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[[Image:1qrq1.png|left|200px|thumb|Crystal structure of voltage-dependent potassium channel, [[1qrq]]]]
[[Image:1qrq1.png|left|200px|thumb|Crystal structure of voltage-dependent potassium channel, [[1qrq]]]]
{{STRUCTURE_1qrq|  PDB=1qrq  | SIZE=300| SCENE=Ion_channels/Cv/1 |right|CAPTION=voltage-dependent potassium channel, [[1qrq]] }}
{{STRUCTURE_1qrq|  PDB=1qrq  | SIZE=300| SCENE=Ion_channels/Cv/1 |right|CAPTION=voltage-dependent potassium channel, [[1qrq]] }}
== PART I ==
 
[[Ion channels]] are membrane proteins that catalyze the passive transport of ions through the cell membrane. Most ion channels are specific to an ion, like the [[sodium channels]], or the [[chloride channels]]. Some, like the [[TRP channels]], let through various cations. Another property of ion channels is that they can be either driven by voltage or concentration gradients, or they can be gated (by voltage, ligands, touch and other sensory signal). [[Potassium Channel|Potassium channels]] (KCh) are subdivided to voltage-gated KCh and calcium-dependent KCh.  The latter are subdivided into high- (BK, LKCa), intermediate- and small-conductance KCh (human SK1, rat SK2, SKCa).
[[Ion channels]] are membrane proteins that catalyze the passive transport of ions through the cell membrane. Most ion channels are specific to an ion, like the [[sodium channels]], or the [[chloride channels]]. Some, like the [[TRP channels]], let through various cations. Another property of ion channels is that they can be either driven by voltage or concentration gradients, or they can be gated (by voltage, ligands, touch and other sensory signal). [[Potassium Channel|Potassium channels]] (KCh) are subdivided to voltage-gated KCh and calcium-dependent KCh.  The latter are subdivided into high- (BK, LKCa), intermediate- and small-conductance KCh (human SK1, rat SK2, SKCa).
MthK is a calcium-dependent potassium channel from ''Methanobacterium thermoautrophicum''.  MscL and MscS are large- and small-conductance mechanosensitive channels which protect bacteria from osmotic shock by allowing ions to flow across the cell membrane. Voltage-Dependent Calcium Channels (VDCC) allow Ca<sup>++</sup> to enter the cell resulting in muscle contraction, neuron excitation or hormone release.  VDCC are composed of several subunits and are named as a ''Cav'' gene product. Finally, ion channels are the fastest of all membrane transporters, with 10<sup>6</sup> to 10<sup>8</sup> transported units per second versus 10<sup>2</sup> to 10<sup>4</sup> molecules per second for porters/carriers, or 10<sup>0</sup> to 10<sup>3</sup> for ATP-driven pumps. The images at the left and at the right correspond to one representative ion channel structure, ''i.e.'' the crystal structure of voltage-dependent potassium channel from ''Rattus norvegicus'' ([[1qrq]]).
MthK is a calcium-dependent potassium channel from ''Methanobacterium thermoautrophicum''.  MscL and MscS are large- and small-conductance mechanosensitive channels which protect bacteria from osmotic shock by allowing ions to flow across the cell membrane. Voltage-Dependent Calcium Channels (VDCC) allow Ca<sup>++</sup> to enter the cell resulting in muscle contraction, neuron excitation or hormone release.  VDCC are composed of several subunits and are named as a ''Cav'' gene product. Finally, ion channels are the fastest of all membrane transporters, with 10<sup>6</sup> to 10<sup>8</sup> transported units per second versus 10<sup>2</sup> to 10<sup>4</sup> molecules per second for porters/carriers, or 10<sup>0</sup> to 10<sup>3</sup> for ATP-driven pumps. The images at the left and at the right correspond to one representative ion channel structure, ''i.e.'' the crystal structure of voltage-dependent potassium channel from ''Rattus norvegicus'' ([[1qrq]]).
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== Available structures ==
== Available 3D 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 &alpha;-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 == === Potassium channel ===
* the [[voltage-dependent potassium channel]] K<sub>1</sub> from ''Rattus norvegicus'' ([[1qrq]], [[1exb]], [[1t1d]], [[2a79]], [[2r9r]], [[3eau]], [[3eb3]], [[3eb4]])
 
