2idv: Difference between revisions

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 ==Crystal structure of wheat C113S mutant EIF4E bound TO 7-methyl-GDP==
-<StructureSection load='2idv' size='340' side='right' caption='[[2idv]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='2idv' size='340' side='right'caption='[[2idv]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2idv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Canadian_hard_winter_wheat Canadian hard winter wheat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IDV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2idv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Triticum_aestivum Triticum aestivum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IDV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M7G:7N-METHYL-8-HYDROGUANOSINE-5-DIPHOSPHATE'>M7G</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2idr|2idr]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M7G:7N-METHYL-8-HYDROGUANOSINE-5-DIPHOSPHATE'>M7G</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2idv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2idv OCA], [http://pdbe.org/2idv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2idv RCSB], [http://www.ebi.ac.uk/pdbsum/2idv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2idv ProSAT]</span></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=2idv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2idv OCA], [https://pdbe.org/2idv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2idv RCSB], [https://www.ebi.ac.uk/pdbsum/2idv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2idv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/IF4E1_WHEAT IF4E1_WHEAT]] Component of the protein complex eIF4F, which is involved in the recognition of the mRNA cap, ATP-dependent unwinding of 5'-terminal secondary structure and recruitment of mRNA to the ribosome. Recognizes and binds the 7-methylguanosine-containing mRNA cap during an early step in the initiation of protein synthesis and facilitates ribosome binding by inducing the unwinding of the mRNAs secondary structures.
+[https://www.uniprot.org/uniprot/IF4E1_WHEAT IF4E1_WHEAT] Component of the protein complex eIF4F, which is involved in the recognition of the mRNA cap, ATP-dependent unwinding of 5'-terminal secondary structure and recruitment of mRNA to the ribosome. Recognizes and binds the 7-methylguanosine-containing mRNA cap during an early step in the initiation of protein synthesis and facilitates ribosome binding by inducing the unwinding of the mRNAs secondary structures.
 == 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/id/2idv_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/id/2idv_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 20: @@
 </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=2idv ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Eukaryotic translation initiation factor-4E (eIF4E) recognizes and binds the m(7) guanosine nucleotide at the 5' end of eukaryotic messenger RNAs; this protein-RNA interaction is an essential step in the initiation of protein synthesis. The structure of eIF4E from wheat (Triticum aestivum) was investigated using a combination of x-ray crystallography and nuclear magnetic resonance (NMR) methods. The overall fold of the crystallized protein was similar to eIF4E from other species, with eight beta-strands, three alpha-helices, and three extended loops. Surprisingly, the wild-type protein did not crystallize with m(7)GTP in its binding site, despite the ligand being present in solution; conformational changes in the cap-binding loops created a large cavity at the usual cap-binding site. The eIF4E crystallized in a dimeric form with one of the cap-binding loops of one monomer inserted into the cavity of the other. The protein also contained an intramolecular disulfide bridge between two cysteines (Cys) that are conserved only in plants. A Cys-to-serine mutant of wheat eIF4E, which lacked the ability to form the disulfide, crystallized with m(7)GDP in its binding pocket, with a structure similar to that of the eIF4E-cap complex of other species. NMR spectroscopy was used to show that the Cys that form the disulfide in the crystal are reduced in solution but can be induced to form the disulfide under oxidizing conditions. The observation that the disulfide-forming Cys are conserved in plants raises the possibility that their oxidation state may have a role in regulating protein function. NMR provided evidence that in oxidized eIF4E, the loop that is open in the ligand-free crystal dimer is relatively flexible in solution. An NMR-based binding assay showed that the reduced wheat eIF4E, the oxidized form with the disulfide, and the Cys-to-serine mutant protein each bind m(7)GTP in a similar and labile manner, with dissociation rates in the range of 20 to 100 s(-1).
-The structure of eukaryotic translation initiation factor-4E from wheat reveals a novel disulfide bond.,Monzingo AF, Dhaliwal S, Dutt-Chaudhuri A, Lyon A, Sadow JH, Hoffman DW, Robertus JD, Browning KS Plant Physiol. 2007 Apr;143(4):1504-18. Epub 2007 Feb 23. PMID:17322339<ref>PMID:17322339</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2idv" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Eukaryotic initiation factor|Eukaryotic initiation factor]]
+*[[Eukaryotic initiation factor 3D structures|Eukaryotic initiation factor 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Canadian hard winter wheat]]
+[[Category: Large Structures]]
-[[Category: Browning, K S]]
+[[Category: Triticum aestivum]]
-[[Category: Dhaliwal, S]]
+[[Category: Browning KS]]
-[[Category: Dutt-Chaudhuri, A]]
+[[Category: Dhaliwal S]]
-[[Category: Hoffman, D W]]
+[[Category: Dutt-Chaudhuri A]]
-[[Category: Monzingo, A F]]
+[[Category: Hoffman DW]]
-[[Category: Robertus, J D]]
+[[Category: Monzingo AF]]
-[[Category: Sadow, J]]
+[[Category: Robertus JD]]
-[[Category: Cap]]
+[[Category: Sadow J]]
-[[Category: Eif4e]]
-[[Category: Eukaryotic initiation factor 4e]]
-[[Category: Methyl-7-gdp]]
-[[Category: Translation regulator]]