Summary: ATP P2X receptor
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 "P2X purinoreceptor". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
P2X purinoreceptor Edit Wikipedia article
|ATP P2X receptor|
The ATP-gated P2X Receptor Cation Channel (P2X Receptor) Family (TC# 1.A.7) consists of cation-permeable ligand gated ion channels that open in response to the binding of extracellular adenosine 5'-triphosphate (ATP). They belong to a larger family of receptors known as the ENaC/P2X superfamily. ENaC and P2X receptors have similar 3-D structures and are homologous. P2X receptors are present in a diverse array of organisms including humans, mouse, rat, rabbit, chicken, zebrafish, bullfrog[disambiguation needed], fluke, and amoeba.
- Modulation of cardiac rhythm and contractility
- Modulation of vascular tone
- Mediation of nociception, especially chronic pain 
- Contraction of the vas deferens during ejaculation
- Contraction of the urinary bladder during micturition 
- Platelet aggregation
- Macrophage activation
- Neuronal-glial integration
P2X receptors are expressed in cells from a wide variety of animal tissues. On presynaptic and postsynaptic nerve terminals and glial cells throughout the central, peripheral and autonomic nervous systems, P2X receptors have been shown to modulate synaptic transmission. Furthermore, P2X receptors are able to initiate contraction in cells of the heart muscle, skeletal muscle, and various smooth muscle tissues, including that of the vasculature, vas deferens and urinary bladder. P2X receptors are also expressed on leukocytes, including lymphocytes and macrophages, and are present on blood platelets. There is some degree of subtype specificity as to which P2X receptor subtypes are expressed on specific cell types, with P2X1 receptors being particularly prominent in smooth muscle cells, and P2X2 being widespread throughout the autonomic nervous system. However, such trends are very general and there is considerable overlap in subunit distribution, with most cell types expressing more than one subunits. For example, P2X2 and P2X3 subunits are commonly found co-expressed in sensory neurons, where they often co-assemble into functional P2X2/3 receptors.
Basic structure and nomenclature
|receptor subtype||HUGO gene name||chromosomal location|
The proteins of the P2X receptors are quite similar in sequence (>35% identity), but they possess 380-1000 amino acyl residues per subunit with variability in length. The subunits all share a common topology, possessing two transmembrane domains (one about 30-50 residues from their N-termini, the other near residues 320-340), a large extracellular loop and intracellular carboxyl and amino termini (Figure 1) The extracellular receptor domains between these two segments (of about 270 residues) are well conserved with several conserved glycyl residues and 10 conserved cysteyl residues. The amino termini contain a consensus site for protein kinase C phosphorylation, indicating that the phosphorylation state of P2X subunits may be involved in receptor functioning. Additionally, there is a great deal of variability (25 to 240 residues) in the C termini, indicating that they might serve subunit specific properties.
Generally speaking, most subunits can form functional homomeric or heteromeric receptors. Receptor nomenclature dictates that naming is determined by the constituent subunits; e.g. a homomeric P2X receptor made up of only P2X1 subunits is called a P2X1 receptor, and a heteromeric receptor containing P2X2 and P2X3 subunits is called a P2X2/3 receptor. The general consensus is that P2X6 cannot form a functional homomeric receptor and that P2X7 cannot form a functional heteromeric receptor.
Topologically, they resemble the epithelial Na+ channel proteins in possessing (a) N- and C-termini localized intracellularly, (b) two putative transmembrane segments, (c) a large extracellular loop domain, and (d) many conserved extracellular cysteyl residues. P2X receptor channels transport small monovalent cations, although some also transport Ca2+.
Evidence from early molecular biological and functional studies has strongly indicated that the functional P2X receptor protein is a trimer, with the three peptide subunits arranged around an ion-permeable channel pore. This view was recently confirmed by the use of X-ray crystallography to resolve the three-dimensional structure of the zebrafish P2X4 receptor(Figure 2). These findings indicate that the second transmembrane domain of each subunit lines the ion-conducting pore and is therefore responsible for channel gating.
The relationship between the structure and function of P2X receptors has been the subject of considerable research, and key protein domains responsible for regulating ATP binding, ion permeation, pore dilation and desensitization have been identified.
Activation and channel opening
Three ATP molecules are thought to be required to activate a P2X receptor, suggesting that ATP needs to bind to each of the three subunits in order to open the channel pore, though recent evidence suggests that ATP binds at the three subunit interfaces. Once ATP binds to the extracellular loop of the P2X receptor, it evokes a conformational change in the structure of the ion channel that results in the opening of the ion-permeable pore. The most commonly accepted theory of channel opening involves the rotation and separation of the second transmembrane domain (TM) helices, allowing cations such as Na+ and Ca2+ to access the ion-conducting pore through three lateral fenestrations above the TM domains. The entry of cations leads to the depolarization of the cell membrane and the activation of various Ca2+-sensitive intracellular processes. The channel opening time is dependent upon the subunit makeup of the receptor. For example, P2X1 and P2X3 receptors desensitize rapidly (a few hundred milliseconds) in the continued presence of ATP, whereas the P2X2 receptor channel remains open for as long as ATP is bound to it.
