2yfp: Difference between revisions

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-{{Seed}}
-[[Image:2yfp.png|left|200px]]
-<!--
+==STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP==
-The line below this paragraph, containing "STRUCTURE_2yfp", creates the "Structure Box" on the page.
+<StructureSection load='2yfp' size='340' side='right'caption='[[2yfp]], [[Resolution|resolution]] 2.60&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'>[[2yfp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YFP 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]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr>
-{{STRUCTURE_2yfp|  PDB=2yfp  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yfp OCA], [https://pdbe.org/2yfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yfp RCSB], [https://www.ebi.ac.uk/pdbsum/2yfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yfp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
+== 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/yf/2yfp_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=2yfp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Because of its ability to spontaneously generate its own fluorophore, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria is used extensively as a fluorescent marker in molecular and cell biology. The yellow fluorescent proteins (YFPs) have the longest wavelength emissions of all GFP variants examined to date. This shift in the spectrum is the result of a T203Y substitution (single-letter amino acid code), a mutation rationally designed on the basis of the X-ray structure of GFP S65T. RESULTS: We have determined the crystal structures of YFP T203Y/S65G/V68L/S72A and YFP H148G to 2.5 and 2.6 A resolution, respectively. Both structures show clear electron density for nearly coplanar pi-pi stacking between Tyr203 and the chromophore. The chromophore has been displaced by nearly 1 A in comparison to other available structures. Although the H148G mutation results in the generation of a solvent channel to the chromophore cavity, intense fluorescence is maintained. The chromophore in the intact protein can be titrated, and the two variants have pKa values of 7.0 (YFP) and 8.0 (YFP H148G). CONCLUSIONS: The observed red shift of the T203Y YFP variant is proposed to be mainly due to the additional polarizability of the pi-stacked Tyr203. The altered location of the chromophore suggests that the exact positions of nearby residues are not crucial for the chemistry of chromophore formation. The YFPs significantly extend the pH range over which GFPs may be employed as pH indicators in live cells.
-===STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP===
+Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein.,Wachter RM, Elsliger MA, Kallio K, Hanson GT, Remington SJ Structure. 1998 Oct 15;6(10):1267-77. PMID:9782051<ref>PMID:9782051</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2yfp" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9782051}}, adds the Publication Abstract to the page
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9782051 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9782051}}
+__TOC__
+</StructureSection>
-==About this Structure==
-YFP is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YFP OCA].
-==Reference==
-<ref group="xtra">PMID:9782051</ref><references group="xtra"/>
 [[Category: Aequorea victoria]]
-[[Category: Elsliger, M A.]]
+[[Category: Large Structures]]
-[[Category: Hanson, G T.]]
+[[Category: Elsliger MA]]
-[[Category: Kallio, K.]]
+[[Category: Hanson GT]]
-[[Category: Remington, S J.]]
+[[Category: Kallio K]]
-[[Category: Wachter, R M.]]
+[[Category: Remington SJ]]
-[[Category: Bioluminescence]]
+[[Category: Wachter RM]]
-[[Category: Fluorescent tag]]
-[[Category: Green fluorescent protein]]
-[[Category: Photoactive protein]]
-[[Category: Photosynthesis]]
-[[Category: Yellow-emission variant]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 15:09:16 2009''