3c9m: Difference between revisions

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-[[Image:3c9m.png|left|200px]]
-<!--
+==Structure of a mutant bovine rhodopsin in hexagonal crystal form==
-The line below this paragraph, containing "STRUCTURE_3c9m", creates the "Structure Box" on the page.
+<StructureSection load='3c9m' size='340' side='right'caption='[[3c9m]], [[Resolution|resolution]] 3.40&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'>[[3c9m]] is a 1 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=3C9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C9M 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]] 3.4&#8491;</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-{{STRUCTURE_3c9m|  PDB=3c9m  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c9m OCA], [https://pdbe.org/3c9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c9m RCSB], [https://www.ebi.ac.uk/pdbsum/3c9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c9m 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/c9/3c9m_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3c9m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The space-group symmetry of two crystal forms of rhodopsin (PDB codes 1gzm and 2j4y; space group P3(1)) can be re-interpreted as hexagonal (space group P6(4)). Two molecules of the G protein-coupled receptor are present in the asymmetric unit in the trigonal models. However, the noncrystallographic twofold axes parallel to the c axis can be treated as crystallographic symmetry operations in the hexagonal space group. This halves the asymmetric unit and makes all of the protein molecules equivalent in these structures. Corrections for merohedral twinning were also applied in the refinement in the higher symmetry space group for one of the structures (2j4y).
-===Structure of a mutant bovine rhodopsin in hexagonal crystal form===
+Alternative models for two crystal structures of bovine rhodopsin.,Stenkamp RE Acta Crystallogr D Biol Crystallogr. 2008 Aug;D64(Pt 8):902-4. Epub 2008, Jul 17. PMID:18645239<ref>PMID:18645239</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3c9m" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18645239}}, adds the Publication Abstract to the page
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18645239 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18645239}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3c9m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C9M OCA].
-==Reference==
-<ref group="xtra">PMID:18645239</ref><ref group="xtra">PMID:17825322</ref><references group="xtra"/>
 [[Category: Bos taurus]]
-[[Category: Stenkamp, R E.]]
+[[Category: Large Structures]]
-[[Category: Acetylation]]
+[[Category: Stenkamp RE]]
-[[Category: Alternate space group]]
-[[Category: Chromophore]]
-[[Category: G-protein coupled receptor]]
-[[Category: Glycoprotein]]
-[[Category: Integral membrane protein]]
-[[Category: Lipoprotein]]
-[[Category: Palmitate]]
-[[Category: Phosphoprotein]]
-[[Category: Phosphorylation]]
-[[Category: Photoreceptor]]
-[[Category: Photoreceptor protein]]
-[[Category: Receptor]]
-[[Category: Retinal protein]]
-[[Category: Sensory transduction]]
-[[Category: Signaling protein]]
-[[Category: Transducer]]
-[[Category: Transmembrane]]
-[[Category: Vision membrane]]
-[[Category: Visual pigment]]