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322  structures 1287  species 3  interactions 28664  sequences 736  architectures

Family: Ion_trans (PF00520)

Summary: Ion transport protein

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 "Ion channel family". More...

Ion channel family Edit Wikipedia article

Ion channel (eukaryotic)
2r9r opm.png
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.
Identifiers
Symbol Ion_trans
Pfam PF00520
InterPro IPR005821
SCOP 1bl8
SUPERFAMILY 1bl8
TCDB 1.A.1
OPM superfamily 8
OPM protein 2a79
Ion channel (bacterial)
1r3j.png
Potassium channel KcsA. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
Identifiers
Symbol Ion_trans_2
Pfam PF07885
InterPro IPR013099
SCOP 1bl8
SUPERFAMILY 1bl8
OPM protein 1r3j

Transmembrane cation channel superfamily was defined in InterPro and Pfam as the family of tetrameric ion channels. These include the sodium, potassium,[1] 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.

Human channels with 6 TM helices

Cation

Transient receptor potential channel

Canonical TRP Channels
Melastatin TRP Channels
Vanilloid TRP Channels
Mucolipin TRP Channels
Ankyrin TRP Channels
TRPP

Calcium

Voltage-dependent calcium channel

Cation channels of sperm

Ryanodine receptor

Potassium

Voltage-gated potassium channels

Delayed rectifier
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)
Outward-rectifying
  • Kvα10.x: Kv10.2 (KCNH5)
Inwardly-rectifying
Slowly activating
Modifier/silencer

Calcium-activated potassium channel

BK channel
SK channel
  • 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
IK channel
Other subfamilies

Inward-rectifier potassium ion channel

Sodium

Cyclic nucleotide-gated

Proton

Related Proteins

Human channels with 2 TM helices in each subunit

Potassium

Tandem pore domain potassium channel

Non-human Channels

Two-pore channels

Pore-only Potassium Channels

Ligand Gated Potassium Channel

Voltage-gated Potassium Channels

Prokaryotic KCa Channels

Voltage and Cyclic Nucleotide Gated Potassium Channel

Sodium Channels

Non-Selective Channels

Prokaryotic Inward-rectifier potassium channels

Engineered Channels

References

  1. ^ Choe S (February 2002). "Potassium channel structures". Nat. Rev. Neurosci. 3 (2): 115–21. doi:10.1038/nrn727. PMID 11836519. 
  2. ^ 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. PMID 10617203. 
  3. ^ 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. PMID 12721618. 
  4. ^ 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. PMID 8170937. 
  5. ^ 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. PMID 11301020. 
  6. ^ 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. 
  7. ^ 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. 
  8. ^ 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. 
  9. ^ 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. PMID 20371380. 
  10. ^ 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. PMID 23085076. 
  11. ^ 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 3077569. PMID 21317882. 
  12. ^ 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 3726529. PMID 23598339. 
  13. ^ 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. 
  14. ^ 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 3510474. PMID 23240087. 
  15. ^ 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 4380455. PMID 25826626. 
  16. ^ 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. PMID 18216238. 
  17. ^ Ren, D; Navarro, B; Xu, H; Yue, L; Shi, Q; Clapham, DE (14 December 2001). "A prokaryotic voltage-gated sodium channel.". Science (New York, N.Y.) 294 (5550): 2372–5. PMID 11743207. 
  18. ^ 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. PMID 21743477. 
  19. ^ 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. PMID 24120938. 
  20. ^ 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. PMID 22678295. 
  21. ^ 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. PMID 23033078. 
  22. ^ 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. PMID 16467789. 
  23. ^ Durell, SR; Guy, HR (2001). "A family of putative Kir potassium channels in prokaryotes.". BMC evolutionary biology 1: 14. PMID 11806753. 
  24. ^ 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. PMID 21187421. 
  25. ^ 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. PMID 21933962. 

External links

This article incorporates text from the public domain Pfam and InterPro IPR005821

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.

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

External database links

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.

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, the UniProtKB sequence database, 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
(243)
Full
(28664)
Representative proteomes UniProt
(51621)
NCBI
(124675)
Meta
(2285)
RP15
(7224)
RP35
(12812)
RP55
(19961)
RP75
(25185)
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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
(243)
Full
(28664)
Representative proteomes UniProt
(51621)
NCBI
(124675)
Meta
(2285)
RP15
(7224)
RP35
(12812)
RP55
(19961)
RP75
(25185)
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
(243)
Full
(28664)
Representative proteomes UniProt
(51621)
NCBI
(124675)
Meta
(2285)
RP15
(7224)
RP35
(12812)
RP55
(19961)
RP75
(25185)
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.

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: Pfam-B_33 (release 1.0)
Previous IDs: ion_trans;
Type: Family
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 245
Family (HMM) version: 29
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Interactions

There are 3 interactions for this family. More...

Ion_trans DSPc PTEN_C2

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 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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