2ayv: Difference between revisions

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-[[Image:2ayv.png|left|200px]]
-{{STRUCTURE_2ayv|  PDB=2ayv  |  SCENE=  }}
+==Crystal structure of a putative ubiquitin-conjugating enzyme E2 from Toxoplasma gondii==
+<StructureSection load='2ayv' size='340' side='right'caption='[[2ayv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ayv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Toxoplasma_gondii Toxoplasma gondii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AYV 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]] 2.001&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=2ayv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ayv OCA], [https://pdbe.org/2ayv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ayv RCSB], [https://www.ebi.ac.uk/pdbsum/2ayv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ayv ProSAT]</span></td></tr>
+</table>
+== 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/ay/2ayv_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=2ayv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Parasites from the protozoan phylum Apicomplexa are responsible for diseases, such as malaria, toxoplasmosis and cryptosporidiosis, all of which have significantly higher rates of mortality and morbidity in economically underdeveloped regions of the world. Advances in vaccine development and drug discovery are urgently needed to control these diseases and can be facilitated by production of purified recombinant proteins from Apicomplexan genomes and determination of their 3D structures. To date, both heterologous expression and crystallization of Apicomplexan proteins have seen only limited success. In an effort to explore the effectiveness of producing and crystallizing proteins on a genome-scale using a standardized methodology, over 400 distinct Plasmodium falciparum target genes were chosen representing different cellular classes, along with select orthologues from four other Plasmodium species as well as Cryptosporidium parvum and Toxoplasma gondii. From a total of 1008 genes from the seven genomes, 304 (30.2%) produced purified soluble proteins and 97 (9.6%) crystallized, culminating in 36 crystal structures. These results demonstrate that, contrary to previous findings, a standardized platform using Escherichia coli can be effective for genome-scale production and crystallography of Apicomplexan proteins. Predictably, orthologous proteins from different Apicomplexan genomes behaved differently in expression, purification and crystallization, although the overall success rates of Plasmodium orthologues do not differ significantly. Their differences were effectively exploited to elevate the overall productivity to levels comparable to the most successful ongoing structural genomics projects: 229 of the 468 target genes produced purified soluble protein from one or more organisms, with 80 and 32 of the purified targets, respectively, leading to crystals and ultimately structures from one or more orthologues.
-===Crystal structure of a putative ubiquitin-conjugating enzyme E2 from Toxoplasma gondii===
+Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.,Vedadi M, Lew J, Artz J, Amani M, Zhao Y, Dong A, Wasney GA, Gao M, Hills T, Brokx S, Qiu W, Sharma S, Diassiti A, Alam Z, Melone M, Mulichak A, Wernimont A, Bray J, Loppnau P, Plotnikova O, Newberry K, Sundararajan E, Houston S, Walker J, Tempel W, Bochkarev A, Kozieradzki I, Edwards A, Arrowsmith C, Roos D, Kain K, Hui R Mol Biochem Parasitol. 2007 Jan;151(1):100-10. Epub 2006 Nov 13. PMID:17125854<ref>PMID:17125854</ref>
-{{ABSTRACT_PUBMED_17125854}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2ayv" style="background-color:#fffaf0;"></div>
-[[2ayv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Toxoplasma_gondii Toxoplasma gondii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AYV OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:017125854</ref><references group="xtra"/>
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Toxoplasma gondii]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Alam Z]]
-[[Category: Alam, Z.]]
+[[Category: Amani M]]
-[[Category: Amani, M.]]
+[[Category: Arrowsmith C]]
-[[Category: Arrowsmith, C.]]
+[[Category: Bochkarev A]]
-[[Category: Bochkarev, A.]]
+[[Category: Dong A]]
-[[Category: Dong, A.]]
+[[Category: Edwards A]]
-[[Category: Edwards, A.]]
+[[Category: Hui R]]
-[[Category: Hui, R.]]
+[[Category: Kozieradzki I]]
-[[Category: Kozieradzki, I.]]
+[[Category: Lew J]]
-[[Category: Lew, J.]]
+[[Category: Melone M]]
-[[Category: Melone, M.]]
+[[Category: Sundstrom M]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Tempel W]]
-[[Category: Sundstrom, M.]]
+[[Category: Vedadi M]]
-[[Category: Tempel, W.]]
+[[Category: Wasney G]]
-[[Category: Vedadi, M.]]
+[[Category: Weigelt J]]
-[[Category: Wasney, G.]]
+[[Category: Zhao Y]]
-[[Category: Weigelt, J.]]
-[[Category: Zhao, Y.]]
-[[Category: Ligase]]
-[[Category: Sgc]]
-[[Category: Structural genomic]]
-[[Category: Structural genomics consortium]]
-[[Category: Ubiquitin]]
-[[Category: Ubiquitin-conjugating enzyme]]