4lmj: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-{{STRUCTURE_4lmj|  PDB=4lmj  |  SCENE=  }}
-===GLIC Liganded-closed-channel Conformation, Mutant T25'A===
-==Function==
+==GLIC Liganded-closed-channel Conformation, Mutant T25'A==
-[[http://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>
+<StructureSection load='4lmj' size='340' side='right'caption='[[4lmj]], [[Resolution|resolution]] 3.44&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4lmj]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloeobacter_violaceus Gloeobacter violaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LMJ 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]] 3.44&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></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=4lmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lmj OCA], [https://pdbe.org/4lmj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lmj RCSB], [https://www.ebi.ac.uk/pdbsum/4lmj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lmj 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 ==
+Cryoelectron microscopy and X-ray crystallography have recently been used to generate structural models that likely represent the unliganded closed-channel conformation and the fully liganded open-channel conformation of different members of the nicotinic-receptor superfamily. To characterize the structure of the closed-channel conformation in its liganded state, we identified a number of positions in the loop between transmembrane segments 2 (M2) and 3 (M3) of a proton-gated ortholog from the bacterium Gloeobacter violaceus (GLIC) where mutations to alanine reduce the liganded-gating equilibrium constant, and solved the crystal structures of two such mutants (T25'A and Y27'A) at pH approximately 4.0. At the level of backbone atoms, the liganded closed-channel model presented here differs from the liganded open-channel structure of GLIC in the pre-M1 linker, the M3-M4 loop, and much more prominently, in the extracellular half of the pore lining, where the more pronounced tilt of the closed-channel M2 alpha-helices toward the pore's long axis narrows the permeation pathway. On the other hand, no differences between the liganded closed-channel and open-channel models could be detected at the level of the extracellular domain, where conformational changes are expected to underlie the low-to-high proton-affinity switch that drives gating of proton-bound channels. Thus, the liganded closed-channel model is nearly indistinguishable from the recently described "locally closed" structure. However, because cross-linking strategies (which could have stabilized unstable conformations) and mutations involving ionizable side chains (which could have affected proton-gated channel activation) were purposely avoided, we favor the notion that this structure represents one of the end states of liganded gating rather than an unstable intermediate.
-==About this Structure==
+Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography.,Gonzalez-Gutierrez G, Cuello LG, Nair SK, Grosman C Proc Natl Acad Sci U S A. 2013 Oct 28. PMID:24167270<ref>PMID:24167270</ref>
-[[4lmj]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Gloeobacter_violaceus Gloeobacter violaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LMJ OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<references group="xtra"/><references/>
+</div>
+<div class="pdbe-citations 4lmj" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ion channels 3D structures|Ion channels 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Gloeobacter violaceus]]
-[[Category: Gonzalez-Gutierrez, G.]]
+[[Category: Large Structures]]
-[[Category: Grosman, C.]]
+[[Category: Gonzalez-Gutierrez G]]
-[[Category: Membrane protein]]
+[[Category: Grosman C]]
-[[Category: Pentameric ligand-gated ion channel]]
-[[Category: Prokaryotic cys-loop receptor]]
-[[Category: Transport protein]]