2zfe: Difference between revisions

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-{{Seed}}
-[[Image:2zfe.jpg|left|200px]]
-<!--
+==Crystal structure of bacteriorhodopsin-xenon complex==
-The line below this paragraph, containing "STRUCTURE_2zfe", creates the "Structure Box" on the page.
+<StructureSection load='2zfe' size='340' side='right'caption='[[2zfe]], [[Resolution|resolution]] 2.50&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'>[[2zfe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZFE 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=SGA:O3-SULFONYLGALACTOSE'>SGA</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-{{STRUCTURE_2zfe|  PDB=2zfe  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [https://pdbe.org/2zfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [https://www.ebi.ac.uk/pdbsum/2zfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zfe ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump.
+== 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/zf/2zfe_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=2zfe ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+To understand the functional role of apolar cavities in bacteriorhodopsin, a light-driven proton pump found in Halobacterium salinarum, we investigated the crystal structure in pressurized xenon or krypton. Diffraction data from the P622 crystal showed that one Xe or Kr atom binds to a preexisting hydrophobic cavity buried between helices C and D, located at the same depth from the membrane surface as Asp96, a key residue in the proton uptake pathway. The occupation fraction of Xe or Kr was calculated as approximately 0.32 at a pressure of 1 MPa. In the unphotolyzed state, the binding of Xe or Kr caused no large deformation of the cavity. However, the proton pumping cycle was greatly perturbed when an aqueous suspension of purple membrane was pressurized with xenon gas; that is, the decay of the M state was accelerated significantly (~5 times at full occupancy), while the decay of an equilibrium state of N and O was slightly decelerated. A similar but much smaller perturbation in the reaction kinetics was observed upon pressurization with krypton gas. In a glycerol/water mixture, xenon-induced acceleration of M decay became less significant in proportion to the water activity. Together with the structure of the xenon-bound protein, these observations suggest that xenon binding helps water molecules permeate into apolar cavities in the proton uptake pathway, thereby accelerating the water-mediated proton transfer from Asp96 to the Schiff base.
-===Crystal structure of bacteriorhodopsin-xenon complex===
+Effect of xenon binding to a hydrophobic cavity on the proton pumping cycle in bacteriorhodopsin.,Hayakawa N, Kasahara T, Hasegawa D, Yoshimura K, Murakami M, Kouyama T J Mol Biol. 2008 Dec 26;384(4):812-23. Epub 2008 Oct 9. PMID:18930734<ref>PMID:18930734</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2zfe" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18930734}}, adds the Publication Abstract to the page
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18930734 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18930734}}
+__TOC__
+</StructureSection>
-==About this Structure==
-ZFE is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA].
-==Reference==
-Effect of Xenon Binding to a Hydrophobic Cavity on the Proton Pumping Cycle in Bacteriorhodopsin., Hayakawa N, Kasahara T, Hasegawa D, Yoshimura K, Murakami M, Kouyama T, J Mol Biol. 2008 Oct 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18930734 18930734]
 [[Category: Halobacterium salinarum]]
-[[Category: Kouyama, T.]]
+[[Category: Large Structures]]
-[[Category: Chromophore]]
+[[Category: Kouyama T]]
-[[Category: Hydrogen ion transport]]
-[[Category: Hydrophobic cavity]]
-[[Category: Ion transport]]
-[[Category: Membrane]]
-[[Category: Photoreceptor protein]]
-[[Category: Proton transport]]
-[[Category: Pyrrolidone carboxylic acid]]
-[[Category: Receptor]]
-[[Category: Retinal protein]]
-[[Category: Sensory transduction]]
-[[Category: Transmembrane]]
-[[Category: Transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 12 10:44:17 2008''