3h3d: Difference between revisions

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OCA

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 ==Drosophila Pumilio RNA binding domain (Puf domain)==
-<StructureSection load='3h3d' size='340' side='right' caption='[[3h3d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3h3d' size='340' side='right'caption='[[3h3d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3h3d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3H3D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3h3d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H3D FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pumilio ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</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='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=3h3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3h3d RCSB], [http://www.ebi.ac.uk/pdbsum/3h3d 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=3h3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h3d OCA], [https://pdbe.org/3h3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h3d RCSB], [https://www.ebi.ac.uk/pdbsum/3h3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h3d ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PUM_DROME PUM_DROME] Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding to the Nanos Response Element (NRE), a 16 bp sequence in the hb mRNA 3'-UTR and prevents its translation. Required for abdominal development and to support proliferation and self-renewal of germ cells. Pum is the only gene required for nos activity that is not also required for posterior localization of germline determinants. Pum is required during embryogenesis when nos activity apparently moves anteriorly from the posterior pole.<ref>PMID:1459455</ref> <ref>PMID:1576962</ref> <ref>PMID:9660969</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/h3/3h3d_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h3/3h3d_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3h3d ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Translation regulation plays an essential role in the differentiation and development of animal cells. One well-studied case is the control of hunchback mRNA during early Drosophila embryogenesis by the trans-acting factors Pumilio, Nanos, and Brain Tumor. We report here a crystal structure of the critical region of Pumilio, the Puf domain, that organizes a multivalent repression complex on the 3' untranslated region of hunchback mRNA. The structure reveals an extended, rainbow shaped molecule, with tandem helical repeats that bear unexpected resemblance to the armadillo repeats in beta-catenin and the HEAT repeats in protein phosphatase 2A. Based on the structure and genetic experiments, we identify putative interaction surfaces for hunchback mRNA and the cofactors Nanos and Brain Tumor. This analysis suggests that similar features in helical repeat proteins are used to bind extended peptides and RNA.
-Structure of Pumilio reveals similarity between RNA and peptide binding motifs.,Edwards TA, Pyle SE, Wharton RP, Aggarwal AK Cell. 2001 Apr 20;105(2):281-9. PMID:11336677<ref>PMID:11336677</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 == References ==
 <references/>
@@ Line 29: / Line 24: @@
 </StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Aggarwal, A K]]
+[[Category: Large Structures]]
-[[Category: Edwards, T A]]
+[[Category: Aggarwal AK]]
-[[Category: Wharton, R P]]
+[[Category: Edwards TA]]
-[[Category: Developmental protein]]
+[[Category: Wharton RP]]
-[[Category: Phosphoprotein]]
-[[Category: Puf]]
-[[Category: Pumilio]]
-[[Category: Repressor]]
-[[Category: Rna binding domain]]
-[[Category: Rna binding protein]]
-[[Category: Rna-binding]]
-[[Category: Translation regulation]]