2e1r: Difference between revisions

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-{{Seed}}
-[[Image:2e1r.png|left|200px]]
-<!--
+==Structure of eEF2 in complex with a sordarin derivative==
-The line below this paragraph, containing "STRUCTURE_2e1r", creates the "Structure Box" on the page.
+<StructureSection load='2e1r' size='340' side='right'caption='[[2e1r]], [[Resolution|resolution]] 3.15&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'>[[2e1r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1R 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]] 3.15&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SOD:(1S,4S,5S,6R,9S,11S)-6-CHLORO-9-FORMYL-13-ISOPROPYL-5-METHYL-2-({[(3AR,5R,7R+,7AS)-7-METHYL-3-METHYLENEHEXAHYDRO-2H-FURO[2,3-C]PYRAN-5-YL]OXY}METHYL)TETR+ACYCLO[7.4.0.02,11.04,8]TRIDEC-12-ENE-1-CARBOXYLIC+ACI'>SOD</scene></td></tr>
-{{STRUCTURE_2e1r|  PDB=2e1r  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1r OCA], [https://pdbe.org/2e1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1r RCSB], [https://www.ebi.ac.uk/pdbsum/2e1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1r ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/EF2_YEAST EF2_YEAST]
+== 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/e1/2e1r_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=2e1r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The sordarins are fungal specific inhibitors of the translation factor eEF2, which catalyzes the translocation of tRNA and mRNA after peptide bond formation. We have determined the crystal structures of eEF2 in complex with two novel sordarin derivatives. In both structures, the three domains of eEF2 that form the ligand-binding pocket are oriented in a different manner relative to the rest of eEF2 compared with our previous structure of eEF2 in complex with the parent natural product sordarin. Yeast eEF2 is also shown to bind adenylic nucleotides, which can be displaced by sordarin, suggesting that ADP or ATP also bind to the three C-terminal domains of eEF2. Fusidic acid is a universal inhibitor of translation that targets EF-G or eEF2 and is widely used as an antibiotic against Gram-positive bacteria. Based on mutations conferring resistance to fusidic acid, cryo-EM reconstructions, and x-ray structures of eEF2, EF-G, and an EF-G homolog, we suggest that the conformation of EF-G stalled on the 70 S ribosome by fusidic acid is similar to that of eEF2 trapped on the 80 S ribosome by sordarin.
-===Structure of eEF2 in complex with a sordarin derivative===
+Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2.,Soe R, Mosley RT, Justice M, Nielsen-Kahn J, Shastry M, Merrill AR, Andersen GR J Biol Chem. 2007 Jan 5;282(1):657-66. Epub 2006 Nov 2. PMID:17082187<ref>PMID:17082187</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2e1r" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17082187}}, 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 17082187 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17082187}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-E1R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1R OCA].
-==Reference==
-Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2., Soe R, Mosley RT, Justice M, Nielsen-Kahn J, Shastry M, Merrill AR, Andersen GR, J Biol Chem. 2007 Jan 5;282(1):657-66. Epub 2006 Nov 2. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17082187 17082187]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Andersen GR]]
-[[Category: Andersen, G R.]]
+[[Category: Mosley RT]]
-[[Category: Mosley, R T.]]
+[[Category: Soe R]]
-[[Category: Soe, R.]]
-[[Category: G-protein]]
-[[Category: Protein-ligand complex]]
-[[Category: Translation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 13 13:41:50 2008''