1dze: Difference between revisions

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-{{Seed}}
-[[Image:1dze.png|left|200px]]
-<!--
+==Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K==
-The line below this paragraph, containing "STRUCTURE_1dze", creates the "Structure Box" on the page.
+<StructureSection load='1dze' size='340' side='right'caption='[[1dze]], [[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'>[[1dze]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. The March 2002 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Bacteriorhodopsin''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2002_3 10.2210/rcsb_pdb/mom_2002_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DZE 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=GAL:BETA-D-GALACTOSE'>GAL</scene>, <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=L4P:3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL'>L4P</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-{{STRUCTURE_1dze|  PDB=1dze  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dze OCA], [https://pdbe.org/1dze PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dze RCSB], [https://www.ebi.ac.uk/pdbsum/1dze PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dze 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/dz/1dze_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=1dze ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Structural changes in the proton pumping cycle of wild-type bacteriorhodopsin were investigated by using a 3D crystal (space group P622)prepared by the membrane fusion method. Protein-protein contacts in the crystal elongate the lifetime of the M intermediate by a factor of approximately 100,allowing high levels of the M intermediate to accumulate under continuous illumination. When the M intermediate generated at room temperature was exposed to a low flux of X-rays (approximately 10(14) photons/mm2), this yellow intermediate was converted into a blue species having an absorption maximum at 650 nm. This color change is suggested to accompany a configuration change in the retinal-Lys216 chain. The true conformational change associated with formation of the M intermediate was analyzed by taking the X-radiation-induced structural change into account. Our result indicates that, upon formation of the M intermediate, helix G move stowards the extra-cellular side by, on average, 0.5 angstroms. This movement is coupled with several reactions occurring at distal sites in the protein: (1) reorientation of the side-chain of Leu93 contacting the C13 methyl group of retinal, which is accompanied by detachment of a water molecule from the Schiff base; (2) a significant distortion in the F-G loop, triggering destruction of a hydrogen bonding interaction between a pair of glutamate groups (Glu194 and Glu204); (3) formation of a salt bridge between the carboxylate group of Glu204 and the guanidinium ion of Arg82, which is accompanied by a large distortion in the extra-cellular half of helix C; (4)noticeable movements of the AB loop and the cytoplasmic end of helix B. But, no appreciable change is induced in the peptide backbone of helices A,D, E and F. These structural changes are discussed from the viewpoint of translocation of water molecules.
-===STRUCTURE OF THE M INTERMEDIATE OF BACTERIORHODOPSIN TRAPPED AT 100K===
+Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix.,Takeda K, Matsui Y, Kamiya N, Adachi S, Okumura H, Kouyama T J Mol Biol. 2004 Aug 20;341(4):1023-37. PMID:15328615<ref>PMID:15328615</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1dze" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15328615}}, adds the Publication Abstract to the page
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15328615 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15328615}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DZE is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. The March 2002 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Bacteriorhodopsin''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2002_3 10.2210/rcsb_pdb/mom_2002_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZE OCA].
-==Reference==
-<ref group="xtra">PMID:15328615</ref><ref group="xtra">PMID:10393291</ref><references group="xtra"/>
 [[Category: Bacteriorhodopsin]]
 [[Category: Halobacterium salinarum]]
-[[Category: Adachi, S.]]
+[[Category: Large Structures]]
-[[Category: Hino, T.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Iizuka, T.]]
+[[Category: Adachi S]]
-[[Category: Kamiya, N.]]
+[[Category: Hino T]]
-[[Category: Kanamori, E.]]
+[[Category: Iizuka T]]
-[[Category: Kouyama, T.]]
+[[Category: Kamiya N]]
-[[Category: Matsui, Y.]]
+[[Category: Kanamori E]]
-[[Category: Okumura, H.]]
+[[Category: Kouyama T]]
-[[Category: Sato, H.]]
+[[Category: Matsui Y]]
-[[Category: Takeda, K.]]
+[[Category: Okumura H]]
-[[Category: Yamane, T.]]
+[[Category: Sato H]]
-[[Category: Bacteriorhodopsin]]
+[[Category: Takeda K]]
-[[Category: Halobacteria]]
+[[Category: Yamane T]]
-[[Category: Helix]]
-[[Category: Ion pump]]
-[[Category: Membrane protein]]
-[[Category: Photoreceptor]]
-[[Category: Proton pump]]
-[[Category: Reaction intermediate]]
-[[Category: Retinal protein]]
-[[Category: Sliding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 10:32:18 2009''