4ifd

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

Structural highlights

4ifd is a 10 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.805Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RRP6_YEAST Nuclear-specific 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. 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. RRP6 has 3'-5' exonuclease activity which is not modulated upon association with Exo-9 suggesting that the complex inner RNA-binding path is not used to access its active site.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The exosome is the major 3'-5' RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44. In the nucleus, the Exo-10 core recruits another nuclease, Rrp6. Here we crystallized an approximately 440-kilodalton complex of Saccharomyces cerevisiae Exo-10 bound to a carboxy-terminal region of Rrp6 and to an RNA duplex with a 3'-overhang of 31 ribonucleotides. The 2.8 A resolution structure shows how RNA is funnelled into the Exo-9 channel in a single-stranded conformation by an unwinding pore. Rrp44 adopts a closed conformation and captures the RNA 3'-end that exits from the side of Exo-9. Exo-9 subunits bind RNA with sequence-unspecific interactions reminiscent of archaeal exosomes. The substrate binding and channelling mechanisms of 3'-5' RNA degradation complexes are conserved in all kingdoms of life.

Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.,Makino DL, Baumgartner M, Conti E Nature. 2013 Mar 7;495(7439):70-5. doi: 10.1038/nature11870. Epub 2013 Feb 3. PMID:23376952^[5]

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

References

↑ Briggs MW, Burkard KT, Butler JS. Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3' end formation. J Biol Chem. 1998 May 22;273(21):13255-63. PMID:9582370
↑ Allmang C, Petfalski E, Podtelejnikov A, Mann M, Tollervey D, Mitchell P. The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases. Genes Dev. 1999 Aug 15;13(16):2148-58. PMID:10465791
↑ Burkard KT, Butler JS. A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p. Mol Cell Biol. 2000 Jan;20(2):604-16. PMID:10611239
↑ Hieronymus H, Yu MC, Silver PA. Genome-wide mRNA surveillance is coupled to mRNA export. Genes Dev. 2004 Nov 1;18(21):2652-62. Epub 2004 Oct 15. PMID:15489286 doi:http://dx.doi.org/gad.1241204
↑ Makino DL, Baumgartner M, Conti E. Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Nature. 2013 Mar 7;495(7439):70-5. doi: 10.1038/nature11870. Epub 2013 Feb 3. PMID:23376952 doi:http://dx.doi.org/10.1038/nature11870

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ifd"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Conti E | Makino DL

@@ Line 1: / Line 1: @@
-[[Image:4ifd.jpg|left|200px]]
-{{STRUCTURE_4ifd|  PDB=4ifd  |  SCENE=  }}
+==Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA==
+<StructureSection load='4ifd' size='340' side='right'caption='[[4ifd]], [[Resolution|resolution]] 2.81&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ifd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IFD 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]] 2.805&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=4ifd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ifd OCA], [https://pdbe.org/4ifd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ifd RCSB], [https://www.ebi.ac.uk/pdbsum/4ifd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ifd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RRP6_YEAST RRP6_YEAST] Nuclear-specific 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. 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. RRP6 has 3'-5' exonuclease activity which is not modulated upon association with Exo-9 suggesting that the complex inner RNA-binding path is not used to access its active site.<ref>PMID:9582370</ref> <ref>PMID:10465791</ref> <ref>PMID:10611239</ref> <ref>PMID:15489286</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The exosome is the major 3'-5' RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44. In the nucleus, the Exo-10 core recruits another nuclease, Rrp6. Here we crystallized an approximately 440-kilodalton complex of Saccharomyces cerevisiae Exo-10 bound to a carboxy-terminal region of Rrp6 and to an RNA duplex with a 3'-overhang of 31 ribonucleotides. The 2.8 A resolution structure shows how RNA is funnelled into the Exo-9 channel in a single-stranded conformation by an unwinding pore. Rrp44 adopts a closed conformation and captures the RNA 3'-end that exits from the side of Exo-9. Exo-9 subunits bind RNA with sequence-unspecific interactions reminiscent of archaeal exosomes. The substrate binding and channelling mechanisms of 3'-5' RNA degradation complexes are conserved in all kingdoms of life.
-===Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA===
+Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.,Makino DL, Baumgartner M, Conti E Nature. 2013 Mar 7;495(7439):70-5. doi: 10.1038/nature11870. Epub 2013 Feb 3. PMID:23376952<ref>PMID:23376952</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4ifd" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[4ifd]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFD OCA].
+*[[Exosome 3D structures|Exosome 3D structures]]
-[[Category: Saccharomyces cerevisiae s288c]]
+== References ==
-[[Category: Conti, E.]]
+<references/>
-[[Category: Makino, D L.]]
+__TOC__
-[[Category: Dis3]]
+</StructureSection>
-[[Category: Endonuclease]]
+[[Category: Large Structures]]
-[[Category: Exonuclease]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Exosome]]
+[[Category: Conti E]]
-[[Category: Hydrolase]]
+[[Category: Makino DL]]
-[[Category: Hydrolase-rna complex]]
-[[Category: Nuclease]]
-[[Category: Pin]]
-[[Category: Ribonuclease]]
-[[Category: Rna]]
-[[Category: Rna processing]]
-[[Category: Rrp44]]
-[[Category: Rrp6]]

4ifd

From Proteopedia

Current revision

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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