2bgg

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[[Image:2bgg.gif|left|200px]]<br /><applet load="2bgg" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2bgg, resolution 2.20&Aring;" />
 
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'''THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT SIRNA DUPLEX.'''<br />
 
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==Overview==
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==The structure of a Piwi protein from Archaeoglobus fulgidus complexed with a 16nt siRNA duplex.==
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RNA interference and related RNA silencing phenomena use short antisense, guide RNA molecules to repress the expression of target genes. Argonaute, proteins, containing amino-terminal PAZ (for PIWI/Argonaute/Zwille), domains and carboxy-terminal PIWI domains, are core components of these, mechanisms. Here we show the crystal structure of a Piwi protein from, Archaeoglobus fulgidus (AfPiwi) in complex with a small interfering RNA, (siRNA)-like duplex, which mimics the 5' end of a guide RNA strand bound, to an overhanging target messenger RNA. The structure contains a highly, conserved metal-binding site that anchors the 5' nucleotide of the guide, RNA. The first base pair of the duplex is unwound, separating the 5', nucleotide of the guide from the complementary nucleotide on the target, strand, which exits with the 3' overhang through a short channel. The, remaining base-paired nucleotides assume an A-form helix, accommodated, within a channel in the PIWI domain, which can be extended to place the, scissile phosphate of the target strand adjacent to the putative slicer, catalytic site. This study provides insights into mechanisms of target, mRNA recognition and cleavage by an Argonaute-siRNA guide complex.
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<StructureSection load='2bgg' size='340' side='right'caption='[[2bgg]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2bgg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BGG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BGG FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bgg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bgg OCA], [https://pdbe.org/2bgg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bgg RCSB], [https://www.ebi.ac.uk/pdbsum/2bgg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bgg ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PIWI_ARCFU PIWI_ARCFU] Required for RNA-mediated gene silencing (RNAi). Binds to short RNAs such as short interfering RNAs (siRNAs), and may cleave or repress the translation of mRNAs which are complementary to them (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bg/2bgg_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2bgg ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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RNA interference and related RNA silencing phenomena use short antisense guide RNA molecules to repress the expression of target genes. Argonaute proteins, containing amino-terminal PAZ (for PIWI/Argonaute/Zwille) domains and carboxy-terminal PIWI domains, are core components of these mechanisms. Here we show the crystal structure of a Piwi protein from Archaeoglobus fulgidus (AfPiwi) in complex with a small interfering RNA (siRNA)-like duplex, which mimics the 5' end of a guide RNA strand bound to an overhanging target messenger RNA. The structure contains a highly conserved metal-binding site that anchors the 5' nucleotide of the guide RNA. The first base pair of the duplex is unwound, separating the 5' nucleotide of the guide from the complementary nucleotide on the target strand, which exits with the 3' overhang through a short channel. The remaining base-paired nucleotides assume an A-form helix, accommodated within a channel in the PIWI domain, which can be extended to place the scissile phosphate of the target strand adjacent to the putative slicer catalytic site. This study provides insights into mechanisms of target mRNA recognition and cleavage by an Argonaute-siRNA guide complex.
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==About this Structure==
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Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex.,Parker JS, Roe SM, Barford D Nature. 2005 Mar 31;434(7033):663-6. PMID:15800628<ref>PMID:15800628</ref>
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2BGG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Site: <scene name='pdbsite=AC1:Mn Binding Site For Chain B'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BGG OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex., Parker JS, Roe SM, Barford D, Nature. 2005 Mar 31;434(7033):663-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15800628 15800628]
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</div>
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<div class="pdbe-citations 2bgg" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Barford, D.]]
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[[Category: Barford D]]
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[[Category: Parker, J.S.]]
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[[Category: Parker JS]]
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[[Category: Roe, S.M.]]
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[[Category: Roe SM]]
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[[Category: MN]]
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[[Category: argonaute]]
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[[Category: piwi domain]]
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[[Category: protein/rna complex]]
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[[Category: risc]]
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[[Category: rnai]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 18:45:58 2007''
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Current revision

The structure of a Piwi protein from Archaeoglobus fulgidus complexed with a 16nt siRNA duplex.

PDB ID 2bgg

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