2f8s

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[[Image:2f8s.gif|left|200px]]
 
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{{Structure
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==Crystal structure of Aa-Ago with externally-bound siRNA==
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|PDB= 2f8s |SIZE=350|CAPTION= <scene name='initialview01'>2f8s</scene>, resolution 3.00&Aring;
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<StructureSection load='2f8s' size='340' side='right'caption='[[2f8s]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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<table><tr><td colspan='2'>[[2f8s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. The February 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Small Interfering RNA'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_2 10.2210/rcsb_pdb/mom_2008_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F8S FirstGlance]. <br>
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|ACTIVITY=
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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]] 3&#8491;</td></tr>
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|GENE=
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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=2f8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8s OCA], [https://pdbe.org/2f8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f8s RCSB], [https://www.ebi.ac.uk/pdbsum/2f8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f8s ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=[[2f8t|2F8T]]
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8s OCA], [http://www.ebi.ac.uk/pdbsum/2f8s PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2f8s RCSB]</span>
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[https://www.uniprot.org/uniprot/O67434_AQUAE O67434_AQUAE]
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}}
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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/f8/2f8s_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=2f8s 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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Argonaute proteins are key components of the RNA-induced silencing complex (RISC). They provide both architectural and catalytic functionalities associated with small interfering RNA (siRNA) guide strand recognition and subsequent guide strand-mediated cleavage of complementary mRNAs. We report on the 3.0 A crystal structures of 22-mer and 26-mer siRNAs bound to Aquifex aeolicus Argonaute (Aa-Ago), where one 2 nt 3' overhang of the siRNA inserts into a cavity positioned on the outer surface of the PAZ-containing lobe of the bilobal Aa-Ago architecture. The first overhang nucleotide stacks over a tyrosine ring, while the second overhang nucleotide, together with the intervening sugar-phosphate backbone, inserts into a preformed surface cavity. Photochemical crosslinking studies on Aa-Ago with 5-iodoU-labeled single-stranded siRNA and siRNA duplex provide support for this externally bound siRNA-Aa-Ago complex. The structure and biochemical data together provide insights into a protein-RNA recognition event potentially associated with the RISC-loading pathway.
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'''Crystal structure of Aa-Ago with externally-bound siRNA'''
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A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA.,Yuan YR, Pei Y, Chen HY, Tuschl T, Patel DJ Structure. 2006 Oct;14(10):1557-65. PMID:17027504<ref>PMID:17027504</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2f8s" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Argonaute proteins are key components of the RNA-induced silencing complex (RISC). They provide both architectural and catalytic functionalities associated with small interfering RNA (siRNA) guide strand recognition and subsequent guide strand-mediated cleavage of complementary mRNAs. We report on the 3.0 A crystal structures of 22-mer and 26-mer siRNAs bound to Aquifex aeolicus Argonaute (Aa-Ago), where one 2 nt 3' overhang of the siRNA inserts into a cavity positioned on the outer surface of the PAZ-containing lobe of the bilobal Aa-Ago architecture. The first overhang nucleotide stacks over a tyrosine ring, while the second overhang nucleotide, together with the intervening sugar-phosphate backbone, inserts into a preformed surface cavity. Photochemical crosslinking studies on Aa-Ago with 5-iodoU-labeled single-stranded siRNA and siRNA duplex provide support for this externally bound siRNA-Aa-Ago complex. The structure and biochemical data together provide insights into a protein-RNA recognition event potentially associated with the RISC-loading pathway.
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*[[Argonaute 3D structures|Argonaute 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2F8S is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8S OCA].
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__TOC__
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</StructureSection>
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==Reference==
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A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA., Yuan YR, Pei Y, Chen HY, Tuschl T, Patel DJ, Structure. 2006 Oct;14(10):1557-65. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17027504 17027504]
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[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Chen, H Y.]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Patel, D J.]]
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[[Category: Small Interfering RNA]]
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[[Category: Yuan, Y R.]]
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[[Category: Chen HY]]
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[[Category: argonaute]]
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[[Category: Patel DJ]]
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[[Category: risc loading complex]]
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[[Category: Yuan YR]]
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[[Category: sirna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:59:25 2008''
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Current revision

Crystal structure of Aa-Ago with externally-bound siRNA

PDB ID 2f8s

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