Summary: Ion transport protein
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Ion channel family Edit Wikipedia article
|Ion channel (eukaryotic)|
Potassium channel Kv1.2 (with beta2 auxiliary subunits), structure in a membrane-like environment. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
|Ion channel (bacterial)|
Potassium channel KcsA. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
Transmembrane cation channel superfamily was defined in InterPro and Pfam as the family of tetrameric ion channels. These include the sodium, potassium, calcium, ryanodine receptor, HCN, CNG, CatSper, and TRP channels. This large group of ion channels apparently includes families 1.A.1, 1.A.2, 1.A.3, and 1.A.4 of the TCDB transporter classification.
They are described as minimally having two transmembrane helices flanking a loop which determines the ion selectivity of the channel pore. Many eukaryotic channels have four additional transmembrane helices (TM) (Pfam PF00520), related to or vestigial of voltage gating. The proteins with only two transmembrane helices (Pfam PF07885) are most commonly found in bacteria. This also includes the 2-TM Inward-rectifier potassium channels (Pfam PF01007) found primarily in eukaryotes. There are commonly additional regulatory domains which serve to regulate ion conduction and channel gating. The pores may also be homotetramers or hetrotetramers; where hetrotetramers may be encoded as distinct genes or as multiple pore domains within a single polypepetide. Interestingly, the HVCN1 and Putative tyrosine-protein phosphatase proteins do not contain an expected ion conduction pore domain, but rather have homology only to the voltage sensor domain of voltage gated ion channels.
- 1 Human channels with 6 TM helices
- 1.1 Cation
- 1.2 Calcium
- 1.3 Potassium
- 1.3.1 Voltage-gated potassium channels
- 1.3.2 Calcium-activated potassium channel
- 1.3.3 Inward-rectifier potassium ion channel
- 1.4 Sodium
- 1.5 Cyclic nucleotide-gated
- 1.6 Proton
- 1.7 Related Proteins
- 2 Human channels with 2 TM helices in each subunit
- 3 Non-human Channels
- 3.1 Two-pore channels
- 3.2 Pore-only Potassium Channels
- 3.3 Ligand Gated Potassium Channel
- 3.4 Voltage-gated Potassium Channels
- 3.5 Prokaryotic KCa Channels
- 3.6 Voltage and Cyclic Nucleotide Gated Potassium Channel
- 3.7 Sodium Channels
- 3.8 Non-Selective Channels
- 3.9 Prokaryotic Inward-rectifier potassium channels
- 3.10 Engineered Channels
- 4 References
- 5 External links
Human channels with 6 TM helices
- Kvα1.x - Shaker-related: Kv1.1 (KCNA1), Kv1.2 (KCNA2), Kv1.3 (KCNA3), Kv1.5 (KCNA5), Kv1.6 (KCNA6), Kv1.7 (KCNA7), Kv1.8 (KCNA10)
- Kvα2.x - Shab-related: Kv2.1 (KCNB1), Kv2.2 (KCNB2)
- Kvα3.x - Shaw-related: Kv3.1 (KCNC1), Kv3.2 (KCNC2)
- Kvα7.x: Kv7.1 (KCNQ1) - KvLQT1, Kv7.2 (KCNQ2), Kv7.3 (KCNQ3), Kv7.4 (KCNQ4), Kv7.5 (KCNQ5)
- Kvα10.x: Kv10.1 (KCNH1)
A-type potassium channel
- Kvα1.x - Shaker-related: Kv1.4 (KCNA4)
- Kvα3.x - Shaw-related: Kv3.3 (KCNC3), Kv3.4 (KCNC4)
- Kvα4.x - Shal-related: Kv4.1 (KCND1), Kv4.2 (KCND2), Kv4.3 (KCND3)
- Kvα10.x: Kv10.2 (KCNH5)
- Kvα5.x: Kv5.1 (KCNF1)
- Kvα6.x: Kv6.1 (KCNG1), Kv6.2 (KCNG2), Kv6.3 (KCNG3), Kv6.4 (KCNG4)
- Kvα8.x: Kv8.1 (KCNV1), Kv8.2 (KCNV2)
- Kvα9.x: Kv9.1 (KCNS1), Kv9.2 (KCNS2), Kv9.3 (KCNS3)
- KCa2.x: KCa2.1 (KCNN1) - SK1, KCa2.2 (KCNN2) - SK2, KCa2.3 (KCNN3) - SK3
- KCa3.x: KCa3.1 (KCNN4) - SK4
- KCa4.x: KCa4.1 (KCNT1) - SLACK, KCa4.2 (KCNT2) - SLICK
- SCN1A; SCN2A; SCN2A2; SCN3A; SCN4A; SCN5A; SCN7A; SCN8A; SCN9A; SCN10A; SCN11A
- SLC9A10; SLC9A11
Human channels with 2 TM helices in each subunit
- KCNK1; KCNK2; KCNK3; KCNK4; KCNK5; KCNK6; KCNK7; KCNK9; KCNK10; KCNK12; KCNK13; KCNK15; KCNK16; KCNK17; KCNK18
Ligand Gated Potassium Channel
Voltage and Cyclic Nucleotide Gated Potassium Channel
Prokaryotic Inward-rectifier potassium channels
- Choe S (February 2002). "Potassium channel structures". Nat. Rev. Neurosci. 3 (2): 115–21. doi:10.1038/nrn727. PMID 11836519.
