User:Ralf Stephan/Sandbox 2: Difference between revisions
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== Classification == | == Classification == | ||
TCDB, the most sophisticated classification of transport proteins to date, classify ion channels as a heterogenous subset of all '''α-type channels''', whose singular property is to consist mainly of [[alpha helix|α-helices]] that span the membrane. They are distinct in this from the [[beta-barrel porins]], but also from non-ribosomally synthesized channels like [[gramicidin]], [[polyglutamine]] or [[digitoxin]]. All these proteins are '''passive''' transport proteins. | TCDB, the most sophisticated classification of transport proteins to date, classify ion channels as a heterogenous subset of all '''α-type channels''', whose singular property is to consist mainly of [[alpha helix|α-helices]] that span the membrane. They are distinct in this from the [[beta-barrel porins]], the [[pore-forming toxins]], but also from non-ribosomally synthesized channels like [[gramicidin]], [[polyglutamine]] or [[digitoxin]]. All these proteins are '''passive''' transport proteins. | ||
== Available structures == | == Available structures == | ||
Membrane transport proteins are notoriously difficult to crystallize while in a working state. So, it's no surprise that there are preciously few structure data for ion channels. At the moment, the following α-type ion channels have been at least partly resolved: | Membrane transport proteins are notoriously difficult to crystallize while in a working state. So, it's no surprise that there are preciously few structure data for ion channels. At the moment, the following α-type ion channels have been at least partly resolved: | ||
* the [[voltage-dependent potassium channel]] from ''Rattus norvegicus'' ([[1exb]], [[2a79]], [[2r9r]]) | * the [[voltage-dependent potassium channel]] K<sub>v</sub>1 from ''Rattus norvegicus'' ([[1qrq]], [[1exb]], [[1t1d]], [[2a79]], [[2r9r]], [[3eau]], [[3eb3]], [[3eb4]]) | ||
* the [[voltage-dependent calcium channel]] from ''Rattus norvegicus'' (L-type: [[3bxk]], R-type: [[3bxl]]) | * the [[voltage-dependent calcium channel]] from ''Rattus norvegicus'' (L-type: [[1t0h]], [[1t0j]], [[1vyt]], [[1vyu]], [[1vyv]], [[2vay]], [[3bxk]], R-type: [[3bxl]]) | ||
* the [[voltage-gated potassium channel]] from ''Streptomyces lividans'' with the structures [[1bl8]], [[1k4c]], [[1k4d]] | * the [[voltage-gated potassium channel]] KcsA from ''Streptomyces lividans'' with the structures [[1bl8]], [[1k4c]], [[1k4d]], [[2bob]], [[2boc]], [[2itc]], [[2itd]], [[2k1e]], [[2nlj]] | ||
* the [[voltage-gated potassium channel]] K<sub>v</sub>AP from ''Aeropyrum pernix'' ([[1orq]], [[2a0l]]), and human K<sub>v</sub>7 ([[2ovc]]) | * the [[voltage-gated potassium channel]] K<sub>v</sub>AP from ''Aeropyrum pernix'' ([[1orq]], [[2a0l]]), and human K<sub>v</sub>7 ([[2ovc]], [[3bj4]]) | ||
* the [[voltage-gated | * the [[voltage-gated sodium channel]] Na<sub>v</sub>1.2 ([[1byy]], [[2kav]]) and Na<sub>v</sub>1.2 ([[2kbi]]) | ||
* the [[calcium-gated potassium channel mthK]] from ''Methanobacterium thermoautotrophicum'' ([[1lnq]]) | * the [[calcium-gated potassium channel mthK]] from ''Methanobacterium thermoautotrophicum'' ([[1lnq]], [[2fy8]]) | ||
* the hyperpolarization-activated and cyclic nucleotide-gated K+ channel [[HCN]] from ''Mus musculus'' ([[1q3e]], [[1q43]], [[1q5o]], [[2ptm]], [[2q0a]], [[3bpz]]) | * the hyperpolarization-activated and cyclic nucleotide-gated K+ channel [[HCN]] from ''Mus musculus'' ([[1q3e]], [[1q43]], [[1q5o]], [[2ptm]], [[2q0a]], [[3bpz]]) | ||
* the [[inward rectifier potassium channels]] KirBac3.1 ([[1xl4]],[[1xl6]]) and Kir3.1 (Cyt. only: [[1n9p]], [[1u4e]], [[1u4f]], [[1p7b]], [[2e4f]]) | * the [[inward rectifier potassium channels]] KirBac3.1 ([[1xl4]],[[1xl6]]) and Kir3.1 (Cyt. only: [[1n9p]], [[1u4e]], [[1u4f]], [[1p7b]], [[2e4f]]) | ||
* the acid-sensitive (proton-gated) cation channel [[ASIC]] from ''Gallus gallus'' ([[2qts]]) | * the acid-sensitive (proton-gated) cation channel [[ASIC]] from ''Gallus gallus'' ([[2qts]]) | ||
* the [[nicotinic acetylcholine-activated cation-selective channel]] from ''Torpedo marmorata'' ([[1oed]], [[2bg9]]) | * the human [[intracellular chloride channel]] CLIC-2 ([[2per]], [[2r4v]], [[2r5g]]) | ||
* the [[nicotinic acetylcholine-activated cation-selective channel]] from ''Torpedo marmorata'' ([[1oed]], [[2bg9]], [[2k58]], [[2k59]]) | |||
* a [[potassium channel]] from ''Burkholderia pseudomallei'' ([[1p7b]]) | * a [[potassium channel]] from ''Burkholderia pseudomallei'' ([[1p7b]]) | ||
* the [[ammonium transporter]] from ''Archaeoglobus fulgidus'' ([[2b2f]]) | * the [[ammonium transporter]] from ''Archaeoglobus fulgidus'' ([[2b2f]]) | ||
* the small-conductance [[mechanosensitive channel]] from ''E. coli'' K12 ([[2oau]]) | * the small-conductance [[mechanosensitive channel]] from ''E. coli'' K12 ([[2oau]], [[2vv5]], see also [[2k2b]]) | ||
* [[TRP channels]] ([[3e7k]]) | * [[TRP channels]] ([[2rfa]], [[3e7k]]) | ||
* human [[phospholamban]] ([[1zll]]) | * human [[phospholamban]] ([[1zll]]) | ||
* the P7 [[viroporin]] of Hepatitis C virus ([[2k8j]]) | * the P7 [[viroporin]] of Hepatitis C virus ([[2k8j]]) | ||
* the [[M2 protein]] from Influenza A ([[2rlf]], [[3c9j]]) | * the [[M2 protein]] from Influenza A ([[2kad]], [[2rlf]], [[3c9j]]) | ||
Additionally the following non-ribosomally synthesized channel proteins constitute ion channels, and have their structure resolved: | Additionally the following non-ribosomally synthesized channel proteins constitute ion channels, and have their structure resolved: | ||