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1r4k

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[[Image:1r4k.gif|left|200px]]
 
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{{Structure
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==Solution Structure of the Drosophila Argonaute 1 PAZ Domain==
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|PDB= 1r4k |SIZE=350|CAPTION= <scene name='initialview01'>1r4k</scene>
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<StructureSection load='1r4k' size='340' side='right'caption='[[1r4k]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1r4k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R4K 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">Solution NMR</td></tr>
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|GENE= Ago1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])
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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=1r4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r4k OCA], [https://pdbe.org/1r4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r4k RCSB], [https://www.ebi.ac.uk/pdbsum/1r4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r4k ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r4k OCA], [http://www.ebi.ac.uk/pdbsum/1r4k PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r4k RCSB]</span>
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[https://www.uniprot.org/uniprot/Q32KD4_DROME Q32KD4_DROME]
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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/r4/1r4k_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=1r4k 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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The discovery of RNA-mediated gene-silencing pathways, including RNA interference, highlights a fundamental role of short RNAs in eukaryotic gene regulation and antiviral defence. Members of the Dicer and Argonaute protein families are essential components of these RNA-silencing pathways. Notably, these two families possess an evolutionarily conserved PAZ (Piwi/Argonaute/Zwille) domain whose biochemical function is unknown. Here we report the nuclear magnetic resonance solution structure of the PAZ domain from Drosophila melanogaster Argonaute 1 (Ago1). The structure consists of a left-handed, six-stranded beta-barrel capped at one end by two alpha-helices and wrapped on one side by a distinctive appendage, which comprises a long beta-hairpin and a short alpha-helix. Using structural and biochemical analyses, we demonstrate that the PAZ domain binds a 5-nucleotide RNA with 1:1 stoichiometry. We map the RNA-binding surface to the open face of the beta-barrel, which contains amino acids conserved within the PAZ domain family, and we define the 5'-to-3' orientation of single-stranded RNA bound within that site. Furthermore, we show that PAZ domains from different human Argonaute proteins also bind RNA, establishing a conserved function for this domain.
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'''Solution Structure of the Drosophila Argonaute 1 PAZ Domain'''
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Structure and conserved RNA binding of the PAZ domain.,Yan KS, Yan S, Farooq A, Han A, Zeng L, Zhou MM Nature. 2003 Nov 27;426(6965):468-74. Epub 2003 Nov 16. PMID:14615802<ref>PMID:14615802</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 1r4k" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The discovery of RNA-mediated gene-silencing pathways, including RNA interference, highlights a fundamental role of short RNAs in eukaryotic gene regulation and antiviral defence. Members of the Dicer and Argonaute protein families are essential components of these RNA-silencing pathways. Notably, these two families possess an evolutionarily conserved PAZ (Piwi/Argonaute/Zwille) domain whose biochemical function is unknown. Here we report the nuclear magnetic resonance solution structure of the PAZ domain from Drosophila melanogaster Argonaute 1 (Ago1). The structure consists of a left-handed, six-stranded beta-barrel capped at one end by two alpha-helices and wrapped on one side by a distinctive appendage, which comprises a long beta-hairpin and a short alpha-helix. Using structural and biochemical analyses, we demonstrate that the PAZ domain binds a 5-nucleotide RNA with 1:1 stoichiometry. We map the RNA-binding surface to the open face of the beta-barrel, which contains amino acids conserved within the PAZ domain family, and we define the 5'-to-3' orientation of single-stranded RNA bound within that site. Furthermore, we show that PAZ domains from different human Argonaute proteins also bind RNA, establishing a conserved function for this domain.
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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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1R4K is a [[Single protein]] structure of 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=1R4K OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Structure and conserved RNA binding of the PAZ domain., Yan KS, Yan S, Farooq A, Han A, Zeng L, Zhou MM, Nature. 2003 Nov 27;426(6965):468-74. Epub 2003 Nov 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14615802 14615802]
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[[Category: Drosophila melanogaster]]
[[Category: Drosophila melanogaster]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Farooq, A.]]
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[[Category: Farooq A]]
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[[Category: Han, A.]]
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[[Category: Han A]]
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[[Category: Yan, K S.]]
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[[Category: Yan KS]]
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[[Category: Yan, S.]]
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[[Category: Yan S]]
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[[Category: Zeng, L.]]
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[[Category: Zeng L]]
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[[Category: Zhou, M M.]]
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[[Category: Zhou M-M]]
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[[Category: beta barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:23:09 2008''
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Current revision

Solution Structure of the Drosophila Argonaute 1 PAZ Domain

PDB ID 1r4k

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