- Chen, GQ; Cui, C; Mayer, ML; Gouaux, E (16 December 1999). "Functional characterization of a potassium-selective prokaryotic glutamate receptor.". Nature. 402 (6763): 817–21. doi:10.1038/45568. PMID 10617203.
- Jiang, Y; Lee, A; Chen, J; Ruta, V; Cadene, M; Chait, BT; MacKinnon, R (1 May 2003). "X-ray structure of a voltage-dependent K+ channel.". Nature. 423 (6935): 33–41. doi:10.1038/nature01580. PMID 12721618.
- Milkman R (Apr 1994). "An Escherichia coli homologue of eukaryotic potassium channel proteins". Proceedings of the National Academy of Sciences of the United States of America. 91 (9): 3510–4. doi:10.1073/pnas.91.9.3510. PMC . PMID 8170937.
- Jiang Y, Pico A, Cadene M, Chait BT, MacKinnon R (Mar 2001). "Structure of the RCK domain from the E. coli K+ channel and demonstration of its presence in the human BK channel". Neuron. 29 (3): 593–601. doi:10.1016/s0896-6273(01)00236-7. PMID 11301020.
- Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R (May 2002). "Crystal structure and mechanism of a calcium-gated potassium channel". Nature. 417 (6888): 515–22. Bibcode:2002Natur.417..515J. doi:10.1038/417515a. PMID 12037559.
- Smith FJ, Pau VP, Cingolani G, Rothberg BS (2013). "Structural basis of allosteric interactions among Ca2+-binding sites in a K+ channel RCK domain". Nature Communications. 4: 2621. Bibcode:2013NatCo...4E2621S. doi:10.1038/ncomms3621. PMID 24126388.
- Ye S, Li Y, Chen L, Jiang Y (Sep 2006). "Crystal structures of a ligand-free MthK gating ring: insights into the ligand gating mechanism of K+ channels". Cell. 126 (6): 1161–73. doi:10.1016/j.cell.2006.08.029. PMID 16990139.
- Dvir H, Valera E, Choe S (Aug 2010). "Structure of the MthK RCK in complex with cadmium". Journal of Structural Biology. 171 (2): 231–7. doi:10.1016/j.jsb.2010.03.020. PMC . PMID 20371380.
- Smith FJ, Pau VP, Cingolani G, Rothberg BS (Dec 2012). "Crystal structure of a Ba(2+)-bound gating ring reveals elementary steps in RCK domain activation". Structure. 20 (12): 2038–47. doi:10.1016/j.str.2012.09.014. PMC . PMID 23085076.
- Cao Y, Jin X, Huang H, Derebe MG, Levin EJ, Kabaleeswaran V, et al. (Mar 2011). "Crystal structure of a potassium ion transporter, TrkH". Nature. 471 (7338): 336–40. Bibcode:2011Natur.471..336C. doi:10.1038/nature09731. PMC . PMID 21317882.
- Cao Y, Pan Y, Huang H, Jin X, Levin EJ, Kloss B, et al. (Apr 2013). "Gating of the TrkH ion channel by its associated RCK protein TrkA". Nature. 496 (7445): 317–22. Bibcode:2013Natur.496..317C. doi:10.1038/nature12056. PMC . PMID 23598339.
- Vieira-Pires RS, Szollosi A, Morais-Cabral JH (Apr 2013). "The structure of the KtrAB potassium transporter". Nature. 496 (7445): 323–8. Bibcode:2013Natur.496..323V. doi:10.1038/nature12055. PMID 23598340.
- Kong C, Zeng W, Ye S, Chen L, Sauer DB, Lam Y, et al. (2012). "Distinct gating mechanisms revealed by the structures of a multi-ligand gated K(+) channel". eLife. 1: e00184. doi:10.7554/eLife.00184. PMC . PMID 23240087.