* the [[voltage-dependent calcium channel]] from ''Rattus norvegicus'' (L-type: [[1t0h]], [[1t0j]], [[1vyt]], [[1vyu]], [[1vyv]], [[2vay]], [[3bxk]], R-type: [[3bxl]])
See: [[Potassium_Channel#Additional_Structures_of_Potassium_Channels|Potassium Channels]]
* the [[voltage-gated potassium channel]] KcsA from ''Streptomyces lividans'' and ''Mus musculus'' with the structures [[1bl8]], [[1k4c]], [[1jq2]], [[1k4d]], [[2bob]], [[2boc]], [[2hg5]],[[2h8p]], [[2hfe]], [[2itc]], [[2itd]], [[2k1e]], [[2nlj]]
=== BK channel ===
* the [[voltage-gated potassium channel]] K<sub>AP</sub> from ''Aeropyrum pernix'' ([[1orq]], [[2a0l]]), and human K<sub>7</sub> ([[2ovc]], [[3bj4]])
 
* the [[voltage-gated sodium channel]] Na<sub>1.2</sub> ([[1byy]], [[2kav]]) and Na<sub>1.5</sub> ([[2kbi]])
[[3mt5]] – hBK cytoplasmic domain<br />
* the [[ligand-gated ion channel]] that is the [[Glutamate receptor (GluA2)|glutamate receptor]] from ''Rattus norvegicus'' ([[Glutamate receptor (GluA2)|3kg2]])
[[1jo6]] – BK beta 2 N- terminal KCNMB2 encoded LKCa  - NMR
* 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 [[inward rectifier potassium channels]] KirBac3.1 ([[1xl4]],[[1xl6]]) and Kir3.1 (Cyt. only: [[1n9p]], [[1u4e]], [[1u4f]], [[1p7b]], [[2e4f]])
=== MthK ===
* the acid-sensitive (proton-gated) cation channel [[ASIC]] from ''Gallus gallus'' ([[2qts]])
 
* the human [[intracellular chloride channel]] CLIC-2 ([[2per]], [[2r4v]], [[2r5g]])
[[1kxd]] – MthK RCK domain+Cd - ''Methanobacterium thermoautrophicum''<br />
* the [[nicotinic acetylcholine-activated cation-selective channel]] from ''Torpedo marmorata'' ([[1oed]], [[2bg9]], [[2k58]], [[2k59]])
[[2ogu]], [[2fy8]], [[2aej]], [[2aem]], [[1lnq]] - MthK RCK domain<br />
* a [[potassium channel]] from ''Burkholderia pseudomallei'' ([[1p7b]])
[[2aef]] - MthK RCK domain+Ca
* the [[ammonium transporter]] from ''Archaeoglobus fulgidus'' ([[2b2f]]) and from ''Nitrosomonas europaea'' ([[3b9y]], [[3b9z]], [[3bhs]])
 
* the small-conductance [[mechanosensitive channel]] from ''E.&nbsp;coli'' K12 ([[2oau]], [[2vv5]], see also [[2k2b]])
 
* [[TRP channels]] ([[2rfa]], [[3e7k]])
=== Calcium channel ===
* human [[phospholamban]] ([[1zll]], [[2hyn]])
 
