3m7n: Difference between revisions
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< | ==archaeoglobus fulgidus exosome with RNA bound to the active site== | ||
<StructureSection load='3m7n' size='340' side='right'caption='[[3m7n]], [[Resolution|resolution]] 2.40Å' scene=''> | |||
You may | == Structural highlights == | ||
or the | <table><tr><td colspan='2'>[[3m7n]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M7N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M7N 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]] 2.4Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3m7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m7n OCA], [https://pdbe.org/3m7n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m7n RCSB], [https://www.ebi.ac.uk/pdbsum/3m7n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m7n ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CSL4_ARCFU CSL4_ARCFU] Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Increases the RNA binding and the efficiency of RNA degradation. Helpful for the interaction of the exosome with A-poor RNAs (Probable).<ref>PMID:16285927</ref> <ref>PMID:20392821</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/m7/3m7n_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=3m7n ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
RNA exosomes are large multisubunit assemblies involved in controlled RNA processing. The archaeal exosome possesses a heterohexameric processing chamber with three RNase-PH-like active sites, capped by Rrp4- or Csl4-type subunits containing RNA-binding domains. RNA degradation by RNA exosomes has not been studied in a quantitative manner because of the complex kinetics involved, and exosome features contributing to efficient RNA degradation remain unclear. Here we derive a quantitative kinetic model for degradation of a model substrate by the archaeal exosome. Markov Chain Monte Carlo methods for parameter estimation allow for the comparison of reaction kinetics between different exosome variants and substrates. We show that long substrates are degraded in a processive and short RNA in a more distributive manner and that the cap proteins influence degradation speed. Our results, supported by small angle X-ray scattering, suggest that the Rrp4-type cap efficiently recruits RNA but prevents fast RNA degradation of longer RNAs by molecular friction, likely by RNA contacts to its unique KH-domain. We also show that formation of the RNase-PH like ring with entrapped RNA is not required for high catalytic efficiency, suggesting that the exosome chamber evolved for controlled processivity, rather than for catalytic chemistry in RNA decay. | |||
Quantitative analysis of processive RNA degradation by the archaeal RNA exosome.,Hartung S, Niederberger T, Hartung M, Tresch A, Hopfner KP Nucleic Acids Res. 2010 Aug;38(15):5166-76. Epub 2010 Apr 14. PMID:20392821<ref>PMID:20392821</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3m7n" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Exosome 3D structures|Exosome 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Archaeoglobus fulgidus]] | [[Category: Archaeoglobus fulgidus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Hartung S]] | ||
[[Category: | [[Category: Hopfner K-P]] | ||
Latest revision as of 19:30, 1 November 2023
archaeoglobus fulgidus exosome with RNA bound to the active sitearchaeoglobus fulgidus exosome with RNA bound to the active site
Structural highlights
FunctionCSL4_ARCFU Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Increases the RNA binding and the efficiency of RNA degradation. Helpful for the interaction of the exosome with A-poor RNAs (Probable).[1] [2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedRNA exosomes are large multisubunit assemblies involved in controlled RNA processing. The archaeal exosome possesses a heterohexameric processing chamber with three RNase-PH-like active sites, capped by Rrp4- or Csl4-type subunits containing RNA-binding domains. RNA degradation by RNA exosomes has not been studied in a quantitative manner because of the complex kinetics involved, and exosome features contributing to efficient RNA degradation remain unclear. Here we derive a quantitative kinetic model for degradation of a model substrate by the archaeal exosome. Markov Chain Monte Carlo methods for parameter estimation allow for the comparison of reaction kinetics between different exosome variants and substrates. We show that long substrates are degraded in a processive and short RNA in a more distributive manner and that the cap proteins influence degradation speed. Our results, supported by small angle X-ray scattering, suggest that the Rrp4-type cap efficiently recruits RNA but prevents fast RNA degradation of longer RNAs by molecular friction, likely by RNA contacts to its unique KH-domain. We also show that formation of the RNase-PH like ring with entrapped RNA is not required for high catalytic efficiency, suggesting that the exosome chamber evolved for controlled processivity, rather than for catalytic chemistry in RNA decay. Quantitative analysis of processive RNA degradation by the archaeal RNA exosome.,Hartung S, Niederberger T, Hartung M, Tresch A, Hopfner KP Nucleic Acids Res. 2010 Aug;38(15):5166-76. Epub 2010 Apr 14. PMID:20392821[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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