3tmr: Difference between revisions

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-[[Image:3tmr.png|left|200px]]
-<!--
+==IrisFP, planar chromophore==
-The line below this paragraph, containing "STRUCTURE_3tmr", creates the "Structure Box" on the page.
+<StructureSection load='3tmr' size='340' side='right'caption='[[3tmr]], [[Resolution|resolution]] 2.00&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'>[[3tmr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lobophyllia_hemprichii Lobophyllia hemprichii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TMR 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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR8:2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE'>CR8</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3tmr|  PDB=3tmr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tmr OCA], [https://pdbe.org/3tmr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tmr RCSB], [https://www.ebi.ac.uk/pdbsum/3tmr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tmr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5S6Z9_LOBHE Q5S6Z9_LOBHE]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Fluorescent proteins (FPs) of the green fluorescent protein family blink and bleach like all fluorophores. However, contrary to organic dyes, the mechanisms by which transient losses of fluorescence occur in FPs have received little attention. Here, we focus on the photoactivatable IrisFP, for which a transient non-fluorescent chromophoric state with distorted geometry was recently reported (Adam, V.; et al. J. Am. Chem. Soc.2009, 131, 18063). We investigated the chemical nature of this blinked state by employing quantum chemical/molecular mechanical calculations. Our findings suggest two previously unidentified dark states that display similar distorted chromophores with a transiently ruptured pi-electron system. Both are protonated at atom C(alpha) of the chromophore methylene bridge. Transient protonation may occur via proton transfer from the nearby Arg66 either in the triplet state T(1) after intersystem crossing or in an anionic radical (doublet) ground state. As Arg66 is conserved in green-to-red photoconvertible FPs, these dark states are predicted to be common to all these proteins. We also suggest that C(alpha) protonated dark states may accelerate photobleaching by favoring decarboxylation of the fully conserved Glu212.
-===IrisFP, planar chromophore===
+The Nature of Transient Dark States in a Photoactivatable Fluorescent Protein.,Roy A, Field MJ, Adam V, Bourgeois D J Am Chem Soc. 2011 Oct 31. PMID:22039963<ref>PMID:22039963</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_22039963}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3tmr" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 22039963 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22039963}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3tmr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lobophyllia_hemprichii Lobophyllia hemprichii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TMR OCA].
-==Reference==
-<ref group="xtra">PMID:022039963</ref><references group="xtra"/>
 [[Category: Lobophyllia hemprichii]]
-[[Category: Adam, V.]]
+[[Category: Adam V]]
-[[Category: Bourgeois, D.]]
+[[Category: Bourgeois D]]
-[[Category: Carpentier, P.]]
+[[Category: Carpentier P]]
-[[Category: Field, M.]]
+[[Category: Field M]]
-[[Category: Roy, A.]]
+[[Category: Roy A]]
-[[Category: Beta-can]]
-[[Category: Fluorescent protein]]