4NPP

The GLIC-His10 wild-type structure in equilibrium between the open and locally-closed (LC) forms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation.

Sauguet, L.Shahsavar, A.Poitevin, F.Huon, C.Menny, A.Nemecz, A.Haouz, A.Changeux, J.P.Corringer, P.J.Delarue, M.

(2014) Proc.Natl.Acad.Sci.USA 111: 966-971

  • DOI: 10.1073/pnas.1314997111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pentameric ligand-gated ion channels mediate fast chemical transmission of nerve signals. The structure of a bacterial proton-gated homolog has been established in its open and locally closed conformations at acidic pH. Here we report its crystal str ...

    Pentameric ligand-gated ion channels mediate fast chemical transmission of nerve signals. The structure of a bacterial proton-gated homolog has been established in its open and locally closed conformations at acidic pH. Here we report its crystal structure at neutral pH, thereby providing the X-ray structures of the two end-points of the gating mechanism in the same pentameric ligand-gated ion channel. The large structural variability in the neutral pH structure observed in the four copies of the pentamer present in the asymmetric unit has been used to analyze the intrinsic fluctuations in this state, which are found to prefigure the transition to the open state. In the extracellular domain (ECD), a marked quaternary change is observed, involving both a twist and a blooming motion, and the pore in the transmembrane domain (TMD) is closed by an upper bend of helix M2 (as in locally closed form) and a kink of helix M1, both helices no longer interacting across adjacent subunits. On the tertiary level, detachment of inner and outer β sheets in the ECD reshapes two essential cavities at the ECD-ECD and ECD-TMD interfaces. The first one is the ligand-binding cavity; the other is close to a known divalent cation binding site in other pentameric ligand-gated ion channels. In addition, a different crystal form reveals that the locally closed and open conformations coexist as discrete ones at acidic pH. These structural results, together with site-directed mutagenesis, physiological recordings, and coarse-grained modeling, have been integrated to propose a model of the gating transition pathway.


    Organizational Affiliation

    Unité de Dynamique Structurale des Macromolécules, Unité Mixte de Recherche (UMR) 3528 du Centre National de la Recherche Scientifique (CNRS), Institut Pasteur, 75015 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proton-gated ion channel
A, B, C, D, E
329Gloeobacter violaceus (strain PCC 7421)Mutation(s): 0 
Gene Names: glvI
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Cys-Loop Receptor Family
Protein: 
Prokaryotic pentameric ligand-gated ion channel (GLIC)
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain PCC 7421))
Go to UniProtKB:  Q7NDN8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A, B, C, D, E
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 113.554α = 90.00
b = 127.618β = 90.00
c = 185.807γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary