

Mowrey, D.Chen, Q.Liang, Y.Liang, J.Xu, Y.Tang, P.

(2013) Plos One 8: e64326-e64326

  • DOI: 10.1371/journal.pone.0064326

  • PubMed Abstract: 
  • The mechanisms of allosteric action within pentameric ligand-gated ion channels (pLGICs) remain to be determined. Using crystallography, site-directed mutagenesis, and two-electrode voltage clamp measurements, we identified two functionally relevant ...

    The mechanisms of allosteric action within pentameric ligand-gated ion channels (pLGICs) remain to be determined. Using crystallography, site-directed mutagenesis, and two-electrode voltage clamp measurements, we identified two functionally relevant sites in the extracellular (EC) domain of the bacterial pLGIC from Gloeobacter violaceus (GLIC). One site is at the C-loop region, where the NQN mutation (D91N, E177Q, and D178N) eliminated inter-subunit salt bridges in the open-channel GLIC structure and thereby shifted the channel activation to a higher agonist concentration. The other site is below the C-loop, where binding of the anesthetic ketamine inhibited GLIC currents in a concentration dependent manner. To understand how a perturbation signal in the EC domain, either resulting from the NQN mutation or ketamine binding, is transduced to the channel gate, we have used the Perturbation-based Markovian Transmission (PMT) model to determine dynamic responses of the GLIC channel and signaling pathways upon initial perturbations in the EC domain of GLIC. Despite the existence of many possible routes for the initial perturbation signal to reach the channel gate, the PMT model in combination with Yen's algorithm revealed that perturbation signals with the highest probability flow travel either via the β1-β2 loop or through pre-TM1. The β1-β2 loop occurs in either intra- or inter-subunit pathways, while pre-TM1 occurs exclusively in inter-subunit pathways. Residues involved in both types of pathways are well supported by previous experimental data on nAChR. The direct coupling between pre-TM1 and TM2 of the adjacent subunit adds new insight into the allosteric signaling mechanism in pLGICs.


    Organizational Affiliation

    Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proton-gated ion channel
A, B, C, D, E
317Gloeobacter violaceus (strain PCC 7421)Mutation(s): 3 
Gene Names: glvI
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain PCC 7421))
Go to UniProtKB:  Q7NDN8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D, E
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PC1
Query on PC1

Download SDF File 
Download CCD File 
A, B, C, D, E
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
OXL
Query on OXL

Download SDF File 
Download CCD File 
A, B, C, D, E
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
LMD
Query on LMD

Download SDF File 
Download CCD File 
A, C, E
tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
n-Tetradecyl-b-D-maltopyranosid
C26 H50 O11
UKPROSIGWJBJGA-IWODYCRQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 182.030α = 90.00
b = 133.620β = 102.57
c = 161.430γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-05-01
    Type: Structure summary
  • Version 1.2: 2013-05-22
    Type: Database references