The generalized transport reaction is:
- Monovalent cations or Ca2+ (out) ⇌ monovalent cations or Ca2+ (in)
The pharmacology of a given P2X receptor is largely determined by its subunit makeup. Different subunits exhibit different sensitivities to purinergic agonists such as ATP, α,β-meATP and BzATP; and antagonists such as pyridoxalphosphate-6-azophenyl-2',4'-disulphonic acid (PPADS) and suramin. Of continuing interest is the fact that some P2X receptors (P2X2, P2X4, human P2X5, and P2X7) exhibit multiple open states in response to ATP, characterized by a time-dependent increase in the permeabilities of large organic ions such as N-methyl-D-glucamine (NMDG+) and nucleotide binding dyes such as propidium iodide (YO-PRO-1). Whether this change in permeability is due to a widening of the P2X receptor channel pore itself or the opening of a separate ion-permeable pore is the subject of continued investigation.
Synthesis and trafficking
P2X receptors are synthesized in the rough endoplasmic reticulum. After complex glycosylation in the Golgi apparatus, they are transported to the plasma membrane, whereby docking is achieved through specific members of the SNARE protein family. A YXXXK motif in the C terminus is common to all P2X subunits and seems to be important for trafficking and stabilization of P2X receptors in the membrane. Removal of P2X receptors occurs via clathrin-mediated endocytosis of receptors to endosomes where they are sorted into vesicles for degradation or recycling.
The sensitivity of P2X receptors to ATP is strongly modulated by changes in extracellular pH and by the presence of heavy metals (e.g. zinc and cadmium). For example, the ATP sensitivity of P2X1, P2X3 and P2X4 receptors is attenuated when the extracellular pH<7, whereas the ATP sensitivity of P2X2 is significantly increased. On the other hand, zinc potentiates ATP-gated currents through P2X2, P2X3 and P2X4, and inhibits currents through P2X1. The allosteric modulation of P2X receptors by pH and metals appears to be conferred by the presence of histidine side chains in the extracellular domain. In contrast to the other members of the P2X receptor family, P2X4 receptors are also very sensitive to modulation by the macrocyclic lactone, ivermectin. Ivermectin potentiates ATP-gated currents through P2X4 receptors by increasing the open probability of the channel in the presence of ATP, which it appears to do by interacting with the transmembrane domains from within the lipid bilayer.
- P2RX1 InterPro: IPR003044
- P2RX2 InterPro: IPR003045
- P2RX3 InterPro: IPR003046
- P2RX4 InterPro: IPR003047
- P2RX5 InterPro: IPR003048
- P2RX6 InterPro: IPR003049
- P2RX7 InterPro: IPR003050
Human proteins containing this domain
- North RA (2002). "Molecular physiology of P2X receptors". Physiological reviews. 82 (4): 1013–1067. doi:10.1152/physrev.00015.2002. PMID 12270951.
- Khakh BS, North RA (2006). "P2X receptors as cell-surface ATP sensors in health and disease". Nature. 442 (7102): 527–32. doi:10.1038/nature04886. PMID 16885977.
- Vassort G (2001). "Adenosine 5'-triphosphate: a P2-purinergic agonist in the myocardium". Physiol. Rev. 81 (2): 767–806. PMID 11274344.
- Chizh BA, Illes P (2001). "P2X receptors and nociception". Pharmacol. Rev. 53 (4): 553–68. PMID 11734618.
- Fowler CJ, Griffiths D, de Groat WC (2008). "The neural control of micturition". Nat Rev Neurosci. 9 (6): 453–466. doi:10.1038/nrn2401. PMC . PMID 18490916.
- Gachet C (2006). "Regulation of Platelet Functions by P2 Receptors". Annual Review of Pharmacology and Toxicology. 46: 277–300. doi:10.1146/annurev.pharmtox.46.120604.141207. PMID 16402906.
- Wewers MD, Sarkar A (2009). "P2X7 receptor and macrophage function". Purinergic Signalling. 5 (2): 189–195. doi:10.1007/s11302-009-9131-9. PMC . PMID 19214778.
- Kawano A, Tsukimoto M, Noguchi T, Hotta N, Harada H, Takenouchi T, Kitani H, Kojima S (2012). "Involvement of P2X4 receptor in P2X7 receptor-dependent cell death of mouse macrophages". Biochemical and Biophysical Research Communications. 419 (2): 374–380. doi:10.1016/j.bbrc.2012.01.156. PMID 22349510.
