2ntu: Difference between revisions

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-{{Seed}}
-[[Image:2ntu.png|left|200px]]
-<!--
+==Bacteriorhodopsin, wild type, before illumination==
-The line below this paragraph, containing "STRUCTURE_2ntu", creates the "Structure Box" on the page.
+<StructureSection load='2ntu' size='340' side='right'caption='[[2ntu]], [[Resolution|resolution]] 1.53&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'>[[2ntu]] 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=2NTU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NTU 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]] 1.53&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-{{STRUCTURE_2ntu|  PDB=2ntu  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ntu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ntu OCA], [https://pdbe.org/2ntu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ntu RCSB], [https://www.ebi.ac.uk/pdbsum/2ntu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ntu 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/nt/2ntu_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=2ntu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The L to M reaction of the bacteriorhodopsin photocycle includes the crucial proton transfer from the retinal Schiff base to Asp85. In spite of the importance of the L state in deciding central issues of the transport mechanism in this pump, the serious disagreements among the three published crystallographic structures of L have remained unresolved. Here, we report on the X-ray diffraction structure of the L state, to 1.53-1.73 A resolutions, from replicate data sets collected from six independent crystals. Unlike earlier studies, the partial occupancy refinement uses diffraction intensities from the same crystals before and after the illumination to produce the trapped L state. The high reproducibility of inter-atomic distances, and bond angles and torsions of the retinal, lends credibility to the structural model. The photoisomerized 13-cis retinal in L is twisted at the C(13)=C(14) and C(15)=NZ double-bonds, and the Schiff base does not lose its connection to Wat402 and, therefore, to the proton acceptor Asp85. The protonation of Asp85 by the Schiff base in the L--&gt;M reaction is likely to occur, therefore, via Wat402. It is evident from the structure of the L state that various conformational changes involving hydrogen-bonding residues and bound water molecules begin to propagate from the retinal to the protein at this stage already, and in both extracellular and cytoplasmic directions. Their rationales in the transport can be deduced from the way their amplitudes increase in the intermediates that follow L in the reaction cycle, and from the proton transfer reactions with which they are associated.
-===Bacteriorhodopsin, wild type, before illumination===
+Structural changes in the L photointermediate of bacteriorhodopsin.,Lanyi JK, Schobert B J Mol Biol. 2007 Feb 2;365(5):1379-92. Epub 2006 Nov 10. PMID:17141271<ref>PMID:17141271</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ntu" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17141271}}, adds the Publication Abstract to the page
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17141271 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17141271}}
+__TOC__
+</StructureSection>
-==About this Structure==
-NTU is a [[Single protein]] 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=2NTU OCA].
-==Reference==
-Structural changes in the L photointermediate of bacteriorhodopsin., Lanyi JK, Schobert B, J Mol Biol. 2007 Feb 2;365(5):1379-92. Epub 2006 Nov 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17141271 17141271]
 [[Category: Halobacterium salinarum]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Lanyi, J K.]]
+[[Category: Lanyi JK]]
-[[Category: Schobert, B.]]
+[[Category: Schobert B]]
-[[Category: 7-transmembrane]]
-[[Category: Haloarchaea]]
-[[Category: Ion pump]]
-[[Category: Ion transport]]
-[[Category: Lipid]]
-[[Category: Membrane protein]]
-[[Category: Photoreceptor]]
-[[Category: Retinal protein]]
-[[Category: Serpentine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:15:24 2008''