* the P7 [[viroporin]] of Hepatitis C virus ([[2k8j]])
[[3bxx]] – rCav2.1 alpha 1A subunit+calmodulin<br />
* the [[M2 proton channel]] from Influenza A ([[3bkd]], [[1nyj]], [[2kad]], [[2rlf]], [[3c9j]])
[[3bxl]] - rCav2.3 alpha 1E subunit+calmodulin<br />
**featured in a morph at [[Proton Channels]].
[[2f3y]], [[2f3z]], [[2be6]] – hCav1.2 alpha 1C subunit+calmodulin<br />
* [[aquaporins]] from several species:
[[1t0h]] – rVDCC beta 2A subunit <br />
** ''Methanobacterium thermoautotrophicum'' (aqpM, [[2evu]], [[2f2c]])
[[1t0j]] – rVDCC beta 2A+alpha 1C <br />
** ''E.&nbsp;coli'' K12 (Aquaporin Z, [[1r2c]], [[2abm]])
[[1vyt]] - rVDCC beta 3+alpha 1C <br />
** the [[glycerol uptake facilitator]] from ''E.&nbsp;coli'' K12 (GlpF, [[1lda]], [[1ldf]], [[1ldi]], [[1fx8]])
[[1vyu]] – rVDCC beta 3<br />
** ''Homo sapiens'' (AQP-1, [[1fqy]], [[1ih5]])
[[1vyv]] - rVDCC beta 4<br />
** ''Bos taurus'' (Aquaporin-0, [[1ymg]], [[2b6p]])
[[1t3l]] - raVDCC beta 2+alpha 1S – rabbit<br />
[[1t3s]] - raVDCC beta 2<br />
[[2d46]] – hVDCC beta 4a – NMR<br />
[[3dve]], [[3dvj]], [[3dvk]], [[3dvm]], [[3g43]] - rCav2.2 alpha 1B subunit+hCalmodulin<br />
[[3oxq]] - hCav2.1 alpha 1C subunit IQ domain+hCalmodulin<br />
[[1hvd]], [[1hve]], [[1hvf]], [[1hvg]] – hAnnexin V (mutant)
 
 
=== NH4+ channel ===
 
[[2nmr]], [[2nop]], [[2now]], [[2npc]], [[2npd]], [[2npe]], [[2npj]], [[2npg]], [[2npk]], [[1u77]], [[1u7c]], [[1u7g]], [[1xqe]], [[1xqf]] – EcAmCh – ''Escherichia coli''<br />
[[2b2h]], [[2b2i]], [[2b2j]] – AmCh – ''Archaeglobus fulgidus''<br />
[[3b9w]], [[3b9y]] – AmCh – ''Nitrosomonas  europaea''
 
=== MscL and MscS ===
 
[[3hzq]] – MscL – ''Staphylococcus aureus''<br />
[[2oar]] – MscL – ''Mycobacterium tuberculosis''<br />
[[2oau]], [[2vv5]] - EcMscS
 
 
=== Chloride channel ===
 
[[2ahe]], [[2d2z]] – hClCh protein 4<br />
[[1rk4]] - hClCh protein 1<br />
[[3o3t]], [[3p8w]], [[3p90]], [[1k0o]] - hClCh protein 1 (mutant)
 
 
=== Anion Channel ===
 
[[2jk4]] – hVDAC
 
 
=== Ligand-gated ion channel ===
 
[[2vl0]] – LGIC – ''Erwinia chrysanthemi''<br />
[[2xq3]], [[2xq4]], [[2xq5]], [[2xq6]], [[2xq7]], [[2xqa]], [[2xq8]] – GvLGIC+inhibitor – ''Gloeobacter violaceus''<br />
[[3eam]], [[3ehz]] – GvLGIC<br />
[[3igq]] – GvLGIC N-terminal<br />
[[2xq9]] – GvLGIC (mutant)+inhibitor<br />
[[3lsv]] – GvLGIC (mutant)
 
