2ped: Difference between revisions

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{{Seed}}
[[Image:2ped.png|left|200px]]


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==Crystallographic model of 9-cis-rhodopsin==
The line below this paragraph, containing "STRUCTURE_2ped", creates the "Structure Box" on the page.
<StructureSection load='2ped' size='340' side='right'caption='[[2ped]], [[Resolution|resolution]] 2.95&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'>[[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>
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]] 2.95&#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=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>
{{STRUCTURE_2ped|  PDB=2ped  |  SCENE= }}
<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.


===Crystallographic model of 9-cis-rhodopsin===
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>


From MEDLINE&reg;/PubMed&reg;, 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==
The line below this paragraph, {{ABSTRACT_PUBMED_17449675}}, adds the Publication Abstract to the page
*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17449675 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17449675}}
__TOC__
 
</StructureSection>
==About this Structure==
2PED is a [[Single protein]] structure of 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=2PED OCA].
 
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/17449675 17449675]
 
Protein assistance in the photoisomerization of rhodopsin and 9-cis-rhodopsin--insights from experiment and theory., Sekharan S, Sugihara M, Weingart O, Okada T, Buss V, J Am Chem Soc. 2007 Feb 7;129(5):1052-4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17263385 17263385]
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Nakamichi, H.]]
[[Category: Nakamichi H]]
[[Category: Okada, T.]]
[[Category: Okada T]]
[[Category: G protein-coupled receptor]]
[[Category: Rhodopsin]]
[[Category: Signaling protein]]
[[Category: Visual pigment]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:05:29 2008''
Retrieved from "https://proteopedia.org/2ped"