3ip2: Difference between revisions

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-[[Image:3ip2.png|left|200px]]
-{{STRUCTURE_3ip2|  PDB=3ip2  |  SCENE=  }}
+==Crystal structure of red fluorescent protein Neptune at pH 7.0==
+<StructureSection load='3ip2' size='340' side='right'caption='[[3ip2]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ip2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Entacmaea_quadricolor Entacmaea quadricolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IP2 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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NRQ:{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>NRQ</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=3ip2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ip2 OCA], [https://pdbe.org/3ip2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ip2 RCSB], [https://www.ebi.ac.uk/pdbsum/3ip2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ip2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RFP_ENTQU RFP_ENTQU] Pigment protein.<ref>PMID:12185250</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/ip/3ip2_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=3ip2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Fluorescent proteins have become valuable tools for biomedical research as protein tags, reporters of gene expression, biosensor components, and cell lineage tracers. However, applications of fluorescent proteins for deep tissue imaging in whole mammals have been constrained by the opacity of tissues to excitation light below 600 nm, because of absorbance by hemoglobin. Fluorescent proteins that excite efficiently in the "optical window" above 600 nm are therefore highly desirable. We report here the evolution of far-red fluorescent proteins with peak excitation at 600 nm or above. The brightest one of these, Neptune, performs well in imaging deep tissues in living mice. The crystal structure of Neptune reveals a novel mechanism for red-shifting involving the acquisition of a new hydrogen bond with the acylimine region of the chromophore.
-===Crystal structure of red fluorescent protein Neptune at pH 7.0===
+Autofluorescent proteins with excitation in the optical window for intravital imaging in mammals.,Lin MZ, McKeown MR, Ng HL, Aguilera TA, Shaner NC, Campbell RE, Adams SR, Gross LA, Ma W, Alber T, Tsien RY Chem Biol. 2009 Nov 25;16(11):1169-79. PMID:19942140<ref>PMID:19942140</ref>
-{{ABSTRACT_PUBMED_19942140}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3ip2" style="background-color:#fffaf0;"></div>
-[[3ip2]] is a 1 chain structure of [[Alyssa Marsico/Sandbox 1]], [[Devon McCarthy/Sandbox 1]], [[Green Fluorescent Protein]], [[Sandbox104]] and [[User:Joanne Lau/Sandbox 5]] with sequence from [http://en.wikipedia.org/wiki/Entacmaea_quadricolor Entacmaea quadricolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IP2 OCA].
 ==See Also==
-*[[Alyssa Marsico/Sandbox 1|Alyssa Marsico/Sandbox 1]]
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
-*[[Devon McCarthy/Sandbox 1|Devon McCarthy/Sandbox 1]]
+== References ==
-*[[Green Fluorescent Protein|Green Fluorescent Protein]]
+<references/>
-*[[Sandbox104|Sandbox104]]
+__TOC__
-*[[User:Joanne Lau/Sandbox 5|User:Joanne Lau/Sandbox 5]]
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:019942140</ref><references group="xtra"/>
 [[Category: Entacmaea quadricolor]]
-[[Category: Adams, S R.]]
+[[Category: Large Structures]]
-[[Category: Aguilera, T A.]]
+[[Category: Adams SR]]
-[[Category: Alber, T.]]
+[[Category: Aguilera TA]]
-[[Category: Campbell, R E.]]
+[[Category: Alber T]]
-[[Category: Lin, M Z.]]
+[[Category: Campbell RE]]
-[[Category: Ma, W.]]
+[[Category: Lin MZ]]
-[[Category: McKeown, M R.]]
+[[Category: Ma W]]
-[[Category: Ng, H L.]]
+[[Category: McKeown MR]]
-[[Category: Shaner, N C.]]
+[[Category: Ng HL]]
-[[Category: Tsien, R Y.]]
+[[Category: Shaner NC]]
-[[Category: Fluorescent protein]]
+[[Category: Tsien RY]]