2ja9: Difference between revisions
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< | ==Structure of the N-terminal deletion of yeast exosome component Rrp40== | ||
<StructureSection load='2ja9' size='340' side='right'caption='[[2ja9]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
or the | <table><tr><td colspan='2'>[[2ja9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JA9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JA9 FirstGlance]. <br> | ||
or | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</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=2ja9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja9 OCA], [https://pdbe.org/2ja9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ja9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ja9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ja9 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RRP40_YEAST RRP40_YEAST] Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. RRP40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.<ref>PMID:10465791</ref> <ref>PMID:17173052</ref> <ref>PMID:19060898</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/ja/2ja9_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=2ja9 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The exosome is a protein complex that is important in both degradation and 3'-processing of eukaryotic RNAs. We present the crystal structure of the Rrp40 exosome subunit from Saccharomyces cerevisiae at a resolution of 2.2 A. The structure comprises an S1 domain and an unusual KH (K homology) domain. Close packing of the S1 and KH domains is stabilized by a GxNG sequence, which is uniquely conserved in exosome KH domains. Nuclear magnetic resonance data reveal the presence of a manganese-binding site at the interface of the two domains. Isothermal titration calorimetry shows that Rrp40 and archaeal Rrp4 alone have very low intrinsic affinity for RNA. The affinity of an archaeal core exosome for RNA is significantly increased in the presence of the S1-KH subunit Rrp4, indicating that multiple subunits might contribute to cooperative binding of RNA substrates by the exosome. | |||
Structural and biochemical characterization of the yeast exosome component Rrp40.,Oddone A, Lorentzen E, Basquin J, Gasch A, Rybin V, Conti E, Sattler M EMBO Rep. 2007 Jan;8(1):63-9. Epub 2006 Dec 8. PMID:17159918<ref>PMID:17159918</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2ja9" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Exosome 3D structures|Exosome 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Basquin | [[Category: Basquin J]] | ||
[[Category: Conti | [[Category: Conti E]] | ||
[[Category: Gasch | [[Category: Gasch A]] | ||
[[Category: Lorentzen | [[Category: Lorentzen E]] | ||
[[Category: Oddone | [[Category: Oddone A]] | ||
[[Category: Rybin | [[Category: Rybin V]] | ||
[[Category: Sattler | [[Category: Sattler M]] | ||