3aym: Difference between revisions

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-[[Image:3aym.png|left|200px]]
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+==Crystal structure of the batho intermediate of squid rhodopsin==
-The line below this paragraph, containing "STRUCTURE_3aym", creates the "Structure Box" on the page.
+<StructureSection load='3aym' size='340' side='right'caption='[[3aym]], [[Resolution|resolution]] 2.80&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'>[[3aym]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Todarodes_pacificus Todarodes pacificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AYM 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]] 2.8&#8491;</td></tr>
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+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=PC1:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PC1</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3aym|  PDB=3aym  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3aym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aym OCA], [https://pdbe.org/3aym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aym RCSB], [https://www.ebi.ac.uk/pdbsum/3aym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aym ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OPSD_TODPA OPSD_TODPA] Visual pigments such as rhodopsin and porphyropsin are light-absorbing molecules that mediate vision. Rhodopsin consists of an apoprotein, opsin, covalently linked to 11-cis-retinal. This receptor is coupled to the activation of phospholipase C. Porphyropsin consists of opsin covalently linked to 11-cis 3,4-didehydroretinal.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Visual signal transduction is initiated by the photoisomerization of 11-cis retinal upon rhodopsin ligation. Unlike vertebrate rhodopsin, which interacts with Gt-type G-protein to stimulate the cyclic GMP signaling pathway, invertebrate rhodopsin interacts with Gq-type G-protein to stimulate a signaling pathway that is based on inositol 1,4,5-triphosphate. Since the inositol 1,4,5-triphosphate signaling pathway is utilized by mammalian nonvisual pigments and a large number of G-protein-coupled receptors, it is important to elucidate how the activation mechanism of invertebrate rhodopsin differs from that of vertebrate rhodopsin. Previous crystallographic studies of squid and bovine rhodopsins have shown that there is a profound difference in the structures of the retinal-binding pockets of these photoreceptors. Here, we report the crystal structures of all-trans bathorhodopsin (Batho; the first photoreaction intermediate) and the artificial 9-cis isorhodopsin (Iso) of squid rhodopsin. Upon the formation of Batho, the central moiety of the retinal was observed to move largely towards the cytoplasmic side, while the Schiff base and the ionone ring underwent limited movements (i.e., the all-trans retinal in Batho took on a right-handed screwed configuration). Conversely, the 9-cis retinal in Iso took on a planar configuration. Our results suggest that the light energy absorbed by squid rhodopsin is mostly converted into the distortion energy of the retinal polyene chain and surrounding residues.
-===Crystal structure of the batho intermediate of squid rhodopsin===
+Crystallographic analysis of the primary photochemical reaction of squid rhodopsin.,Murakami M, Kouyama T J Mol Biol. 2011 Oct 28;413(3):615-27. Epub 2011 Aug 31. PMID:21906602<ref>PMID:21906602</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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+</div>
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+<div class="pdbe-citations 3aym" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 21906602 is the PubMed ID number.
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-{{ABSTRACT_PUBMED_21906602}}
-==About this Structure==
-[[3aym]] is a 2 chain structure of [[Rhodopsin]] with sequence from [http://en.wikipedia.org/wiki/Todarodes_pacificus Todarodes pacificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AYM OCA].
 ==See Also==
-*[[Rhodopsin]]
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:021906602</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Todarodes pacificus]]
-[[Category: Kouyama, T.]]
+[[Category: Kouyama T]]
-[[Category: Murakami, M.]]
+[[Category: Murakami M]]
-[[Category: Chromophore]]
-[[Category: Glycoprotein]]
-[[Category: Gq-type g-protein]]
-[[Category: Lipoprotein]]
-[[Category: Membrane]]
-[[Category: Phosphorylation]]
-[[Category: Photoreceptor]]
-[[Category: Signaling protein]]
-[[Category: Transmembrane protein]]