- Burnstock G (2013). "Introduction to Purinergic Signalling in the Brain". Advances in Experimental Medicine and Biology. 986: 1–12. doi:10.1007/978-94-007-4719-7_1. ISBN 978-94-007-4718-0. PMID 22879061.
- Burnstock G (2000). "P2X receptors in sensory neurones". Br J Anaesth. 84 (4): 476–88. doi:10.1093/oxfordjournals.bja.a013473. PMID 10823099.
- Gever JR, Cockayne DA, Dillon MP, Burnstock G, Ford AP (2006). "Pharmacology of P2X channels". Pflugers Arch. 452 (5): 513–37. doi:10.1007/s00424-006-0070-9. PMID 16649055.
- Boué-Grabot E, Archambault V, Séguéla P (2000). "A protein kinase C site highly conserved in P2X subunits controls the desensitization kinetics of P2X(2) ATP-gated channels". The Journal of Biological Chemistry. 275 (14): 10190–10195. doi:10.1074/jbc.275.14.10190. PMID 10744703.
- Surprenant A, North RA (2009). "Signaling at Purinergic P2X Receptors". Annual Review of Physiology. 71: 333–359. doi:10.1146/annurev.physiol.70.113006.100630. PMID 18851707.
- Kaczmarek-Hájek K, Lörinczi E, Hausmann R, Nicke A (2012). "Molecular and functional properties of P2X receptors—recent progress and persisting challenges". Purinergic Signalling. 8 (3): 375–417. doi:10.1007/s11302-012-9314-7. PMC . PMID 22547202.
- Barrera NP, Ormond SJ, Henderson RM, Murrell-Lagnado RD, Edwardson JM (2005). "Atomic Force Microscopy Imaging Demonstrates that P2X2 Receptors Are Trimers but That P2X6 Receptor Subunits Do Not Oligomerize". Journal of Biological Chemistry. 280 (11): 10759–10765. doi:10.1074/jbc.M412265200. PMID 15657042.
- Torres GE, Egan TM, Voigt MM (1999). "Hetero-oligomeric assembly of P2X receptor subunits. Specificities exist with regard to possible partners". The Journal of Biological Chemistry. 274 (10): 6653–6659. doi:10.1074/jbc.274.10.6653. PMID 10037762.
- US Lapsed 6498022, Yale University School Of Medicine, "Isolated nucleic acid molecules encoding human carbonate transporter proteins, and uses thereof", assigned to Applera Corporation, Connecticut This article incorporates text from this source, which is in the public domain.
- Nicke A, Bäumert HG, Rettinger J, Eichele A, Lambrecht G, Mutschler E, Schmalzing G (1998). "P2X1 and P2X3 receptors form stable trimers: a novel structural motif of ligand-gated ion channels". EMBO J. 17 (11): 3016–28. doi:10.1093/emboj/17.11.3016. PMC . PMID 9606184.
- Kawate T, Michel JC, Birdsong WT, Gouaux E (2009). "Crystal structure of the ATP-gated P2X4 ion channel in the closed state". Nature. 460 (7255): 592–598. doi:10.1038/nature08198. PMC . PMID 19641588.
- Migita K, Haines WR, Voigt MM, Egan TM (2001). "Polar Residues of the Second Transmembrane Domain Influence Cation Permeability of the ATP-gated P2X2 Receptor". Journal of Biological Chemistry. 276 (33): 30934–30941. doi:10.1074/jbc.M103366200. PMID 11402044.
- Egan TM, Samways DS, Li Z (2006). "Biophysics of P2X receptors". Pflugers Arch. 452 (5): 501–12. doi:10.1007/s00424-006-0078-1. PMID 16708237.
- Roberts JA, Vial C, Digby HR, Agboh KC, Wen H, Atterbury-Thomas A, Evans RJ (2006). "Molecular properties of P2X receptors". Pflugers Arch. 452 (5): 486–500. doi:10.1007/s00424-006-0073-6. PMID 16607539.
- Evans RJ (2008). "Orthosteric and allosteric binding sites of P2X receptors". Eur. Biophys. J. 38 (3): 319–27. doi:10.1007/s00249-008-0275-2. PMID 18247022.
- Ding S, Sachs F (1999). "Single channel properties of P2X2 purinoceptors". The Journal of General Physiology. 113 (5): 695–720. doi:10.1085/jgp.113.5.695. PMC . PMID 10228183.
- Cao L, Broomhead HE, Young MT, North RA (2009). "Polar Residues in the Second Transmembrane Domain of the Rat P2X2 Receptor That Affect Spontaneous Gating, Unitary Conductance, and Rectification". Journal of Neuroscience. 29 (45): 14257–14264. doi:10.1523/JNEUROSCI.4403-09.2009. PMC . PMID 19906973.
