Summary: Glioma tumor suppressor candidate region
This is the Wikipedia entry entitled "Ion channel family". More...
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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 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
- MCOLN1; MCOLN2; MCOLN3;
- TPCN1; TPCN2
- TRPC1: TRPC3; TRPC4; TRPC5; TRPC6; TRPC7
- TRPM1; TRPM2; TRPM3; TRPM4; TRPM5; TRPM6; TRPM7; TRPM8
- TRPV1; TRPV2; TRPV3; TRPV4; TRPV5; TRPV6
- CACNA1A; CACNA1B; CACNA1C; CACNA1D; CACNA1E; CACNA1F; CACNA1G; CACNA1H; CACNA1I; CACNA1S
- CATSPER1; CATSPER2; CATSPER3; CATSPER4
- RYR1; RYR2; RYR3
- KCNA1; KCNA2; KCNA3; KCNA4; KCNA5; KCNA6; KCNA7; KCNA10
- KCNB1; KCNB2
- KCNC1; KCNC2; KCNC3; KCNC4
- KCND1; KCND2; KCND3
- KCNG1; KCNG2; KCNG3; KCNG4
- KCNH1; KCNH2; KCNH3; KCNH4; KCNH5; KCNH6; KCNH7; KCNH8
- KCNQ1; KCNQ2; KCNQ3; KCNQ4; KCNQ5
- KCNS1; KCNS2; KCNS3
- KCNV1; KCNV2
- SCN1A; SCN2A; SCN2A2; SCN3A; SCN4A; SCN5A; SCN7A; SCN8A; SCN9A; SCN10A; SCN11A
- SLC9A10; SLC9A11
Human channels with two TM helices in each subunit, as in bacteria
- KCNK1; KCNK2; KCNK3; KCNK4; KCNK5; KCNK6; KCNK7; KCNK9; KCNK10; KCNK12; KCNK13; KCNK15; KCNK16; KCNK17; KCNK18
- KCNN1; KCNN2; KCNN3; KCNN4;
- KCNT1; KCNT2
- "Voltage-gated Ion Channels". IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical Pharmacology.
|This membrane protein–related article is a stub. You can help Wikipedia by expanding it.|
Glioma tumor suppressor candidate region Provide feedback
This domain family is found in eukaryotes, and is typically between 105 and 124 amino acids in length. There is a single completely conserved residue F that may be functionally important. Mutations in the gene for this protein in humans leads to the development of oligodendrogliomas . There is evidence that these protein interacts with SH3 domains .
Yang P, Kollmeyer TM, Buckner K, Bamlet W, Ballman KV, Jenkins RB;, Cancer. 2005;103:2363-2372.: Polymorphisms in GLTSCR1 and ERCC2 are associated with the development of oligodendrogliomas. PUBMED:15834925 EPMC:15834925
Wu C, Ma MH, Brown KR, Geisler M, Li L, Tzeng E, Jia CY, Jurisica I, Li SS;, Proteomics. 2007;7:1775-1785.: Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. PUBMED:17474147 EPMC:17474147
External database links
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
- 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
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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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 8 members:GLTSCR1 Ion_trans Ion_trans_2 IRK KdpA Lig_chan PKD_channel TrkH
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 NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
This family is new in this Pfam release.
|Author:||Eberhardt RY, Coggill P, Hetherington K|
|Number in seed:||54|
|Number in full:||193|
|Average length of the domain:||109.40 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||10.45 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||1|
|Download:||download the raw HMM for this family|
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