- Deller MC, Johnson HA, Miller MD, Spraggon G, Elsliger MA, Wilson IA, et al. (2015). "Crystal Structure of a Two-Subunit TrkA Octameric Gating Ring Assembly". PloS One. 10 (3): e0122512. doi:10.1371/journal.pone.0122512. PMC . PMID 25826626.
- Clayton, GM; Altieri, S; Heginbotham, L; Unger, VM; Morais-Cabral, JH (5 February 2008). "Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel.". Proceedings of the National Academy of Sciences of the United States of America. 105 (5): 1511–5. doi:10.1073/pnas.0711533105. PMC . PMID 18216238.
- Ren, D; Navarro, B; Xu, H; Yue, L; Shi, Q; Clapham, DE (14 December 2001). "A prokaryotic voltage-gated sodium channel.". Science. 294 (5550): 2372–5. doi:10.1126/science.1065635. PMID 11743207.
- Payandeh, J; Scheuer, T; Zheng, N; Catterall, WA (10 July 2011). "The crystal structure of a voltage-gated sodium channel.". Nature. 475 (7356): 353–8. doi:10.1038/nature10238. PMC . PMID 21743477.
- Shaya, D; Findeisen, F; Abderemane-Ali, F; Arrigoni, C; Wong, S; Nurva, SR; Loussouarn, G; Minor DL, Jr (23 January 2014). "Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels.". Journal of Molecular Biology. 426 (2): 467–83. doi:10.1016/j.jmb.2013.10.010. PMC . PMID 24120938.
- Zhang, X; Ren, W; DeCaen, P; Yan, C; Tao, X; Tang, L; Wang, J; Hasegawa, K; Kumasaka, T; He, J; Wang, J; Clapham, DE; Yan, N (20 May 2012). "Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel.". Nature. 486 (7401): 130–4. doi:10.1038/nature11054. PMC . PMID 22678295.
- McCusker, EC; Bagnéris, C; Naylor, CE; Cole, AR; D'Avanzo, N; Nichols, CG; Wallace, BA (2012). "Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.". Nature Communications. 3: 1102. doi:10.1038/ncomms2077. PMC . PMID 23033078.
- Shi, N; Ye, S; Alam, A; Chen, L; Jiang, Y (23 March 2006). "Atomic structure of a Na+- and K+-conducting channel.". Nature. 440 (7083): 570–4. doi:10.1038/nature04508. PMID 16467789.
- Durell, SR; Guy, HR (2001). "A family of putative Kir potassium channels in prokaryotes.". BMC Evolutionary Biology. 1: 14. PMC . PMID 11806753.
- Derebe, MG; Sauer, DB; Zeng, W; Alam, A; Shi, N; Jiang, Y (11 January 2011). "Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites.". Proceedings of the National Academy of Sciences of the United States of America. 108 (2): 598–602. doi:10.1073/pnas.1013636108. PMC . PMID 21187421.
- Sauer, DB; Zeng, W; Raghunathan, S; Jiang, Y (4 October 2011). "Protein interactions central to stabilizing the K+ channel selectivity filter in a four-sited configuration for selective K+ permeation.". Proceedings of the National Academy of Sciences of the United States of America. 108 (40): 16634–9. doi:10.1073/pnas.1111688108. PMC . PMID 21933962.
- "Voltage-gated Ion Channels". IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical Pharmacology.
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.
Ion transport protein Provide feedback
This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.
Internal database links
|SCOOP:||IRK Ion_trans_2 PKD_channel|
|Similarity to PfamA using HHSearch:||Ion_trans_2 PKD_channel|
External database links
|PRINTS:||PR00167 PR00169 PR00170|
|Transporter classification:||1.A.3 1.A.4|
This tab holds annotation information from the InterPro database.
InterPro entry IPR005821
This domain is found in sodium, potassium, and calcium ion channels proteins. The proteins have 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some Na channel proteins the domain is repeated four times, whereas in others (e.g. K channels) the protein forms a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not included in the Pfam family due to it lacking the first four helices.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|Molecular function||ion channel activity (GO:0005216)|
|Biological process||transmembrane transport (GO:0055085)|
|ion transport (GO:0006811)|
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.
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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
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_33 (release 1.0)|
|Author:||Finn RD, Eberhardt R|
|Number in seed:||243|
|Number in full:||28664|
|Average length of the domain:||245.90 aa|
|Average identity of full alignment:||15 %|
|Average coverage of the sequence by the domain:||35.80 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||29|
|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 3 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 Ion_trans domain has been found. There are 322 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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