2nub: Difference between revisions

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-[[Image:2nub.png|left|200px]]
-{{STRUCTURE_2nub|  PDB=2nub  |  SCENE=  }}
+==Structure of Aquifex aeolicus Argonuate==
+<StructureSection load='2nub' size='340' side='right'caption='[[2nub]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2nub]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NUB FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</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=2nub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nub OCA], [https://pdbe.org/2nub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nub RCSB], [https://www.ebi.ac.uk/pdbsum/2nub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nub ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O67434_AQUAE O67434_AQUAE]
+== 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/nu/2nub_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/main_output.php?pdb_ID=2nub ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Gene silencing mediated by RNA interference requires the sequence-specific recognition of target mRNA by the endonuclease Argonaute, the primary enzymatic component of the RNA-induced silencing complex. We report the crystal structure of Aquifex aeolicus Argonaute, refined at 3.2A resolution. Relative to recent Argonaute structures, a 24 degrees reorientation of the PAZ domain in our structure opens a basic cleft between the N-terminal and PAZ domains, exposing the guide strand binding pocket of PAZ. This rearrangement leads to a branched, Y-shaped system of grooves that extends through the molecule and merges in a central channel containing the catalytic residues. A 5.5-ns molecular dynamics simulation of Argonaute shows a strong tendency of the PAZ and N-terminal domains to be mobile. Binding of single-stranded DNA to Argonaute monitored by total internal reflection fluorescence spectroscopy shows biphasic kinetics, also indicative of domain rearrangement upon DNA binding. Conformational rearrangement of the PAZ domain may therefore be critical for the catalytic cycle of Argonaute and the RNA-induced silencing complex.
-===Structure of Aquifex aeolicus Argonuate===
+Structure of Aquifex aeolicus argonaute highlights conformational flexibility of the PAZ domain as a potential regulator of RNA-induced silencing complex function.,Rashid UJ, Paterok D, Koglin A, Gohlke H, Piehler J, Chen JC J Biol Chem. 2007 May 4;282(18):13824-32. Epub 2006 Nov 27. PMID:17130125<ref>PMID:17130125</ref>
-{{ABSTRACT_PUBMED_17130125}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2nub" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2nub]] is a 1 chain structure with 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=2NUB OCA].
+*[[Argonaute 3D structures|Argonaute 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017130125</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Aquifex aeolicus]]
-[[Category: Chen, J C.H.]]
+[[Category: Large Structures]]
-[[Category: Gohlke, H.]]
+[[Category: Chen JC-H]]
-[[Category: Koglin, A.]]
+[[Category: Gohlke H]]
-[[Category: Paterok, D.]]
+[[Category: Koglin A]]
-[[Category: Piehler, J.]]
+[[Category: Paterok D]]
-[[Category: Rashid, U J.]]
+[[Category: Piehler J]]
-[[Category: Argonaute]]
+[[Category: Rashid UJ]]
-[[Category: Ribonuclease]]
-[[Category: Risc]]
-[[Category: Rnai]]
-[[Category: Rnaseh]]
-[[Category: Signaling protein]]