 
=== Cyclic Nucleotide-Gated channel ===
 
[[3etq]], [[3ffq]] – mCNGC C-terminal<br />
[[2zd9]], [[3beh]] - MlCNGC
 
 
=== Acid sensitive ion channel ===
 
[[3hgc]], [[3ij4]] – ASC – chicken
 
 
=== ATP-Gated channel (AGC) ===
 
[[3h9v]], [[3i5d]] – AGC – Zebra fish
 


Calcium-dependent potassium channels from ''Methanobacterium thermoautrophicum'' (MthK):
=== Proton channel ===
* [[1kxd]] – MthK RCK domain+Cd - ''Methanobacterium thermoautrophicum''
* [[2ogu]], [[2fy8]], [[2aej]], [[2aem]], [[1lnq]] - MthK RCK domain
* [[2aef]] - MthK RCK domain+Ca
Large- and small-conductance mechanosensitive channels (MscL and MscS):
* [[3hzq]] – MscL – ''Staphylococcus aureus''
* [[2oar]] – MscL – ''Mycobacterium tuberculosis''
* [[2oau]], [[2vv5]] - EcMscS


Additionally the following non-ribosomally synthesized channel proteins constitute ion channels, and have their structure resolved:
[[2kih]], [[2kwx]] – IVproton channel – Influenza virus<br />
* [[Gramicidin]] ([[1av2]], [[1c4d]], [[1mag]])
[[2kj1]], [[2l0j]] - IVproton channel – NMR
** See also the theoretical model of a [[Gramicidin_Channel_in_Lipid_Bilayer|gramicidin channel in a hydrated lipid bilayer]].
* fungal [[Antiamoebin]] ([[1joh]], [[1gq0]])
* fungal [[Trichotoxin]] ([[1m24]])
* further [[Peptaibol]] antibiotics ([[1ob4]], [[1ob6]], [[1ob7]])


We do not count ClC chloride carriers as ion channels, as they are secondary active [[carriers]].


For additional information see page [[Ion channels (Part II)]]  
== Voltage-gated hydrogen channel (VGHC) ==
[[3a2a]] – hVGHC C-terminal - NMR


== Weblinks ==
== Weblinks ==

Revision as of 20:21, 23 March 2011

File:1qrq1.png
Crystal structure of voltage-dependent potassium channel, 1qrq

Template:STRUCTURE 1qrq

Ion channels are membrane proteins that catalyze the passive transport of ions through the cell membrane. Most ion channels are specific to an ion, like the sodium channels, or the chloride channels. Some, like the TRP channels, let through various cations. Another property of ion channels is that they can be either driven by voltage or concentration gradients, or they can be gated (by voltage, ligands, touch and other sensory signal). Potassium channels (KCh) are subdivided to voltage-gated KCh and calcium-dependent KCh. The latter are subdivided into high- (BK, LKCa), intermediate- and small-conductance KCh (human SK1, rat SK2, SKCa). MthK is a calcium-dependent potassium channel from Methanobacterium thermoautrophicum. MscL and MscS are large- and small-conductance mechanosensitive channels which protect bacteria from osmotic shock by allowing ions to flow across the cell membrane. Voltage-Dependent Calcium Channels (VDCC) allow Ca++ to enter the cell resulting in muscle contraction, neuron excitation or hormone release. VDCC are composed of several subunits and are named as a Cav gene product. Finally, ion channels are the fastest of all membrane transporters, with 106 to 108 transported units per second versus 102 to 104 molecules per second for porters/carriers, or 100 to 103 for ATP-driven pumps. The images at the left and at the right correspond to one representative ion channel structure, i.e. the crystal structure of voltage-dependent potassium channel from Rattus norvegicus (1qrq).

ClassificationClassification

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 α-helices that span the membrane. They are distinct in this from the beta-barrel porins and the pore-forming toxins, as well as from non-ribosomally synthesized channels like gramicidin, polyglutamine or digitoxin. All these proteins are passive transport proteins.

