2ei4: Difference between revisions

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-[[Image:2ei4.png|left|200px]]
-<!--
+==Trimeric complex of archaerhodopsin-2==
-The line below this paragraph, containing "STRUCTURE_2ei4", creates the "Structure Box" on the page.
+<StructureSection load='2ei4' size='340' side='right'caption='[[2ei4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2ei4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_sp._AUS-2 Halobacterium sp. AUS-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EI4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-{{STRUCTURE_2ei4|  PDB=2ei4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ei4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ei4 OCA], [https://pdbe.org/2ei4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ei4 RCSB], [https://www.ebi.ac.uk/pdbsum/2ei4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ei4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BACR2_HALS2 BACR2_HALS2]
+== 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/ei/2ei4_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=2ei4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Archaerhodopsin-2 (aR2), a retinal protein-carotenoid complex found in the claret membrane of Halorubrum sp. aus-2, functions as a light-driven proton pump. In this study, the membrane fusion method was utilized to prepare trigonal P321 crystals (a=b=98.2 A, c=56.2 A) and hexagonal P6(3) crystals (a=b=108.8 A, c=220.7 A). The trigonal crystal is made up of stacked membranes in which the aR2 trimers are arranged on a honeycomb lattice. Similar membranous structures are found in the hexagonal crystal, but four membrane layers with different orientations are contained in the unit cell. In these crystals, the carotenoid bacterioruberin [5,32-bis(2-hydroxypropan-2-yl)-2,8,12,16,21,25,29,35-octamethylhexatriaco nta-6,8,10,12,14,16,18,20,22,24,26,28,30-tridecaene-2,35-diol] binds to crevices between the subunits of the trimer. Its polyene chain is inclined from the membrane normal by an angle of about 20 degrees and, on the cytoplasmic side, it is surrounded by helices AB and DE of neighbouring subunits. This peculiar binding mode suggests that bacterioruberin plays a striking structural role for the trimerization of aR2. When compared with the aR2 structure in another crystal form containing no bacterioruberin, the proton release channel takes a more closed conformation in the P321 or P6(3) crystal; i.e., the native conformation of protein is stabilized in the trimeric protein-bacterioruberin complex. Interestingly, most residues participating in the trimerization are not conserved in bacteriorhodopsin, a homologous protein capable of forming a trimeric structure in the absence of bacterioruberin. Despite a large alteration in the amino acid sequence, the shape of the intratrimer hydrophobic space filled by lipids is highly conserved between aR2 and bacteriorhodopsin. Since a transmembrane helix facing this space undergoes a large conformational change during the proton pumping cycle, it is feasible that trimerization is an important strategy to capture special lipid components that are relevant to the protein activity.
-===Trimeric complex of archaerhodopsin-2===
+Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2.,Yoshimura K, Kouyama T J Mol Biol. 2008 Feb 1;375(5):1267-81. Epub 2007 Nov 22. PMID:18082767<ref>PMID:18082767</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ei4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18082767}}, adds the Publication Abstract to the page
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18082767 is the PubMed ID number.
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_18082767}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-[[2ei4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaea Archaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EI4 OCA].
+[[Category: Halobacterium sp. AUS-2]]
+[[Category: Large Structures]]
-==Reference==
+[[Category: Kouyama T]]
-<ref group="xtra">PMID:18082767</ref><references group="xtra"/>
-[[Category: Archaea]]
-[[Category: Kouyama, T.]]