2ba0: Difference between revisions

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==Archaeal exosome core==
==Archaeal exosome core==
<StructureSection load='2ba0' size='340' side='right' caption='[[2ba0]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='2ba0' size='340' side='right'caption='[[2ba0]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2ba0]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BA0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BA0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2ba0]] is a 9 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=2BA0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BA0 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ba1|2ba1]]</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]] 2.7&#8491;</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=2ba0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ba0 OCA], [http://pdbe.org/2ba0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ba0 RCSB], [http://www.ebi.ac.uk/pdbsum/2ba0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ba0 ProSAT]</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=2ba0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ba0 OCA], [https://pdbe.org/2ba0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ba0 RCSB], [https://www.ebi.ac.uk/pdbsum/2ba0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ba0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RRP4_ARCFU RRP4_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. Confers strong poly(A) specificity to the exosome (Probable).<ref>PMID:16285927</ref> <ref>PMID:20392821</ref> [[http://www.uniprot.org/uniprot/ECX2_ARCFU ECX2_ARCFU]] Probably involved in the 3'->5' degradation of a variety of RNA species (Potential). [[http://www.uniprot.org/uniprot/ECX1_ARCFU ECX1_ARCFU]] Probably involved in the 3'->5' degradation of a variety of RNA species (Potential).
[https://www.uniprot.org/uniprot/RRP4_ARCFU RRP4_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. Confers strong poly(A) specificity to the exosome (Probable).<ref>PMID:16285927</ref> <ref>PMID:20392821</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ba/2ba0_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ba/2ba0_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 19: Line 19:
</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=2ba0 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=2ba0 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Exosomes emerge as central 3'--&gt;5' RNA processing and degradation machineries in eukaryotes and archaea. We determined crystal structures of two 230 kDa nine subunit archaeal exosome isoforms. Both exosome isoforms contain a hexameric ring of RNase phosphorolytic (PH) domain subunits with a central chamber. Tungstate soaks identified three phosphorolytic active sites in this processing chamber. A trimer of Csl4 or Rrp4 subunits forms a multidomain macromolecular interaction surface on the RNase-PH domain ring with central S1 domains and peripheral KH and zinc-ribbon domains. Structural and mutational analyses suggest that the S1 domains and a subsequent neck in the RNase-PH domain ring form an RNA entry pore to the processing chamber that only allows access of unstructured RNA. This structural framework can mechanistically unify observed features of exosomes, including processive degradation of unstructured RNA, the requirement for regulatory factors to degrade structured RNA, and left-over tails in rRNA trimming.
Structural framework for the mechanism of archaeal exosomes in RNA processing.,Buttner K, Wenig K, Hopfner KP Mol Cell. 2005 Nov 11;20(3):461-71. PMID:16285927<ref>PMID:16285927</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ba0" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Exosome|Exosome]]
*[[Exosome 3D structures|Exosome 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arcfl]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Buttner, K]]
[[Category: Large Structures]]
[[Category: Hopfner, K P]]
[[Category: Buttner K]]
[[Category: Wenig, K]]
[[Category: Hopfner KP]]
[[Category: Archaeal]]
[[Category: Wenig K]]
[[Category: Exoribonuclease]]
[[Category: Exosome]]
[[Category: Kh domain]]
[[Category: Rna binding]]
[[Category: Rna binding protein]]
[[Category: Rna degradation]]
[[Category: Rnase ph]]
[[Category: S1domain]]

Latest revision as of 12:16, 14 February 2024

Archaeal exosome coreArchaeal exosome core

Structural highlights

2ba0 is a 9 chain structure with sequence from Archaeoglobus fulgidus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RRP4_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. Confers strong poly(A) specificity to the exosome (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.

See Also

References

  1. ↑ Buttner K, Wenig K, Hopfner KP. Structural framework for the mechanism of archaeal exosomes in RNA processing. Mol Cell. 2005 Nov 11;20(3):461-71. PMID:16285927 doi:10.1016/j.molcel.2005.10.018
  2. ↑ Hartung S, Niederberger T, Hartung M, Tresch A, Hopfner KP. Quantitative analysis of processive RNA degradation by the archaeal RNA exosome. Nucleic Acids Res. 2010 Aug;38(15):5166-76. Epub 2010 Apr 14. PMID:20392821 doi:10.1093/nar/gkq238

2ba0, resolution 2.70Å

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