1r6z: Difference between revisions

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-{{Seed}}
-[[Image:1r6z.png|left|200px]]
-<!--
+==The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion)==
-The line below this paragraph, containing "STRUCTURE_1r6z", creates the "Structure Box" on the page.
+<StructureSection load='1r6z' size='340' side='right'caption='[[1r6z]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1r6z]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R6Z FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene></td></tr>
-{{STRUCTURE_1r6z|  PDB=1r6z  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6z OCA], [https://pdbe.org/1r6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r6z RCSB], [https://www.ebi.ac.uk/pdbsum/1r6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r6z ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.[https://www.uniprot.org/uniprot/AGO2_DROME AGO2_DROME] Essential for RNA interference (RNAi); double-stranded RNA induces potent and specific gene silencing. RNAi is mediated by the RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys or silences messenger RNAs homologous to the silencing trigger.<ref>PMID:11498593</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/r6/1r6z_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=1r6z ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RISC, the RNA-induced silencing complex, uses short interfering RNAs (siRNAs) or micro RNAs (miRNAs) to select its targets in a sequence-dependent manner. Key RISC components are Argonaute proteins, which contain two characteristic domains, PAZ and PIWI. PAZ is highly conserved and is found only in Argonaute proteins and Dicer. We have solved the crystal structure of the PAZ domain of Drosophila Argonaute2. The PAZ domain contains a variant of the OB fold, a module that often binds single-stranded nucleic acids. PAZ domains show low-affinity nucleic acid binding, probably interacting with the 3' ends of single-stranded regions of RNA. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.
-===The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion)===
+The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes.,Song JJ, Liu J, Tolia NH, Schneiderman J, Smith SK, Martienssen RA, Hannon GJ, Joshua-Tor L Nat Struct Biol. 2003 Dec;10(12):1026-32. Epub 2003 Nov 16. PMID:14625589<ref>PMID:14625589</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1r6z" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14625589}}, adds the Publication Abstract to the page
+*[[Argonaute 3D structures|Argonaute 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14625589 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14625589}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Drosophila melanogaster]]
-R6Z is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli,_drosophila_melanogaster Escherichia coli, drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R6Z OCA].
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
-==Reference==
+[[Category: Hannon GJ]]
-The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes., Song JJ, Liu J, Tolia NH, Schneiderman J, Smith SK, Martienssen RA, Hannon GJ, Joshua-Tor L, Nat Struct Biol. 2003 Dec;10(12):1026-32. Epub 2003 Nov 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14625589 14625589]
+[[Category: Joshua-Tor L]]
-[[Category: Escherichia coli, drosophila melanogaster]]
+[[Category: Liu J]]
-[[Category: Single protein]]
+[[Category: Martienssen RA]]
-[[Category: Hannon, G J.]]
+[[Category: Schneiderman J]]
-[[Category: Joshua-Tor, L.]]
+[[Category: Smith SK]]
-[[Category: Liu, J.]]
+[[Category: Song JJ]]
-[[Category: Martienssen, R A.]]
+[[Category: Tolia NH]]
-[[Category: Schneiderman, J.]]
-[[Category: Smith, S K.]]
-[[Category: Song, J J.]]
-[[Category: Tolia, N H.]]
-[[Category: Deviant ob fold]]
-[[Category: Rnai]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 15:13:55 2008''