3dlh: Difference between revisions

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 ==Crystal structure of the guide-strand-containing Argonaute protein silencing complex==
-<StructureSection load='3dlh' size='340' side='right' caption='[[3dlh]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='3dlh' size='340' side='right'caption='[[3dlh]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dlh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DLH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dlh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DLH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dlb|3dlb]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [https://pdbe.org/3dlh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [https://www.ebi.ac.uk/pdbsum/3dlh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dlh ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [http://pdbe.org/3dlh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [http://www.ebi.ac.uk/pdbsum/3dlh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dlh ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q746M7_THET2 Q746M7_THET2]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / Line 20: @@
 </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=3dlh ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.
-Structure of the guide-strand-containing argonaute silencing complex.,Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ Nature. 2008 Nov 13;456(7219):209-13. Epub 2008 Aug 27. PMID:18754009<ref>PMID:18754009</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3dlh" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Argonaute|Argonaute]]
+*[[Argonaute 3D structures|Argonaute 3D structures]]
-*[[RNA Interference|RNA Interference]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Thet2]]
+[[Category: Large Structures]]
-[[Category: Patel, D J]]
+[[Category: Thermus thermophilus HB27]]
-[[Category: Sheng, G]]
+[[Category: Patel DJ]]
-[[Category: Wang, Y]]
+[[Category: Sheng G]]
-[[Category: Argonaute]]
+[[Category: Wang Y]]
-[[Category: Nucleic acid binding protein-dna complex]]
-[[Category: Plasmid]]
-[[Category: Protein-dna complex]]