1rpu: Difference between revisions

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OCA

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 ==Crystal Structure of CIRV p19 bound to siRNA==
-<StructureSection load='1rpu' size='340' side='right' caption='[[1rpu]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='1rpu' size='340' side='right'caption='[[1rpu]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1rpu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cirv Cirv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RPU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1rpu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Carnation_Italian_ringspot_virus Carnation Italian ringspot virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RPU FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">p19 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39443 CIRV])</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]] 2.5&#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=1rpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rpu OCA], [http://pdbe.org/1rpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rpu RCSB], [http://www.ebi.ac.uk/pdbsum/1rpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rpu 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=1rpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rpu OCA], [https://pdbe.org/1rpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rpu RCSB], [https://www.ebi.ac.uk/pdbsum/1rpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rpu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/P19_CIRV P19_CIRV]] Acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. Binds to short interfering RNAs (siRNAs) with high affinity. Acts as a molecular caliper to specifically select siRNAs based on the length of the duplex region of the RNA.<ref>PMID:14697199</ref> <ref>PMID:19254536</ref>
+[https://www.uniprot.org/uniprot/P19_CIRV P19_CIRV] Acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. Binds to short interfering RNAs (siRNAs) with high affinity. Acts as a molecular caliper to specifically select siRNAs based on the length of the duplex region of the RNA.<ref>PMID:14697199</ref> <ref>PMID:19254536</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/rp/1rpu_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rp/1rpu_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / 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=1rpu ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-RNA silencing in plants likely exists as a defense mechanism against molecular parasites such as RNA viruses, retrotransposons, and transgenes. As a result, many plant viruses have adapted mechanisms to evade and suppress gene silencing. Tombusviruses express a 19 kDa protein (p19), which has been shown to suppress RNA silencing in vivo and bind silencing-generated and synthetic small interfering RNAs (siRNAs) in vitro. Here we report the 2.5 A crystal structure of p19 from the Carnation Italian ringspot virus (CIRV) bound to a 21 nt siRNA and demonstrate in biochemical and in vivo assays that CIRV p19 protein acts as a molecular caliper to specifically select siRNAs based on the length of the duplex region of the RNA.
-Size selective recognition of siRNA by an RNA silencing suppressor.,Vargason JM, Szittya G, Burgyan J, Tanaka Hall TM Cell. 2003 Dec 26;115(7):799-811. PMID:14697199<ref>PMID:14697199</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1rpu" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Alignment of 1rpu vs 1r9f|Alignment of 1rpu vs 1r9f]]
+*[[Flock house virus protein B2|Flock house virus protein B2]]
-*[[RNA Interference|RNA Interference]]
+*[[P19|P19]]
-*[[User:Wayne Decatur/Chem791A Work Session|User:Wayne Decatur/Chem791A Work Session]]
+*[[RNA silencing suppressor|RNA silencing suppressor]]
-*[[User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing|User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing]]
+*[[Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]
-*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]]
+*[[Tomato aspermy virus protein 2b Suppression of RNA Silencing|Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
-*[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
-*[[User:Wayne Decatur/Teaching Proteopedia|User:Wayne Decatur/Teaching Proteopedia]]
-*[[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing|User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cirv]]
+[[Category: Carnation Italian ringspot virus]]
-[[Category: Burgyan, J]]
+[[Category: Large Structures]]
-[[Category: Hall, T M.T]]
+[[Category: Burgyan J]]
-[[Category: Szittya, G]]
+[[Category: Hall TMT]]
-[[Category: Vargason, J M]]
+[[Category: Szittya G]]
-[[Category: Protein-rna complex]]
+[[Category: Vargason JM]]
-[[Category: Rna binding protein-rna complex]]
-[[Category: Rna double helix]]
-[[Category: Rna length recognition]]
-[[Category: Rnai]]