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3i5d

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Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5 Angstroms (R3)

Structural highlights

3i5d is a 3 chain structure with sequence from Danio rerio. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.46Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

P2X4A_DANRE ATP-gated nonselective transmembrane cation channel permeable to potassium, sodium and calcium (By similarity). CTP, but not GTP or UTP, functions as a weak affinity agonist for P2RX4 (PubMed:28332633). Activated by extracellularly released ATP, it plays multiple role in immunity and central nervous system physiology (By similarity). Could also function as an ATP-gated cation channel of lysosomal membranes (By similarity).[UniProtKB:P51577][UniProtKB:Q99571][UniProtKB:Q9JJX6]^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

P2X receptors are cation-selective ion channels gated by extracellular ATP, and are implicated in diverse physiological processes, from synaptic transmission to inflammation to the sensing of taste and pain. Because P2X receptors are not related to other ion channel proteins of known structure, there is at present no molecular foundation for mechanisms of ligand-gating, allosteric modulation and ion permeation. Here we present crystal structures of the zebrafish P2X(4) receptor in its closed, resting state. The chalice-shaped, trimeric receptor is knit together by subunit-subunit contacts implicated in ion channel gating and receptor assembly. Extracellular domains, rich in beta-strands, have large acidic patches that may attract cations, through fenestrations, to vestibules near the ion channel. In the transmembrane pore, the 'gate' is defined by an approximately 8 A slab of protein. We define the location of three non-canonical, intersubunit ATP-binding sites, and suggest that ATP binding promotes subunit rearrangement and ion channel opening.

Crystal structure of the ATP-gated P2X(4) ion channel in the closed state.,Kawate T, Michel JC, Birdsong WT, Gouaux E Nature. 2009 Jul 30;460(7255):592-8. PMID:19641588^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kasuya G, Fujiwara Y, Tsukamoto H, Morinaga S, Ryu S, Touhara K, Ishitani R, Furutani Y, Hattori M, Nureki O. Structural insights into the nucleotide base specificity of P2X receptors. Sci Rep. 2017 Mar 23;7:45208. doi: 10.1038/srep45208. PMID:28332633 doi:http://dx.doi.org/10.1038/srep45208
↑ Kawate T, Michel JC, Birdsong WT, Gouaux E. Crystal structure of the ATP-gated P2X(4) ion channel in the closed state. Nature. 2009 Jul 30;460(7255):592-8. PMID:19641588 doi:10.1038/nature08198