3dqa: Difference between revisions

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-{{Seed}}
-[[Image:3dqa.jpg|left|200px]]
-<!--
+==Structure of the Yellow Fluorescent Protein Citrine Frozen at 1250 Atmospheres Number 4: Structure 14 in a Series of 26 High Pressure Structures==
-The line below this paragraph, containing "STRUCTURE_3dqa", creates the "Structure Box" on the page.
+<StructureSection load='3dqa' size='340' side='right'caption='[[3dqa]], [[Resolution|resolution]] 1.44&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'>[[3dqa]] 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=3DQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DQA 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]] 1.44&#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_3dqa|  PDB=3dqa  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dqa OCA], [https://pdbe.org/3dqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dqa RCSB], [https://www.ebi.ac.uk/pdbsum/3dqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dqa 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/dq/3dqa_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=3dqa ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A protein molecule is an intricate system whose function is highly sensitive to small external perturbations. However, no examples that correlate protein function with progressive subangstrom structural perturbations have thus far been presented. To elucidate this relationship, we have investigated a fluorescent protein, citrine, as a model system under high-pressure perturbation. The protein has been compressed to produce deformations of its chromophore by applying a high-pressure cryocooling technique. A closely spaced series of x-ray crystallographic structures reveals that the chromophore undergoes a progressive deformation of up to 0.8 A at an applied pressure of 500 MPa. It is experimentally demonstrated that the structural motion is directly correlated with the progressive fluorescence shift of citrine from yellow to green under these conditions. This protein is therefore highly sensitive to subangstrom deformations and its function must be understood at the subangstrom level. These results have significant implications for protein function prediction and biomolecule design and engineering, because they suggest methods to tune protein function by modification of the protein scaffold.
-===Structure of the Yellow Fluorescent Protein Citrine Frozen at 1250 Atmospheres Number 4: Structure 14 in a Series of 26 High Pressure Structures===
+Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift.,Barstow B, Ando N, Kim CU, Gruner SM Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13362-6. Epub 2008 Sep 3. PMID:18768811<ref>PMID:18768811</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dqa" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18768811}}, 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 18768811 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18768811}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DQA is a [[Single protein]] 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=3DQA OCA].
-==Reference==
-Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift., Barstow B, Ando N, Kim CU, Gruner SM, Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13362-6. Epub 2008 Sep 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18768811 18768811]
-High-pressure cooling of protein crystals without cryoprotectants., Kim CU, Kapfer R, Gruner SM, Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):881-90. Epub 2005, Jun 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15983410 15983410]
 [[Category: Aequorea victoria]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Barstow, B.]]
+[[Category: Barstow B]]
-[[Category: Kim, C U.]]
+[[Category: Kim CU]]
-[[Category: Beta barrel]]
-[[Category: Chromophore]]
-[[Category: Fluorescent protein]]
-[[Category: High pressure]]
-[[Category: Luminescence]]
-[[Category: Luminescent protein]]
-[[Category: Photoprotein]]
-[[Category: Yellow fluorescent protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 24 10:42:13 2008''