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37  structures 1652  species 0  interactions 20399  sequences 434  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.gif
Potassium channel KvAP, 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.gif
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 ion channel family was defined in InterPro and Pfam as the family of tetrameric sodium, potassium, and calcium ion channels, in which two C-terminal transmembrane helices flank a loop which determines ion selectivity of the channel pore. This large group of ion channels apparently includes families 1.A.1, 1.A.2, 1.A.3, and 1.A.4 of transporter classification.

Many eukaryotic channels have four additional transmembrane helices (TMH) (Pfam PF00520), whereas a bacterial structure of the protein has only two transmembrane helices that form the tetrameric channel (Pfam PF07885).

Human channels with 6 TM helices[edit]

Cation

Calcium

Potassium[1]

Sodium

Proton

Cyclic nucleotide-gated

Human channels with two TM helices in each subunit, as in bacteria[edit]

Potassium

References[edit]

  1. ^ Choe S (February 2002). "Potassium channel structures". Nat. Rev. Neurosci. 3 (2): 115–21. doi:10.1038/nrn727. PMID 11836519. 

External links[edit]


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, 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. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices

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 8 members:

GLTSCR1 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(285)
Full
(20399)
Representative proteomes NCBI
(20841)
Meta
(2116)
RP15
(2792)
RP35
(3895)
RP55
(6681)
RP75
(9781)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(285)
Full
(20399)
Representative proteomes NCBI
(20841)
Meta
(2116)
RP15
(2792)
RP35
(3895)
RP55
(6681)
RP75
(9781)
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
(285)
Full
(20399)
Representative proteomes NCBI
(20841)
Meta
(2116)
RP15
(2792)
RP35
(3895)
RP55
(6681)
RP75
(9781)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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
Number in seed: 285
Number in full: 20399
Average length of the domain: 196.60 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 31.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 200
Family (HMM) version: 26
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 Ion_trans domain has been found. There are 37 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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