Additional ResourcesAdditional Resources

For additional information, see: Membrane Channels & Pumps
For additional information, see: Hypertension & Congestive Heart Failure

Available 3D structuresAvailable 3D structures

Membrane transport proteins are notoriously difficult to crystallize while in a working state. So, it's no == === Potassium channel ===

See: Potassium Channels

BK channelBK channel

3mt5 – hBK cytoplasmic domain
1jo6 – BK beta 2 N- terminal KCNMB2 encoded LKCa - NMR


MthKMthK

1kxd – MthK RCK domain+Cd - Methanobacterium thermoautrophicum
2ogu, 2fy8, 2aej, 2aem, 1lnq - MthK RCK domain
2aef - MthK RCK domain+Ca


Calcium channelCalcium channel

3bxx – rCav2.1 alpha 1A subunit+calmodulin
3bxl - rCav2.3 alpha 1E subunit+calmodulin
2f3y, 2f3z, 2be6 – hCav1.2 alpha 1C subunit+calmodulin
1t0h – rVDCC beta 2A subunit
1t0j – rVDCC beta 2A+alpha 1C
1vyt - rVDCC beta 3+alpha 1C
1vyu – rVDCC beta 3
1vyv - rVDCC beta 4
1t3l - raVDCC beta 2+alpha 1S – rabbit
1t3s - raVDCC beta 2
2d46 – hVDCC beta 4a – NMR
3dve, 3dvj, 3dvk, 3dvm, 3g43 - rCav2.2 alpha 1B subunit+hCalmodulin
3oxq - hCav2.1 alpha 1C subunit IQ domain+hCalmodulin
1hvd, 1hve, 1hvf, 1hvg – hAnnexin V (mutant)


NH4+ channelNH4+ channel

2nmr, 2nop, 2now, 2npc, 2npd, 2npe, 2npj, 2npg, 2npk, 1u77, 1u7c, 1u7g, 1xqe, 1xqf – EcAmCh – Escherichia coli
2b2h, 2b2i, 2b2j – AmCh – Archaeglobus fulgidus
3b9w, 3b9y – AmCh – Nitrosomonas europaea

MscL and MscSMscL and MscS

3hzq – MscL – Staphylococcus aureus
2oar – MscL – Mycobacterium tuberculosis
2oau, 2vv5 - EcMscS


Chloride channelChloride channel

2ahe, 2d2z – hClCh protein 4
1rk4 - hClCh protein 1
3o3t, 3p8w, 3p90, 1k0o - hClCh protein 1 (mutant)


Anion ChannelAnion Channel

2jk4 – hVDAC


Ligand-gated ion channelLigand-gated ion channel

2vl0 – LGIC – Erwinia chrysanthemi
2xq3, 2xq4, 2xq5, 2xq6, 2xq7, 2xqa, 2xq8 – GvLGIC+inhibitor – Gloeobacter violaceus
3eam, 3ehz – GvLGIC
3igq – GvLGIC N-terminal
2xq9 – GvLGIC (mutant)+inhibitor
3lsv – GvLGIC (mutant)


Cyclic Nucleotide-Gated channelCyclic Nucleotide-Gated channel

3etq, 3ffq – mCNGC C-terminal
2zd9, 3beh - MlCNGC


Acid sensitive ion channelAcid sensitive ion channel

3hgc, 3ij4 – ASC – chicken


ATP-Gated channel (AGC)ATP-Gated channel (AGC)

3h9v, 3i5d – AGC – Zebra fish


Proton channelProton channel

2kih, 2kwx – IVproton channel – Influenza virus
2kj1, 2l0j - IVproton channel – NMR


Voltage-gated hydrogen channel (VGHC)Voltage-gated hydrogen channel (VGHC)

3a2a – hVGHC C-terminal - NMR

WeblinksWeblinks

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Ralf Stephan, Ilan Samish, Eric Martz, Wayne Decatur, Alexander Berchansky, Michal Harel, David Canner, Jaime Prilusky, Shelly Livne
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