- Kawate T, Robertson JL, Li M, Silberberg SD, Swartz KJ (2011). "Ion access pathway to the transmembrane pore in P2X receptor channels". The Journal of General Physiology. 137 (6): 579–590. doi:10.1085/jgp.201010593. PMC . PMID 21624948.
- Shigetomi E, Kato F (2004). "Action Potential-Independent Release of Glutamate by Ca2+ Entry through Presynaptic P2X Receptors Elicits Postsynaptic Firing in the Brainstem Autonomic Network". Journal of Neuroscience. 24 (12): 3125–3135. doi:10.1523/JNEUROSCI.0090-04.2004. PMID 15044552.
- Koshimizu TA, Van Goor F, Tomić M, Wong AO, Tanoue A, Tsujimoto G, Stojilkovic SS (2000). "Characterization of calcium signaling by purinergic receptor-channels expressed in excitable cells". Molecular Pharmacology. 58 (5): 936–945. PMID 11040040.
- Chaumont S, Jiang LH, Penna A, North RA, Rassendren F (2004). "Identification of a Trafficking Motif Involved in the Stabilization and Polarization of P2X Receptors". Journal of Biological Chemistry. 279 (28): 29628–29638. doi:10.1074/jbc.M403940200. PMID 15126501.
- Royle SJ, Bobanović LK, Murrell-Lagnado RD (2002). "Identification of a Non-canonical Tyrosine-based Endocytic Motif in an Ionotropic Receptor". Journal of Biological Chemistry. 277 (38): 35378–35385. doi:10.1074/jbc.M204844200. PMID 12105201.
- Khakh BS, Proctor WR, Dunwiddie TV, Labarca C, Lester HA (1999). "Allosteric control of gating and kinetics at P2X(4) receptor channels". J. Neurosci. 19 (17): 7289–99. PMID 10460235.
- Priel A, Silberberg SD (2004). "Mechanism of ivermectin facilitation of human P2X4 receptor channels". J. Gen. Physiol. 123 (3): 281–93. doi:10.1085/jgp.200308986. PMC . PMID 14769846.
- Ivar von Kügelgen: Pharmacology of mammalian P2X- and P2Y-receptors, BIOTREND Reviews No. 03, September 2008,© 2008 BIOTREND Chemicals AG
- Ligand-gated ion channel Database (European Bioinformatics Institute)
As of this edit, this article uses content from "1.A.7 ATP-gated P2X Receptor Cation Channel (P2X Receptor) Family", which is licensed in a way that permits reuse under the Creative Commons Attribution-ShareAlike 3.0 Unported License, but not under the GFDL. All relevant terms must be followed.
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.
ATP P2X receptor Provide feedback
No Pfam abstract.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001429
P2X purinoceptors are cell membrane ion channels, gated by adenosine 5'-triphosphate (ATP) and other nucleotides; they have been found to be widely expressed on mammalian cells, and, by means of their functional properties, can be differentiated into three sub-groups. The first group is almost equally well activated by ATP and its analogue alpha,betamethylene-ATP, whereas, the second group is not activated by the latter compound. A third type of receptor (also called P2Z) is distinguished by the fact that repeated or prolonged agonist application leads to the opening of much larger pores, allowing large molecules to traverse the cell membrane. This increased permeability rapidly leads to cell death, and lysis.
Molecular cloning studies have identified seven P2X receptor subtypes, designated P2X1-P2X7. These receptors are proteins that share 35-48% amino acid identity, and possess two putative transmembrane (TM) domains, separated by a long (~270 residues) intervening sequence, which is thought to form an extracellular loop. Around 1/4 of the residues within the loop are invariant between the cloned subtypes, including 10 characteristic cysteines.
Studies of the functional properties of heterologously expressed P2X receptors, together with the examination of their distribution in native tissues, suggests they likely occur as both homo- and heteromultimers in vivo [PUBMED:10414359, PUBMED:12270951].
This entry represents all P2X purinoreceptor subtypes.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||integral component of plasma membrane (GO:0005887)|
|Molecular function||extracellular ATP-gated cation channel activity (GO:0004931)|
|purinergic nucleotide receptor activity (GO:0001614)|
|Biological process||response to ATP (GO:0033198)|
|cation transmembrane transport (GO:0098655)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
If you find these logos useful in your own work, please consider citing the following article:
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.
|Seed source:||Pfam-B_1590 (release 2.1)|
|Number in seed:||72|
|Number in full:||1045|
|Average length of the domain:||268.40 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||81.89 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 P2X_receptor domain has been found. There are 24 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.
Loading structure mapping...