3TLT

The GLIC pentameric Ligand-Gated Ion Channel H11'F mutant in a locally-closed conformation (LC1 subtype)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A locally closed conformation of a bacterial pentameric proton-gated ion channel.

Prevost, M.S.Sauguet, L.Nury, H.Van Renterghem, C.Huon, C.Poitevin, F.Baaden, M.Delarue, M.Corringer, P.J.

(2012) Nat Struct Mol Biol 19: 642-649

  • DOI: https://doi.org/10.1038/nsmb.2307
  • Primary Citation of Related Structures:  
    3TLS, 3TLT, 3TLU, 3TLV, 3TLW, 3UU3, 3UU4, 3UU5, 3UU6, 3UU8, 3UUB

  • PubMed Abstract: 

    Pentameric ligand-gated ion channels mediate signal transduction through conformational transitions between closed-pore and open-pore states. To stabilize a closed conformation of GLIC, a bacterial proton-gated homolog from Gloeobacter violaceus whose open structure is known, we separately generated either four cross-links or two single mutations. We found all six mutants to be in the same 'locally closed' conformation using X-ray crystallography, sharing most of the features of the open form but showing a locally closed pore as a result of a concerted bending of all of its M2 helices. The mutants adopt several variant conformations of the M2-M3 loop, and in all cases an interacting lipid that is observed in the open form disappears. A single cross-linked mutant is functional, according to electrophysiology, and the locally closed structure of this mutant indicates that it has an increased flexibility. Further cross-linking, accessibility and molecular dynamics data suggest that the locally closed form is a functionally relevant conformation that occurs during allosteric gating transitions.


  • Organizational Affiliation

    Institut Pasteur, Groupe Récepteurs-Canaux, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glr4197 protein
A, B, C, D, E
321Gloeobacter violaceusMutation(s): 1 
Gene Names: glr4197
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.37α = 90
b = 129.02β = 102.14
c = 160.53γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references
  • Version 1.2: 2012-06-27
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations