Ion channels

File:1qrq1.png

Crystal structure of voltage-dependent potassium channel, 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 natrium channels, or the chloride channels. Some, like the TRP channels, let through a bunch of 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 10^6 to 10^8 transported units per second versus 10^2 to 10^4 molecules per second for porters/carriers, or 10^0 to 10^3 for ATP-driven pumps.

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, the pore-forming toxins, but also from non-ribosomally synthesized channels like gramicidin, polyglutamine or digitoxin. All these proteins are passive transport proteins.

Available structuresAvailable 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:

• the voltage-dependent potassium channel K_v1 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)
• 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
• the voltage-gated potassium channel K_vAP from Aeropyrum pernix (1orq, 2a0l), and human K_v7 (2ovc, 3bj4)
• the voltage-gated sodium channel Na_v1.2 (1byy, 2kav) and Na_v1.5 (2kbi)
• the ligand-gated ion channel that is the glutamate receptor from Rattus norvegicus (3kg2)
• 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)
• the acid-sensitive (proton-gated) cation channel ASIC from Gallus gallus (2qts)
• 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)
• the ammonium transporter from Archaeoglobus fulgidus (2b2f) and from Nitrosomonas europaea (3b9y, 3b9z, 3bhs)
• the small-conductance mechanosensitive channel from E. coli K12 (2oau, 2vv5, see also 2k2b)
• TRP channels (2rfa, 3e7k)
• human phospholamban (1zll, 2hyn)
• the P7 viroporin of Hepatitis C virus (2k8j)
• the M2 proton channel from Influenza A (3bkd, 1nyj, 2kad, 2rlf, 3c9j)
  • featured in a morph at Proton Channels.
• aquaporins from several species:
  • Methanobacterium thermoautotrophicum (aqpM, 2evu, 2f2c)
  • E. coli K12 (Aquaporin Z, 1r2c, 2abm)
  • the glycerol uptake facilitator from E. coli K12 (GlpF, 1lda, 1ldf, 1ldi, 1fx8)
  • Homo sapiens (AQP-1, 1fqy, 1ih5)
  • Bos taurus (Aquaporin-0, 1ymg, 2b6p)

Additional potassium channels:

• 2wlj – KCh – Magnetospirillum magnetotacticum
• 2k44 – KCh voltage-sensor paddle domain – NMR
• 3e86 – BcKCh transmembrane domain – Bacillus cereus
• 3e8g – BcKCh transmembrane domain +Ca+Na
• 2q67, 2q68, 2q69, 2q6a – BcKCh (mutant)
• 2ahy – BcKCh+Na
• 2ahz – BcKCh+K
• 2pnv – rKCh leucine zipper domain SKCa – from Rattus norvegicus
• 2nz0 – hKCh Kv4.3 N-terminal+KV channel interacting protein 1 – human
• 2i2r - rKCh Kv4.3 N-terminal+KV channel interacting protein 1
• 1s6c - rKCh Kv4.2 N-terminal+KV channel interacting protein 1
• 1qx7 – rKCh SKCa+ calmodulin
• 1g4y – rKCh rSK2 calmodulin binding domain SKCa + calmodulin
• 1j95 – KCh+K+tetrabutylammonium – Streptomyces lividans

BK channels:

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

Calcium-dependent potassium channels from Methanobacterium thermoautrophicum (MthK):

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

Additional calcium channels:

• 3bxx – rCav2.1 alpha 1A subunit+calmodulin
• 2f3y, 2f3z, 2be6 – hCav1.2 alpha 1C subunit+calmodulin
• 1t3l - raVDCC beta 2+alpha 1S – rabbit
• 1t3s - raVDCC beta 2

NH4+ channels

• 2nmr, 2nop, 2now, 2npc, 2npd, 2npe, 2npj, 2npg, 2npk – EcAmCh – Escherichia coli

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:

• Gramicidin (1av2, 1c4d, 1mag)
  • See also the theoretical model of a 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.

WeblinksWeblinks

• The TCDB database
• TCDB: 1.A α-Type channels
• TCDB: Transport proteins with PDB structures