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Resource:Ligand-Gated Ion Channel Database

Name: Resource:Ligand-Gated Ion Channel Database
Description: The LGICdb aims to be a non-redundant, manually curated resource offering access to the large number of subunits composing extracellularly activated ligand-gated ion channels. The Ligand Gated Ion Channel Database currently contains 554 entries of ligand-activated ion channel subunits.


In this database, one may find: the nucleic and proteic sequences of the subunits; multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. In 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.

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, GABAA and GABAC 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.

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

Contents

  • Cys-loop receptor superfamily (5-HT3 and 5-HTmod1 receptors, nicotinic acetylcholine receptors, glycine receptors, GABAA and GABAC 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 or by keywords.

Download the snapshot 60 of the whole database (6 June 2007)

This database is not actively maintained anymore. 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.


Other Name(s): LGIC Database
Parent Organization: Resource:European Bioinformatics Institute
Supporting Agency: the College de France, the Centre National De la Recherche Scientifique, Biotech and Biomed contracts from the Commission of the European communities, the Ministere de i'Enseignement Supereur et de la Recherche, and the Institut Pasteur.
Resource Type(s): Database
Keywords: equilibrium, extracellular, gabaa, gated, gene, genetics, 3d models, alignment, anionic, atomic, atp, cationic, cellular/molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, neuroinformatics, neuroscience, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, protein, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembrane
Resource: Resource
URL: http://www.ebi.ac.uk/compneur-srv/LGICdb/
Id: nif-0000-00037
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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Contributors

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Facts about Resource:Ligand-Gated Ion Channel DatabaseRDF feed
CurationStatuscurated  +
DefiningCitationhttp://www.ebi.ac.uk/compneur-srv/LGICdb/  +
DefinitionThe LGICdb aims to be a non-redundant, man The LGICdb aims to be a non-redundant, manually curated resource offering access to the large number of subunits composing extracellularly activated ligand-gated ion channels. The Ligand Gated Ion Channel Database currently contains 554 entries of ligand-activated ion channel subunits.


In this database, one may find: the nucleic and proteic sequences of the subunits; multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. In 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.

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, GABAA and GABAC 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.

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

Contents

  • Cys-loop receptor superfamily (5-HT3 and 5-HTmod1 receptors, nicotinic acetylcholine receptors, glycine receptors, GABAA and GABAC 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 or by keywords.

Download the snapshot 60 of the whole database (6 June 2007)

This database is not actively maintained anymore. 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.
rot, Ensembl, Protein Databank etc.


Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnif-0000-00037  +
Is part ofResource:European Bioinformatics Institute  +
KeywordsEquilibrium  +, Extracellular  +, Gabaa  +, Gated  +, Gene  +, Genetics  +, 3d models  +, Alignment  +, Anionic  +, Atomic  +, Atp  +, Cationic  +, Cellular/molecular  +, Channel  +, Compartment  +, Computation  +, Conformation  +, Coordinate  +, Cys-loop  +, Glutamate  +, Glycine  +, Histamine  +, Homologous  +, Ion  +, Ion channel  +, Ligand  +, Membrane  +, Neuroinformatics  +, Neuroscience  +, Nicotinic  +, Nucleic acid  +, Phylogenetic  +, Pore  +, Portion  +, Proteic  +, Protein  +, Receptor  +, Segment  +, Sequence  +, Sequence data  +, Serotonin  +, Subunit  +, Superfamily  +, and Transmembrane  +
LabelResource:Ligand-Gated Ion Channel Database  +
ModifiedDate18 May 2011  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
Supporting AgencyThe College de France  +, The Centre National De la Recherche Scientifique  +, Biotech and Biomed contracts from the Commission of the European communities  +, The Ministere de i'Enseignement Supereur et de la Recherche  +, and And the Institut Pasteur.  +
SynonymLGIC Database  +