2ped
From Proteopedia
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(New page: 200px<br /><applet load="2ped" size="350" color="white" frame="true" align="right" spinBox="true" caption="2ped, resolution 2.95Å" /> '''Crystallographic mod...) |
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| - | [[Image:2ped.gif|left|200px]]<br /><applet load="2ped" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2ped, resolution 2.95Å" /> | ||
| - | '''Crystallographic model of 9-cis-rhodopsin'''<br /> | ||
| - | == | + | ==Crystallographic model of 9-cis-rhodopsin== |
| - | The primary photochemical process of the visual function has been | + | <StructureSection load='2ped' size='340' side='right'caption='[[2ped]], [[Resolution|resolution]] 2.95Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2ped]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PED 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]] 2.95Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ped OCA], [https://pdbe.org/2ped PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ped RCSB], [https://www.ebi.ac.uk/pdbsum/2ped PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ped ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/OPSD_BOVIN OPSD_BOVIN] Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).<ref>PMID:16908857</ref> <ref>PMID:17060607</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/pe/2ped_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=2ped ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The primary photochemical process of the visual function has been investigated using the three crystallographic models, 11-cis-rhodopsin, all-trans-bathorhodopsin, and the artificial isomeric 9-cis-rhodopsin. Detailed examination of the atomic displacements and dihedral angle changes of the retinal chromophore involved in the interconversion among these isomers suggests the mechanism of isomerization efficiency. | ||
| - | + | Photoisomerization mechanism of rhodopsin and 9-cis-rhodopsin revealed by x-ray crystallography.,Nakamichi H, Buss V, Okada T Biophys J. 2007 Jun 15;92(12):L106-8. Epub 2007 Apr 20. PMID:17449675<ref>PMID:17449675</ref> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2ped" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[Rhodopsin 3D structures|Rhodopsin 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Bos taurus]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Nakamichi H]] | ||
| + | [[Category: Okada T]] | ||
Current revision
Crystallographic model of 9-cis-rhodopsin
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