Ligand-Gated Ion Channel Database

Dear Colleagues,

The development of the Ligand-Gated Ion Channel database was started in 1994, as part of Le Novère's work on the phylogeny of those receptors' subunits. It grew into a serious data resource, that served the community at large. However, it is not actively maintained anymore. In addition, bioinformatics technology evolved a lot over the last two decades, so that scientists can now generate quickly customised databases from trustworthy primary data resources. Therefore, we decided to officialy freeze the data resource. The resource will not disappear, and all the information and links will stay there. But people should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.

We believe there would be means to rejuvenate the LGICdb, by automatically import sequences and structures, adding functional data and information on channelopathies etc. We just do not have time for it. However, if any user wants to take over the maintainance and development of the LGICdb, we will assist then in the best of our abilities.

Thank-you for your help and fidelity over the years.

Introduction

Ligand-Gated Ion Channels are transmembrane proteins that can exist under different conformations, at least one forming a pore through the membrane connecting the two neighbour compartments. The equilibrium between the various conformations is affected by the binding of ligands on the channels. Phenomenologically, the ligands "open" or "close" the channel.

There are three different superfamilies of extracellularly activated ligand-gated ion channel subunits:

The receptors of the cys-loop superfamily (nicotinic receptors, 5-HT₃ receptors, GABA_A and GABA_C receptors, glycine receptors, and some glutamate, histamine and serotonin activated anionic channels) are made of five homologous subunits, each with four transmembrane segments.
The ATP gated channels (ATP2x receptors) are made of three homologous subunits, each with two transmembrane segments.
The glutamate activated cationic channels (NMDA receptors, AMPA receptors, kainate receptors etc...) are made of four homologous subunits, each with three transmembrane segments.

Due to the lack of evolutionary relationship, these three superfamilies are treated separately.

In the LGIC Database you will find the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available. The LGIC Database redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. See the LGIC Database FAQ for more details about the database construction.

The Ligand Gated Ion Channel Database currently contains 554 entries of ligand-activated ion channel subunits.

Cys-loop receptor superfamily (5-HT₃ and 5-HTmod1 receptors, nicotinic acetylcholine receptors, glycine receptors, GABA_A and GABA_C receptors, anionic glutamate receptors and histamine-gated receptors).

ATP gated channel superfamily (P2x).

Glutamate cationic receptor superfamily (AMPA receptors, kainate receptors, NMDA receptors, etc.).

Download the snapshot 60 of the whole database (6 June 2007) [ChangeLog].

Submit an entry: Send me an email with an accession number, a sequence, or any kind of suggestion, comment, or criticism. You can also design your own entry with the LGICdb Editor.

LGIC Database FAQ.

Acknowledgements

Construction of the LGIC Database

The LGIC database has been initially developed by Nicolas Le Novère within the team of Jean-Pierre Changeux at the Pasteur Institute, with the help of Catherine Letondal. It was further developed at the EMBL-EBI by Marie-Ange Djite and Antonia Mayer. It is now maintained by the Le Novere Lab group at the Babraham Institute.

Submitters

The following people submitted sequences, structures or database accession numbers: Howard Baylis, Igor Baskin, Alain Bessis, Thon De Boer, Thomas Boyd, David C. Chiara, Raphael Courjanet, Steve Ennion, Michael Hollmann, Michaela Jansen, Benoît Lacombe, Pierre Paoletti, David Reeves, Wladimir Saudek, Ralf Schoepfer, Pim van Nierop.

Other helpers

The following people helped with advice, corrections, general comments, etc.: Mikael Andersson, Jim Boulter, Robert Choy, Alban de Kerchove D'Exaerde, Anne Devillers-Thiéry, Marco Donizelli, Aymeric Duclert, Sebastien Dutertre, Ronald Lukas, Daniel McGreal, Alexandre Mourot, Richard Olsen, Yoav Paas, Nicolas Rodriguez, Mike White, Hongjie Yang.

Free (in the sense of freedom) programs used to develop the LGIC Database

The static web pages were written with GNU emacs and Kwrite.
The alignments were performed with the program ClustalW.
The phylogenetic studies were performed with Phylip.
The structures are displayed with JmolApplet.
The different file formats of the database are written with Perl scripts, using bioperl.