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1295  structures 872  species 0  interactions 17215  sequences 316  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
SymbolLig_chan
PfamPF00060
Pfam clanCL0030
InterProIPR001320
SCOPe1gr2 / SUPFAM
TCDB1.A.10
OPM superfamily177
OPM protein3kg2

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. PMC 2964903. PMID 20716669.
  2. ^ Collingridge GL, 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. PMC 2847504. PMID 18655795.
  3. ^ Bliss TV, 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 A, 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. PMC 2964903. PMID 20716669.
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

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 7 members:

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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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
(17215)
Representative proteomes UniProt
(31328)
RP15
(3298)
RP35
(7948)
RP55
(15395)
RP75
(20068)
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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
(17215)
Representative proteomes UniProt
(31328)
RP15
(3298)
RP35
(7948)
RP55
(15395)
RP75
(20068)
Alignment:
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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
(17215)
Representative proteomes UniProt
(31328)
RP15
(3298)
RP35
(7948)
RP55
(15395)
RP75
(20068)
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: 17215
Average length of the domain: 254.70 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 31.15 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -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: 28
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 1295 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
A0A0B4KHJ0 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
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
A0A1D6E1R2 View 3D Structure Click here
A0A1D6EQP7 View 3D Structure Click here
A0A1D6EQP9 View 3D Structure Click here
A0A1D6EXB6 View 3D Structure Click here
A0A1D6GTI6 View 3D Structure Click here
A0A1D6GTI9 View 3D Structure Click here
A0A1D6GTJ2 View 3D Structure Click here
A0A1D6GYP5 View 3D Structure Click here
A0A1D6HMT5 View 3D Structure Click here
A0A1D6HMU4 View 3D Structure Click here
A0A1D6HQP8 View 3D Structure Click here
A0A1D6HQP9 View 3D Structure Click here
A0A1D6I4R9 View 3D Structure Click here
A0A1D6I4S0 View 3D Structure Click here
A0A1D6QCK5 View 3D Structure Click here
A0A1T5HUM0 View 3D Structure Click here
A0A286Y9Q6 View 3D Structure Click here
A0A286YAM5 View 3D Structure Click here
A0A286YAY2 View 3D Structure Click here
A0A2R8PY76 View 3D Structure Click here
A0A2R8Q9Y5 View 3D Structure Click here
A0A2R8QDR4 View 3D Structure Click here
A0A2R8QF68 View 3D Structure Click here
A0A2R8QFE5 View 3D Structure Click here
A0A2R8QLP2 View 3D Structure Click here
A0A3B1E9Z6 View 3D Structure Click here
A2AIR5 View 3D Structure Click here
A2BH14 View 3D Structure Click here
A2CG69 View 3D Structure Click here
B1AS29 View 3D Structure Click here
B3DGS8 View 3D Structure Click here
B7Z069 View 3D Structure Click here
B8JLR6 View 3D Structure Click here
B9G3Q7 View 3D Structure Click here
E7F101 View 3D Structure Click here
E7F1P4 View 3D Structure Click here
E7F1V8 View 3D Structure Click here
E7F3Z4 View 3D Structure Click here
E7F5R2 View 3D Structure Click here
E7F902 View 3D Structure Click here
E7FEG9 View 3D Structure Click here
E7FGL8 View 3D Structure Click here
E7FH62 View 3D Structure Click here
E9NA96 View 3D Structure Click here
E9QGN5 View 3D Structure Click here
F1QA08 View 3D Structure Click here
F1QDE5 View 3D Structure Click here
F1QS78 View 3D Structure Click here
F1R276 View 3D Structure Click here
F6P6I2 View 3D Structure Click here
G5EEH3 View 3D Structure Click here
G5EGQ9 View 3D Structure Click here
I1J8B7 View 3D Structure Click here
I1JST3 View 3D Structure Click here
I1K7B0 View 3D Structure Click here
I1KDN7 View 3D Structure Click here
I1KFC6 View 3D Structure Click here
I1KMD9 View 3D Structure Click here
I1L4P7 View 3D Structure Click here
I1LU56 View 3D Structure Click here
I1LU57 View 3D Structure Click here
I1M440 View 3D Structure Click here
I1M634 View 3D Structure Click here
I1MMT0 View 3D Structure Click here
I3NI77 View 3D Structure Click here
K7KBT8 View 3D Structure Click here
K7L2U8 View 3D Structure Click here
K7LEX1 View 3D Structure Click here
K7LNQ4 View 3D Structure Click here
K7LTZ4 View 3D Structure Click here
