3d3m: Difference between revisions

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 ==The Crystal Structure of the C-terminal region of Death Associated Protein 5(DAP5)==
-<StructureSection load='3d3m' size='340' side='right' caption='[[3d3m]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='3d3m' size='340' side='right'caption='[[3d3m]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3d3m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D3M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3d3m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D3M FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EIF4G2, DAP5, OK/SW-cl.75 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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]] 1.9&#8491;</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=3d3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d3m OCA], [http://pdbe.org/3d3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d3m RCSB], [http://www.ebi.ac.uk/pdbsum/3d3m PDBsum]</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=3d3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d3m OCA], [https://pdbe.org/3d3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d3m RCSB], [https://www.ebi.ac.uk/pdbsum/3d3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d3m ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/IF4G2_HUMAN IF4G2_HUMAN]] Appears to play a role in the switch from cap-dependent to IRES-mediated translation during mitosis, apoptosis and viral infection. Cleaved by some caspases and viral proteases.<ref>PMID:9049310</ref> <ref>PMID:9032289</ref> <ref>PMID:11511540</ref> <ref>PMID:11943866</ref>
+[https://www.uniprot.org/uniprot/IF4G2_HUMAN IF4G2_HUMAN] Appears to play a role in the switch from cap-dependent to IRES-mediated translation during mitosis, apoptosis and viral infection. Cleaved by some caspases and viral proteases.<ref>PMID:9049310</ref> <ref>PMID:9032289</ref> <ref>PMID:11511540</ref> <ref>PMID:11943866</ref>
 == 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/d3/3d3m_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/3d3m_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 18: / Line 19: @@
 </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=3d3m ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-DAP5/p97 (death-associated protein 5) is a member of the eukaryotic translation initiation factor 4G family. It functions as a scaffold protein promoting cap-independent translation of proteins. During apoptosis, DAP5/p97 is cleaved by caspases at position 792, yielding an 86-kDa C-terminal truncated isoform (DAP5/p86) that promotes translation of several mRNAs mediated by an internal ribosome entry site. In this study, we report the crystal structure of the C-terminal region of DAP5/p97 extending between amino acids 730 and 897. This structure consists of four HEAT-Repeats and is homologous to the C-terminal domain of eIF4GI, eIF5, and eIF2Bepsilon. Unlike the other proteins, DAP5/p97 lacks electron density in the loop connecting alpha3 and alpha4, which harbors the caspase cleavage site. Moreover, we observe fewer interactions between these two helices. Thus, previous mapping of this site by mutation analysis is confirmed here by the resolved structure of the DAP5/p97 C-terminus. In addition, we identified the position of two conserved aromatic and acidic boxes in the structure of the DAP5/p97 C-terminus. The acidic residues in the two aromatic and acidic boxes form a continuous negatively charged patch, which is suggested to make specific interactions with other proteins such as eIF2beta. The caspase cleavage of DAP5/p97 removes the subdomain carrying acidic residues in the AA-box motif, which may result in exposure of a hydrophobic surface. These intriguing structural differences between the two DAP5 isoforms suggest that they have different interaction partners and, subsequently, different functions.
-The Crystal Structure of the C-Terminal DAP5/p97 Domain Sheds Light on the Molecular Basis for Its Processing by Caspase Cleavage.,Liberman N, Dym O, Unger T, Albeck S, Peleg Y, Jacobovitch Y, Branzburg A, Eisenstein M, Marash L, Kimchi A J Mol Biol. 2008 Aug 12. PMID:18722383<ref>PMID:18722383</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3d3m" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[C-terminal portion of human eIF4GI|C-terminal portion of human eIF4GI]]
-*[[Death Associated Protein 5|Death Associated Protein 5]]
 *[[Death-associated protein|Death-associated protein]]
-*[[Eukaryotic initiation factor|Eukaryotic initiation factor]]
+*[[Death-associated protein 3D structures|Death-associated protein 3D structures]]
+*[[Eukaryotic initiation factor 3D structures|Eukaryotic initiation factor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Dym, O]]
+[[Category: Large Structures]]
-[[Category: ISPC, Israel Structural Proteomics Center]]
+[[Category: Dym O]]
-[[Category: Heat repeat domain]]
-[[Category: Initiation factor]]
-[[Category: Phosphoprotein]]
-[[Category: Protein biosynthesis]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Repressor]]
-[[Category: Structural genomic]]
-[[Category: Translation]]
-[[Category: Translation regulation]]