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1387  structures 959  species 0  interactions 21543  sequences 330  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

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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

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 ].

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 ].

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 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 8 members:

Ion_trans Ion_trans_2 IRK KdpA Lig_chan PKD_channel Polycystin_dom 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(43)
Full
(21543)
Representative proteomes UniProt
(35057)
RP15
(3969)
RP35
(8883)
RP55
(17337)
RP75
(22711)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(43)
Full
(21543)
Representative proteomes UniProt
(35057)
RP15
(3969)
RP35
(8883)
RP55
(17337)
RP75
(22711)
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
(43)
Full
(21543)
Representative proteomes UniProt
(35057)
RP15
(3969)
RP35
(8883)
RP55
(17337)
RP75
(22711)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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
Sequence Ontology: SO:0100021
Author: Bateman A , Sonnhammer ELL
Number in seed: 43
Number in full: 21543
Average length of the domain: 256.9 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 30.91 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.8 30.8
Trusted cut-off 30.8 30.8
Noise cut-off 30.7 30.7
Model length: 149
Family (HMM) version: 29
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 1387 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044V431 View 3D Structure Click here
A0A044V9U4 View 3D Structure Click here
A0A077YYX9 View 3D Structure Click here
A0A077YZQ7 View 3D Structure Click here
A0A077Z3Y6 View 3D Structure Click here
A0A077Z8K1 View 3D Structure Click here
A0A077ZBF2 View 3D Structure Click here
A0A077ZBW1 View 3D Structure Click here
A0A0B4KHJ0 View 3D Structure Click here
A0A0K0DSZ2 View 3D Structure Click here
A0A0K0DV37 View 3D Structure Click here
A0A0K0DZ37 View 3D Structure Click here
A0A0K0E5S7 View 3D Structure Click here
A0A0K0EE00 View 3D Structure Click here
A0A0K0EH70 View 3D Structure Click here
A0A0K0J2U4 View 3D Structure Click here
A0A0N4U170 View 3D Structure Click here
A0A0N4U761 View 3D Structure Click here
A0A0N4UCU6 View 3D Structure Click here
A0A0N4ULM6 View 3D Structure Click here
A0A0N4UQF3 View 3D Structure Click here
A0A0N7KLP1 View 3D Structure Click here
A0A0P0WTE6 View 3D Structure Click here
A0A0P0WU14 View 3D Structure Click here
A0A0P0XLY5 View 3D Structure Click here
A0A0P0XNE5 View 3D Structure Click here
A0A0R0FUT0 View 3D Structure Click here
A0A0R0FUX9 View 3D Structure Click here
A0A0R0GJI9 View 3D Structure Click here
A0A0R0GSR6 View 3D Structure Click here
A0A0R0H0I1 View 3D Structure Click here
A0A0R0IAP1 View 3D Structure Click here
A0A0R0JFH4 View 3D Structure Click here
A0A0R0JKV3 View 3D Structure Click here
A0A0R0JSN9 View 3D Structure Click here
A0A0R0JT57 View 3D Structure Click here
A0A0R4ID43 View 3D Structure Click here
A0A0R4IG83 View 3D Structure Click here
A0A0R4ING5 View 3D Structure Click here
A0A158Q3R3 View 3D Structure Click here