Ion channel family

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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[edit]

Cation[edit]

Transient receptor potential channel[edit]

Canonical TRP Channels[edit]
Melastatin TRP Channels[edit]
Vanilloid TRP Channels[edit]
Mucolipin TRP Channels[edit]
Ankyrin TRP Channels[edit]
TRPP[edit]

Calcium[edit]

Voltage-dependent calcium channel[edit]

Cation channels of sperm[edit]

Ryanodine receptor[edit]

Potassium[edit]

Voltage-gated potassium channels[edit]

Delayed rectifier[edit]
A-type potassium channel[edit]
  • 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[edit]
  • Kvα10.x: Kv10.2 (KCNH5)
Inwardly-rectifying[edit]
Slowly activating[edit]
Modifier/silencer[edit]

Calcium-activated potassium channel[edit]

BK channel[edit]
SK channel[edit]
  • 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[edit]
Other subfamilies[edit]

Inward-rectifier potassium ion channel[edit]

Sodium[edit]

Cyclic nucleotide-gated[edit]

Proton[edit]

Related Proteins[edit]

Human channels with 2 TM helices in each subunit[edit]

Potassium[edit]

Tandem pore domain potassium channel[edit]

Non-human Channels[edit]

Two-pore channels[edit]

Pore-only Potassium Channels[edit]

Ligand Gated Potassium Channel[edit]

Voltage-gated Potassium Channels[edit]

Prokaryotic KCa Channels[edit]

Voltage and Cyclic Nucleotide Gated Potassium Channel[edit]

Sodium Channels[edit]

Non-Selective Channels[edit]

Prokaryotic Inward-rectifier potassium channels[edit]

Engineered Channels[edit]

References[edit]

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  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. doi:10.1073/pnas.91.9.3510. PMC 43609Freely accessible. 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. doi:10.1016/s0896-6273(01)00236-7. 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. PMC 2956275Freely accessible. 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. PMC 3518701Freely accessible. 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 3077569Freely accessible. 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 3726529Freely accessible. 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 3510474Freely accessible. 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 4380455Freely accessible. 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. doi:10.1073/pnas.0711533105. PMC 2234175Freely accessible. 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. 294 (5550): 2372–5. doi:10.1126/science.1065635. 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. doi:10.1038/nature10238. PMC 3266868Freely accessible. 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. doi:10.1016/j.jmb.2013.10.010. PMC 3947372Freely accessible. 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. doi:10.1038/nature11054. PMC 3979295Freely accessible. 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. doi:10.1038/ncomms2077. PMC 3493636Freely accessible. 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. doi:10.1038/nature04508. PMID 16467789. 
  23. ^ Durell, SR; Guy, HR (2001). "A family of putative Kir potassium channels in prokaryotes.". BMC Evolutionary Biology. 1: 14. PMC 64639Freely accessible. 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. doi:10.1073/pnas.1013636108. PMC 3021048Freely accessible. 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. doi:10.1073/pnas.1111688108. PMC 3189067Freely accessible. PMID 21933962. 

External links[edit]

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