4ilb: Difference between revisions

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-[[Image:4ilb.jpg|left|200px]]
-{{STRUCTURE_4ilb|  PDB=4ilb  |  SCENE=  }}
+==The pentameric ligand-gated ion channel GLIC A237F in complex with Rubidium==
+<StructureSection load='4ilb' size='340' side='right'caption='[[4ilb]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ilb]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloeobacter_violaceus_PCC_7421 Gloeobacter violaceus PCC 7421]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ILB 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]] 3.15&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLC:DIUNDECYL+PHOSPHATIDYL+CHOLINE'>PLC</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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=4ilb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ilb OCA], [https://pdbe.org/4ilb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ilb RCSB], [https://www.ebi.ac.uk/pdbsum/4ilb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ilb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLIC_GLOVI GLIC_GLOVI] Cationic channel with similar permeabilities for Na(+) and K(+), that is activated by an increase of the proton concentration on the extracellular side. Displays no permeability for chloride ions. Shows slow kinetics of activation, no desensitization and a single channel conductance of 8 pS. Might contribute to adaptation to external pH change.<ref>PMID:17167423</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+To understand the molecular mechanism of ion permeation in pentameric ligand-gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a prokaryotic pLGIC, at 2.4 A. Anomalous diffraction data were used to place bound anions and cations. This reveals ordered water molecules at the level of two rings of hydroxylated residues (named Ser6' and Thr2') that contribute to the ion selectivity filter. Two water pentagons are observed, a self-stabilized ice-like water pentagon and a second wider water pentagon, with one sodium ion between them. Single-channel electrophysiology shows that the side-chain hydroxyl of Ser6' is crucial for ion translocation. Simulations and electrostatics calculations complemented the description of hydration in the pore and suggest that the water pentagons observed in the crystal are important for the ion to cross hydrophobic constriction barriers. Simulations that pull a cation through the pore reveal that residue Ser6' actively contributes to ion translocation by reorienting its side chain when the ion is going through the pore. Generalization of these findings to the pLGIC family is proposed.
-===The pentameric ligand-gated ion channel GLIC A237F in complex with Rubidium===
+Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.,Sauguet L, Poitevin F, Murail S, Van Renterghem C, Moraga-Cid G, Malherbe L, Thompson AW, Koehl P, Corringer PJ, Baaden M, Delarue M EMBO J. 2013 Feb 12;32(5):728-41. doi: 10.1038/emboj.2013.17. Epub 2013 Feb 12. PMID:23403925<ref>PMID:23403925</ref>
-{{ABSTRACT_PUBMED_017729286}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4ilb" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[4ilb]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Gloeobacter_violaceus_pcc_7421 Gloeobacter violaceus pcc 7421]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILB OCA].
+*[[Ion channels 3D structures|Ion channels 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017729286</ref><references group="xtra"/>
+__TOC__
-[[Category: Gloeobacter violaceus pcc 7421]]
+</StructureSection>
-[[Category: Corringer, P J.]]
+[[Category: Gloeobacter violaceus PCC 7421]]
-[[Category: Delarue, M.]]
+[[Category: Large Structures]]
-[[Category: Sauguet, L.]]
+[[Category: Corringer PJ]]
-[[Category: Ion channel]]
+[[Category: Delarue M]]
-[[Category: Membrane]]
+[[Category: Sauguet L]]
-[[Category: Membrane protein]]
-[[Category: Pentameric ligand-gated ion channel]]
-[[Category: Transport protein]]