3id5: Difference between revisions

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-[[Image:3id5.png|left|200px]]
-{{STRUCTURE_3id5|  PDB=3id5  |  SCENE=  }}
+==Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA==
+<StructureSection load='3id5' size='340' side='right'caption='[[3id5]], [[Resolution|resolution]] 4.01&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3id5]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ID5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ID5 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]] 4.01&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></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=3id5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3id5 OCA], [https://pdbe.org/3id5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3id5 RCSB], [https://www.ebi.ac.uk/pdbsum/3id5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3id5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q97ZH3_SACS2 Q97ZH3_SACS2]
+== 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/id/3id5_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=3id5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Box C/D guide RNAs are abundant noncoding RNAs that primarily function to direct the 2'-O-methylation of specific nucleotides by base-pairing with substrate RNAs. In archaea, a bipartite C/D RNA assembles with L7Ae, Nop5, and the methyltransferase fibrillarin into a modification enzyme with unique substrate specificity. Here, we determined the crystal structure of an archaeal C/D RNA-protein complex (RNP) composed of all 3 core proteins and an engineered half-guide RNA at 4 A resolution, as well as 2 protein substructures at higher resolution. The RNP structure reveals that the C-terminal domains of Nop5 in the dimeric complex provide symmetric anchoring sites for 2 L7Ae-associated kink-turn motifs of the C/D RNA. A prominent protrusion in Nop5 seems to be important for guide RNA organization and function and for discriminating the structurally related U4 snRNA. Multiple conformations of the N-terminal domain of Nop5 and its associated fibrillarin in different structures indicate the inherent flexibility of the catalytic module, suggesting that a swinging motion of the catalytic module is part of the enzyme mechanism. We also built a model of a native C/D RNP with substrate and fibrillarin in an active conformation. Our results provide insight into the overall organization and mechanism of action of C/D RNA-guided RNA methyltransferases.
-===Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA===
+Structural organization of box C/D RNA-guided RNA methyltransferase.,Ye K, Jia R, Lin J, Ju M, Peng J, Xu A, Zhang L Proc Natl Acad Sci U S A. 2009 Aug 5. PMID:19666563<ref>PMID:19666563</ref>
-{{ABSTRACT_PUBMED_19666563}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3id5" style="background-color:#fffaf0;"></div>
-[[3id5]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ID5 OCA].
 ==See Also==
-*[[Aldehyde dehydrogenase|Aldehyde dehydrogenase]]
+*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
-*[[Ribosomal protein L7|Ribosomal protein L7]]
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:019666563</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Sulfolobus solfataricus]]
+[[Category: Large Structures]]
-[[Category: Ye, K.]]
+[[Category: Saccharolobus solfataricus]]
-[[Category: 2'-o-methylation]]
+[[Category: Ye K]]
-[[Category: C/d guide rna]]
-[[Category: Coiled-coil]]
-[[Category: Methyltransferase]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Rna-binding]]
-[[Category: Rrna processing]]
-[[Category: Splicing-transferase-ribosomal protein-rna complex]]
-[[Category: Transferase]]
-[[Category: Transferase-ribosomal protein-rna complex]]
-[[Category: Trna processing]]