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663  structures 217  species 5  interactions 3764  sequences 102  architectures

Family: Lig_chan (PF00060)

Summary: Ligand-gated ion channel

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This is the Wikipedia entry entitled "Ionotropic glutamate receptor". More...

Ionotropic glutamate receptor Edit Wikipedia article

Lig_chan
PDB 1s50 EBI.jpg
x-ray structure of the glur6 ligand binding core (s1s2a) in complex with glutamate at 1.65 a resolution
Identifiers
Symbol Lig_chan
Pfam PF00060
Pfam clan CL0030
InterPro IPR001320
SCOP 1gr2
SUPERFAMILY 1gr2
TCDB 1.A.10
OPM superfamily 231
OPM protein 3kg2

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are activated by the neurotransmitter glutamate.[1] They mediate the majority of excitatory synaptic transmission throughout the central nervous system and are key players in synaptic plasticity, which is important for learning and memory. iGluRs have been divided into four subtypes on the basis of their ligand binding properties (pharmacology) and sequence similarity: AMPA receptors, kainate receptors, NMDA receptors and delta receptors (see below).[2]

AMPA receptors are the main charge carriers during basal transmission, permitting influx of sodium ions to depolarise the postsynaptic membrane. NMDA receptors are blocked by magnesium ions and therefore only permit ion flux following prior depolarisation. This enables them to act as coincidence detectors for synaptic plasticity. Calcium influx through NMDA receptors leads to persistent modifications in the strength of synaptic transmission.[3][4]

iGluRs are tetramers (they are formed of four subunits). All subunits have a shared architecture with four domain layers: two extracellular clamshell domains called the N-terminal domain (NTD) and ligand-binding domain (LBD; which binds glutamate), the transmembrane domain (TMD) that forms the ion channel, and an intracellular C-terminal domain (CTD).[5]

Human proteins/genes encoding iGluR subunits

AMPA receptors: GluA1/GRIA1; GluA2/GRIA2; GluA3/GRIA3; GluA4/GRIA4;

delta receptors: GluD1/GRID1; GluD2/GRID2;

kainate receptors: GluK1/GRIK1; GluK2/GRIK2; GluK3/GRIK3; GluK4/GRIK4; GluK5/GRIK5;

NMDA receptors: GluN1/GRIN1; GluN2A/GRIN2A; GluN2B/GRIN2B; GluN2C/GRIN2C; GluN2D/GRIN2D; GluN3A/GRIN3A; GluN3B/GRIN3B;

References

  1. ^ Traynelis SF, Wollmuth LP, McBain CJ, Menniti FS, Vance KM, Ogden KK, Hansen KB, Yuan H, Myers SJ, Dingledine R. (September 2010). "Glutamate receptor ion channels: structure, regulation, and function". Pharmacol. Rev. 62 (3): 405–496. doi:10.1124/pr.109.002451. PMID 20716669. 
  2. ^ Collingridge GL1, Olsen RW, Peters J, Spedding M (January 2009). "A nomenclature for ligand-gated ion channels". Neuropharmacology 56 (1): 2–5. doi:10.1016/j.neuropharm.2008.06.063. PMID 18655795. 
  3. ^ Bliss TVP, Collingridge GL (January 1993). "A synaptic model of memory: long-term potentiation in the hippocampus". Nature 361 (6407): 31–39. doi:10.1038/361031a0. PMID 8421494. 
  4. ^ Citri A1, Malenka RC (January 2008). "Synaptic plasticity: multiple forms, functions, and mechanisms". Neuropsychopharmacology 33 (1): 18–41. doi:10.1038/sj.npp.1301559. PMID 17728696. 
  5. ^ Traynelis SF, Wollmuth LP, McBain CJ, Menniti FS, Vance KM, Ogden KK, Hansen KB, Yuan H, Myers SJ, Dingledine R. (September 2010). "Glutamate receptor ion channels: structure, regulation, and function". Pharmacol. Rev. 62 (3): 405–496. doi:10.1124/pr.109.002451. PMID 20716669. 

This article incorporates text from the public domain Pfam and InterPro IPR001320


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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Ligand-gated ion channel Provide feedback

This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.

Literature references

  1. Tong G, Shepherd D, Jahr CE; , Science 1995;267:1510-1512.: Synaptic desensitization of NMDA receptors by calcineurin. PUBMED:7878472 EPMC:7878472


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001320

Ionotropic glutamate receptors (iGluRs) are a highly conserved family of ligand-gated ion channels present in animals, plants, and bacteria, which are best characterised for their roles in synaptic communication in vertebrate nervous systems [PUBMED:14977400]. A variant subfamily of iGluRs, the Ionotropic Receptors (IRs), consist of non-glutamate-binding chemosensory receptors first identified in Drosophila melanogaster. They function in detecting odors and tastants [PUBMED:20808886]. There are three classes of ionotropic glutamate receptors (iGluRs), namely NMDA (N-methyl-D-aspartate), AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole-4-propionic acid) and kainate receptors. They are believed to play critical roles in synaptic plasticity. At many synapses in the brain, transient activation of NMDA receptors leads to a persistent modification in the strength of synaptic transmission mediated by AMPA receptors and kainate receptors can act as the induction trigger for long-term changes in synaptic transmission [PUBMED:10580501].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Ion_channel (CL0030), which has the following description:

This superfamily contains a diverse range of ion channels that share a pair of transmembrane helices in common. This clan is classified as the VIC (Voltage-gated Ion Channel) superfamily in TCDB.

The clan contains the following 7 members:

Ion_trans Ion_trans_2 IRK KdpA Lig_chan PKD_channel TrkH

Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(43)
Full
(3764)
Representative proteomes UniProt
(6547)
NCBI
(12270)
Meta
(56)
RP15
(1116)
RP35
(1910)
RP55
(2893)
RP75
(3495)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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  Seed
(43)
Full
(3764)
Representative proteomes UniProt
(6547)
NCBI
(12270)
Meta
(56)
RP15
(1116)
RP35
(1910)
RP55
(2893)
RP75
(3495)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(43)
Full
(3764)
Representative proteomes UniProt
(6547)
NCBI
(12270)
Meta
(56)
RP15
(1116)
RP35
(1910)
RP55
(2893)
RP75
(3495)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Blastp NMZ1_HUMAN
Previous IDs: lig_chan;
Type: Family
Author: Bateman A, Sonnhammer ELL
Number in seed: 43
Number in full: 3764
Average length of the domain: 254.70 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 32.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.5 26.5
Trusted cut-off 26.5 26.5
Noise cut-off 26.4 26.4
Model length: 149
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 5 interactions for this family. More...

SBP_bac_3 Lig_chan-Glu_bd Lig_chan Lig_chan-Glu_bd SBP_bac_3

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Lig_chan domain has been found. There are 663 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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