K7LWX1 View 3D Structure Click here
K7M0A1 View 3D Structure Click here
K7M1F5 View 3D Structure Click here
K7M291 View 3D Structure Click here
K7M2W3 View 3D Structure Click here
K7MFG6 View 3D Structure Click here
K7MK91 View 3D Structure Click here
K7MNP8 View 3D Structure Click here
K7UT49 View 3D Structure Click here
M9PCT4 View 3D Structure Click here
O01623 View 3D Structure Click here
O04660 View 3D Structure Click here
O15399 View 3D Structure Click here
O43424 View 3D Structure Click here
O60391 View 3D Structure Click here
O81078 View 3D Structure Click here
O81776 View 3D Structure Click here
P19490 View 3D Structure Click here
P19491 View 3D Structure Click here
P19492 View 3D Structure Click here
P19493 View 3D Structure Click here
P22756 View 3D Structure Click here
P23818 View 3D Structure Click here
P23819 View 3D Structure Click here
P34299 View 3D Structure Click here
P35436 View 3D Structure Click here
P35438 View 3D Structure Click here
P35439 View 3D Structure Click here
P39086 View 3D Structure Click here
P39087 View 3D Structure Click here
P42260 View 3D Structure Click here
P42261 View 3D Structure Click here
P42262 View 3D Structure Click here
P42263 View 3D Structure Click here
P42264 View 3D Structure Click here
P48058 View 3D Structure Click here
Q00959 View 3D Structure Click here
Q00960 View 3D Structure Click here
Q00961 View 3D Structure Click here
Q01097 View 3D Structure Click here
Q01098 View 3D Structure Click here
Q01812 View 3D Structure Click here
Q03391 View 3D Structure Click here
Q03445 View 3D Structure Click here
Q05586 View 3D Structure Click here
Q0D972 View 3D Structure Click here
Q0DA37 View 3D Structure Click here
Q0E8N6 View 3D Structure Click here
Q0KI42 View 3D Structure Click here
Q0KIF2 View 3D Structure Click here
Q10914 View 3D Structure Click here
Q12879 View 3D Structure Click here
Q13002 View 3D Structure Click here
Q13003 View 3D Structure Click here
Q13224 View 3D Structure Click here
Q14957 View 3D Structure Click here
Q16099 View 3D Structure Click here
Q16478 View 3D Structure Click here
Q17697 View 3D Structure Click here
Q21415 View 3D Structure Click here
Q24418 View 3D Structure Click here
Q60934 View 3D Structure Click here
Q61625 View 3D Structure Click here
Q61626 View 3D Structure Click here
Q61627 View 3D Structure Click here
Q62640 View 3D Structure Click here
Q62645 View 3D Structure Click here
Q63226 View 3D Structure Click here
Q63273 View 3D Structure Click here
Q68Y21 View 3D Structure Click here
Q69KK7 View 3D Structure Click here
Q69KL0 View 3D Structure Click here
Q69KL2 View 3D Structure Click here
Q69L07 View 3D Structure Click here
Q69L11 View 3D Structure Click here
Q69NA4 View 3D Structure Click here
Q69NA5 View 3D Structure Click here
Q6K4P7 View 3D Structure Click here
Q6ZGL7 View 3D Structure Click here
Q6ZM67 View 3D Structure Click here
Q7XJL2 View 3D Structure Click here
Q7XP59 View 3D Structure Click here
Q84W41 View 3D Structure Click here
Q8BMF5 View 3D Structure Click here
Q8GXJ4 View 3D Structure Click here
Q8LGN0 View 3D Structure Click here
Q8LGN1 View 3D Structure Click here
Q8MXV8 View 3D Structure Click here
Q8TCU5 View 3D Structure Click here
Q8VHN2 View 3D Structure Click here
Q91ZU9 View 3D Structure Click here
Q93YT1 View 3D Structure Click here
Q9C5V5 View 3D Structure Click here
Q9C8E7 View 3D Structure Click here
Q9FH75 View 3D Structure Click here
Q9LFN5 View 3D Structure Click here
Q9LFN8 View 3D Structure Click here
Q9LV72 View 3D Structure Click here
Q9M8W7 View 3D Structure Click here
Q9R1M7 View 3D Structure Click here
Q9SDQ4 View 3D Structure Click here
Q9SHV1 View 3D Structure Click here
Q9SHV2 View 3D Structure Click here
Q9SW97 View 3D Structure Click here
Q9TVI0 View 3D Structure Click here
Q9ULK0 View 3D Structure Click here
Q9V4A0 View 3D Structure Click here
Q9V9N1 View 3D Structure Click here
Q9VDH5 View 3D Structure Click here
Q9VDH6 View 3D Structure Click here
Q9VDN3 View 3D Structure Click here
Q9VMP3 View 3D Structure Click here
Q9VMP4 View 3D Structure Click here
Q9VPI2 View 3D Structure Click here
Q9VPV3 View 3D Structure Click here
Q9VRL4 View 3D Structure Click here
Q9VTH3 View 3D Structure Click here
Q9VVL1 View 3D Structure Click here
Q9VVL2 View 3D Structure Click here
Q9VVU7 View 3D Structure Click here
Q9VW78 View 3D Structure Click here
Q9W365 View 3D Structure Click here
Q9W3P2 View 3D Structure Click here
Q9W581 View 3D Structure Click here
Q9Z2W8 View 3D Structure Click here
Q9Z2W9 View 3D Structure Click here
R4GDN8 View 3D Structure Click here
X1WH07 View 3D Structure Click here