2nlj: Difference between revisions

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-[[Image:2nlj.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2nlj", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2nlj|  PDB=2nlj  |  SCENE=  }}
-'''Potassium Channel KcsA(M96V)-Fab complex in KCl'''
+==Potassium Channel KcsA(M96V)-Fab complex in KCl==
+<StructureSection load='2nlj' size='340' side='right'caption='[[2nlj]], [[Resolution|resolution]] 2.52&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2nlj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NLJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NLJ 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]] 2.52&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGA:DIACYL+GLYCEROL'>DGA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=2nlj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nlj OCA], [https://pdbe.org/2nlj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nlj RCSB], [https://www.ebi.ac.uk/pdbsum/2nlj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nlj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KCSA_STRLI KCSA_STRLI] Acts as a pH-gated potassium ion channel; changing the cytosolic pH from 7 to 4 opens the channel, although it is not clear if this is the physiological stimulus for channel opening. Monovalent cation preference is K(+) > Rb(+) > NH4(+) >> Na(+) > Li(+).<ref>PMID:7489706</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nl/2nlj_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2nlj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Thermodynamic measurements of ion binding to the Streptomyces lividans K(+) channel were carried out using isothermal titration calorimetry, whereas atomic structures of ion-bound and ion-free conformations of the channel were characterized by x-ray crystallography. Here we use these assays to show that the ion radius dependence of selectivity stems from the channel's recognition of ion size (i.e., volume) rather than charge density. Ion size recognition is a function of the channel's ability to adopt a very specific conductive structure with larger ions (K(+), Rb(+), Cs(+), and Ba(2+)) bound and not with smaller ions (Na(+), Mg(2+), and Ca(2+)). The formation of the conductive structure involves selectivity filter atoms that are in direct contact with bound ions as well as protein atoms surrounding the selectivity filter up to a distance of 15 A from the ions. We conclude that ion selectivity in a K(+) channel is a property of size-matched ion binding sites created by the protein structure.
-==Overview==
+Structural and thermodynamic properties of selective ion binding in a K+ channel.,Lockless SW, Zhou M, MacKinnon R PLoS Biol. 2007 May;5(5):e121. PMID:17472437<ref>PMID:17472437</ref>
-Thermodynamic measurements of ion binding to the Streptomyces lividans K(+) channel were carried out using isothermal titration calorimetry, whereas atomic structures of ion-bound and ion-free conformations of the channel were characterized by x-ray crystallography. Here we use these assays to show that the ion radius dependence of selectivity stems from the channel's recognition of ion size (i.e., volume) rather than charge density. Ion size recognition is a function of the channel's ability to adopt a very specific conductive structure with larger ions (K(+), Rb(+), Cs(+), and Ba(2+)) bound and not with smaller ions (Na(+), Mg(2+), and Ca(2+)). The formation of the conductive structure involves selectivity filter atoms that are in direct contact with bound ions as well as protein atoms surrounding the selectivity filter up to a distance of 15 A from the ions. We conclude that ion selectivity in a K(+) channel is a property of size-matched ion binding sites created by the protein structure.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-NLJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NLJ OCA].
+</div>
+<div class="pdbe-citations 2nlj" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural and thermodynamic properties of selective ion binding in a K+ channel., Lockless SW, Zhou M, MacKinnon R, PLoS Biol. 2007 May;5(5):e121. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17472437 17472437]
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Potassium channel 3D structures|Potassium channel 3D structures]]
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
 [[Category: Streptomyces lividans]]
-[[Category: Lockless, S W.]]
+[[Category: Lockless SW]]
-[[Category: MacKinnon, R.]]
+[[Category: MacKinnon R]]
-[[Category: Zhou, M.]]
+[[Category: Zhou M]]
-[[Category: 3d-structure]]
-[[Category: Ion transport]]
-[[Category: Ionic channel]]
-[[Category: K channel]]
-[[Category: Protein-antibody fab complex]]
-[[Category: Transmembrane]]
-[[Category: Voltage-gated channel]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 09:36:46 2008''