2ply: Difference between revisions

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-{{Seed}}
-[[Image:2ply.png|left|200px]]
-<!--
+==Structure of the mRNA binding fragment of elongation factor SelB in complex with SECIS RNA.==
-The line below this paragraph, containing "STRUCTURE_2ply", creates the "Structure Box" on the page.
+<StructureSection load='2ply' size='340' side='right'caption='[[2ply]], [[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'>[[2ply]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Moorella_thermoacetica Moorella thermoacetica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PLY 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_2ply|  PDB=2ply  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ply FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ply OCA], [https://pdbe.org/2ply PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ply RCSB], [https://www.ebi.ac.uk/pdbsum/2ply PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ply ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SELB_MOOTH SELB_MOOTH] Translation factor necessary for the incorporation of selenocysteine into proteins. It probably replaces EF-Tu for the insertion of selenocysteine directed by the UGA codon. SelB binds GTP and GDP.
+== 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/pl/2ply_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=2ply ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Elongation factor SelB is responsible for co-translational incorporation of selenocysteine (Sec) into proteins. The UGA stop codon is recoded as a Sec codon in the presence of a downstream mRNA hairpin. In prokaryotes, in addition to the EF-Tu-like N-terminal domains, a C-terminal extension containing four tandem winged-helix motifs (WH1-4) recognizes the mRNA hairpin. The 2.3-A resolution crystal structure of the Escherichia coli WH3/4 domains bound to mRNA with mutagenesis data reveal that the two WH motifs use the same structural elements to bind RNA. The structure together with the 2.6-A resolution structure of the WH1-4 domains from Moorella thermoacetica bound to RNA revealed that a salt bridge connecting WH2 to WH3 modules is disrupted upon mRNA binding. The results provide a structural basis for the molecular switch that may allow communication between tRNA and mRNA binding sites and illustrate how RNA acts as an activator of the switch. The structures show that tandem WH motifs not only provide an excellent scaffold for RNA binding but can also have an active role in the function of protein-RNA complexes.
-===Structure of the mRNA binding fragment of elongation factor SelB in complex with SECIS RNA.===
+Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB.,Soler N, Fourmy D, Yoshizawa S J Mol Biol. 2007 Jul 20;370(4):728-41. Epub 2007 May 10. PMID:17537456<ref>PMID:17537456</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ply" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17537456}}, adds the Publication Abstract to the page
+*[[Elongation factor 3D structures|Elongation factor 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17537456 is the PubMed ID number.
+*[[SelB|SelB]]
--->
+== References ==
-{{ABSTRACT_PUBMED_17537456}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-PLY is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Moorella_thermoacetica Moorella thermoacetica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLY OCA].
+[[Category: Large Structures]]
-==Reference==
-Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB., Soler N, Fourmy D, Yoshizawa S, J Mol Biol. 2007 Jul 20;370(4):728-41. Epub 2007 May 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17537456 17537456]
-Crystallization and preliminary X-ray analysis of the mRNA-binding domain of elongation factor SelB from Escherichia coli in complex with RNA., Soler N, Fourmy D, Yoshizawa S, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 May 1;63(Pt, 5):419-21. Epub 2007 Apr 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17565186 17565186]
 [[Category: Moorella thermoacetica]]
-[[Category: Protein complex]]
+[[Category: Fourmy D]]
-[[Category: Fourmy, D.]]
+[[Category: Soler N]]
-[[Category: Soler, N.]]
+[[Category: Yoshizawa S]]
-[[Category: Yoshizawa, S.]]
-[[Category: Complex]]
-[[Category: Protein-rna]]
-[[Category: Rna]]
-[[Category: Secis]]
-[[Category: Translation/rna complex]]
-[[Category: Winged helix,selb]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 04:21:49 2008''