3l7z: Difference between revisions

Latest revision as of 10:07, 6 November 2024

Crystal structure of the S. solfataricus archaeal exosome

Structural highlights

3l7z is a 9 chain structure with sequence from Saccharolobus solfataricus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.41Å
Ligands:	SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RRP42_SACS2 Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Contributes to the structuring of the Rrp41 active site.[HAMAP-Rule:MF_00622]^[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 PubMed

BACKGROUND: The exosome complex is an essential RNA 3'-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. METHODOLOGY/PRINCIPAL FINDINGS: Here we report an asymmetric 2.9 A Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation. CONCLUSION/SIGNIFICANCE: This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.

Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.,Lu C, Ding F, Ke A PLoS One. 2010 Jan 15;5(1):e8739. PMID:20090900^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lorentzen E, Walter P, Fribourg S, Evguenieva-Hackenberg E, Klug G, Conti E. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat Struct Mol Biol. 2005 Jul;12(7):575-81. Epub 2005 Jun 12. PMID:15951817 doi:10.1038/nsmb952
↑ Roppelt V, Klug G, Evguenieva-Hackenberg E. The evolutionarily conserved subunits Rrp4 and Csl4 confer different substrate specificities to the archaeal exosome. FEBS Lett. 2010 Jul 2;584(13):2931-6. PMID:20488184 doi:10.1016/j.febslet.2010.05.014
↑ Lu C, Ding F, Ke A. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring. PLoS One. 2010 Jan 15;5(1):e8739. PMID:20090900 doi:10.1371/journal.pone.0008739

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Lorentzen E, Walter P, Fribourg S, Evguenieva-Hackenberg E, Klug G, Conti E. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat Struct Mol Biol. 2005 Jul;12(7):575-81. Epub 2005 Jun 12. PMID:15951817 doi:10.1038/nsmb952

[2] Roppelt V, Klug G, Evguenieva-Hackenberg E. The evolutionarily conserved subunits Rrp4 and Csl4 confer different substrate specificities to the archaeal exosome. FEBS Lett. 2010 Jul 2;584(13):2931-6. PMID:20488184 doi:10.1016/j.febslet.2010.05.014

[3] Lu C, Ding F, Ke A. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring. PLoS One. 2010 Jan 15;5(1):e8739. PMID:20090900 doi:10.1371/journal.pone.0008739

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Crystal structure of the S. solfataricus archaeal exosome==
-<StructureSection load='3l7z' size='340' side='right' caption='[[3l7z]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
+<StructureSection load='3l7z' size='340' side='right'caption='[[3l7z]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3l7z]] is a 9 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=3L7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L7Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3l7z]] is a 9 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=3L7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L7Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.41&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">C20_023, Rrp41/42/4, SSO0732 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus]), SSO0735 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus]), C20_026, SSO0736 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3l7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l7z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l7z RCSB], [http://www.ebi.ac.uk/pdbsum/3l7z PDBsum]</span></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=3l7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l7z OCA], [https://pdbe.org/3l7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l7z RCSB], [https://www.ebi.ac.uk/pdbsum/3l7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l7z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ECX2_SULSO ECX2_SULSO]] Probably involved in the 3'->5' degradation of a variety of RNA species (Potential). [[http://www.uniprot.org/uniprot/ECR1_SULSO ECR1_SULSO]] Probably involved in degradation of a variety of RNA species; could act a RNA-binding component of the exosome (Potential). [[http://www.uniprot.org/uniprot/ECX1_SULSO ECX1_SULSO]] Probably involved in the 3'->5' degradation of a variety of RNA species (Potential).
+[https://www.uniprot.org/uniprot/RRP42_SACS2 RRP42_SACS2] Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Contributes to the structuring of the Rrp41 active site.[HAMAP-Rule:MF_00622]<ref>PMID:15951817</ref> <ref>PMID:20488184</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/l7/3l7z_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l7/3l7z_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3l7z ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3l7z" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Sulfolobus solfataricus]]
+[[Category: Large Structures]]
-[[Category: Ding, F]]
+[[Category: Saccharolobus solfataricus]]
-[[Category: Ke, A]]
+[[Category: Ding F]]
-[[Category: Lu, C]]
+[[Category: Ke A]]
-[[Category: Asymmetry]]
+[[Category: Lu C]]
-[[Category: Conformation flexibility]]
-[[Category: Exosome]]
-[[Category: Hydrolase-rna binding protein complex]]
-[[Category: Rna degradation]]
-[[Category: Rna processing]]
-[[Category: Thermal motion]]

3l7z: Difference between revisions

Latest revision as of 10:07, 6 November 2024

Crystal structure of the S. solfataricus archaeal exosome

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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