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465  structures 277  species 0  interactions 3260  sequences 78  architectures

Family: Lig_chan (PF00060)

Summary: Ligand-gated ion channel

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

The ability of synapses to modify their synaptic strength in response to activity is a fundamental property of the nervous system and may be an essential component of learning and memory. There are four classes of ionotropic glutamate receptors, namely NMDA receptor, AMPA receptor, Delta receptor 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.[1]

This family includes the four regions of the ionotropic glutamate receptors, i.e. the NMDA, AMPA, Delta receptor and kainate receptors.

Human proteins containing this domain[edit]

GRIA1; GRIA2; GRIA3; GRIA4; GRID1; GRID2; GRIK1; GRIK2; GRIK3; GRIK4; GRIK5; GRIN1; GRIN2A; GRIN2B; GRIN2C; GRIN2D; GRIN3A; GRIN3B; NR2A;

References[edit]

  1. ^ Bortolotto ZA, Clarke VR, Delany CM, Parry MC, Smolders I, Vignes M, Ho KH, Miu P, Brinton BT, Fantaske R, Ogden A, Gates M, Ornstein PL, Lodge D, Bleakman D, Collingridge GL (November 1999). "Kainate receptors are involved in synaptic plasticity". Nature 402 (6759): 297–301. doi:10.1038/46290. PMID 10580501. 

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


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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

The ability of synapses to modify their synaptic strength in response to activity is a fundamental property of the nervous system and may be an essential component of learning and memory. There are three classes of ionotropic glutamate receptor, 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

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 contains the following 8 members:

GLTSCR1 Ion_trans Ion_trans_2 IRK KdpA Lig_chan PKD_channel TrkH

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(44)
Full
(3260)
Representative proteomes NCBI
(3242)
Meta
(57)
RP15
(597)
RP35
(867)
RP55
(1417)
RP75
(1868)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(44)
Full
(3260)
Representative proteomes NCBI
(3242)
Meta
(57)
RP15
(597)
RP35
(867)
RP55
(1417)
RP75
(1868)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(44)
Full
(3260)
Representative proteomes NCBI
(3242)
Meta
(57)
RP15
(597)
RP35
(867)
RP55
(1417)
RP75
(1868)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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.

Note: You can also download the data file for the tree.

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: 44
Number in full: 3260
Average length of the domain: 253.80 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 33.83 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.8 24.8
Trusted cut-off 24.8 24.8
Noise cut-off 24.7 24.7
Model length: 148
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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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 465 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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