Ligand-Gated Ion Channel Database

EBI Groups Computational Neurobiology Computing LGICdb

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.).

Search the LGIC Database with FASTA.

Search the LGIC Database by keywords.

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.

Summer Internships

We are looking for summer interns to work on the curation of our Ligand-Gated Ion Channel Database. These internships are not part of a university training. Nevertheless, this is an opportunity for the postholders to gain experience in an international environment. A limited funding is provided to cover for living expenses.

Successful candidates have experience in working with GNU/Linux operating system, and have a good knowledge of the main data resources used in biology. The curation of Ligand-Gated Ion Channel Database requires a good knowledge of nucleotides and protein sequence manipulation. Candidates with a dual training in Biology and computing would be ideal.

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 is now maintained in the Computational Neurobiology group at the European Bioinformatics Institute by Nicolas Le Novère and Antonia Mayer. Thanks to Marie-Ange Djite who migrated the database from the Pasteur Institute and helped to developed the search facility. The FASTA similarity search is maintained by the EBI group External Services.

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 me 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 are written with GNU emacs.
The alignments are performed with the program ClustalW.
The searches by sequence similarity are done with the program FASTA.
The phylogenetic studies are performed with Phylip.
The structures are displayed with JmolApplet.
The different file formats of the database are written with Perl scripts, using bioperl.
The searches by keywords use Xindice and Jakarta Tomcat of the Apache Software Foundation.