View source for 7yxa


==XFEL crystal structure of the human sphingosine 1 phosphate receptor 5 in complex with ONO-5430608==
<StructureSection load='7yxa' size='340' side='right'caption='[[7yxa]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7yxa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YXA FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B2O:4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1~{H}-3-benzazepin-3-ium-3-yl]butanoic+acid'>B2O</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7yxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yxa OCA], [https://pdbe.org/7yxa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yxa RCSB], [https://www.ebi.ac.uk/pdbsum/7yxa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yxa ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX] Electron-transport protein of unknown function.[https://www.uniprot.org/uniprot/S1PR5_HUMAN S1PR5_HUMAN] Receptor for the lysosphingolipid sphingosine 1-phosphate (S1P). S1P is a bioactive lysophospholipid that elicits diverse physiological effect on most types of cells and tissues. Is coupled to both the G(i/0)alpha and G(12) subclass of heteromeric G-proteins (By similarity). May play a regulatory role in the transformation of radial glial cells into astrocytes and may affect proliferative activity of these cells.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The bioactive lysophospholipid sphingosine-1-phosphate (S1P) acts via five different subtypes of S1P receptors (S1PRs) - S1P(1-5). S1P(5) is predominantly expressed in nervous and immune systems, regulating the egress of natural killer cells from lymph nodes and playing a role in immune and neurodegenerative disorders, as well as carcinogenesis. Several S1PR therapeutic drugs have been developed to treat these diseases; however, they lack receptor subtype selectivity, which leads to side effects. In this article, we describe a 2.2 A resolution room temperature crystal structure of the human S1P(5) receptor in complex with a selective inverse agonist determined by serial femtosecond crystallography (SFX) at the Pohang Accelerator Laboratory X-Ray Free Electron Laser (PAL-XFEL) and analyze its structure-activity relationship data. The structure demonstrates a unique ligand-binding mode, involving an allosteric sub-pocket, which clarifies the receptor subtype selectivity and provides a template for structure-based drug design. Together with previously published S1PR structures in complex with antagonists and agonists, our structure with S1P(5)-inverse agonist sheds light on the activation mechanism and reveals structural determinants of the inverse agonism in the S1PR family.

Structural basis for receptor selectivity and inverse agonism in S1P(5) receptors.,Lyapina E, Marin E, Gusach A, Orekhov P, Gerasimov A, Luginina A, Vakhrameev D, Ergasheva M, Kovaleva M, Khusainov G, Khorn P, Shevtsov M, Kovalev K, Bukhdruker S, Okhrimenko I, Popov P, Hu H, Weierstall U, Liu W, Cho Y, Gushchin I, Rogachev A, Bourenkov G, Park S, Park G, Hyun HJ, Park J, Gordeliy V, Borshchevskiy V, Mishin A, Cherezov V Nat Commun. 2022 Aug 12;13(1):4736. doi: 10.1038/s41467-022-32447-1. PMID:35961984<ref>PMID:35961984</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7yxa" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Borshchevskiy V]]
[[Category: Bourenkov G]]
[[Category: Bukhdruker S]]
[[Category: Cherezov V]]
[[Category: Cho Y]]
[[Category: Ergasheva M]]
[[Category: Gerasimov A]]
[[Category: Gordeliy V]]
[[Category: Gusach A]]
[[Category: Gushchin I]]
[[Category: Hu H]]
[[Category: Huyn HJ]]
[[Category: Khorn P]]
[[Category: Khusainov G]]
[[Category: Kovalev K]]
[[Category: Kovaleva M]]
[[Category: Liu W]]
[[Category: Luginina A]]
[[Category: Lyapina E]]
[[Category: Marin E]]
[[Category: Mishin A]]
[[Category: Okhrimenko I]]
[[Category: Orekhov P]]
[[Category: Park G]]
[[Category: Park J]]
[[Category: Park S]]
[[Category: Popov P]]
[[Category: Rogachev A]]
[[Category: Shevtsov M]]
[[Category: Vakhrameev D]]
[[Category: Weierstall U]]