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==Cryo-EM structure of yeast cytoplasmic exosome==
==Cryo-EM structure of yeast cytoplasmic exosome==
<StructureSection load='5g06' size='340' side='right' caption='[[5g06]], [[Resolution|resolution]] 4.20&Aring;' scene=''>
<SX load='5g06' size='340' side='right' viewer='molstar' caption='[[5g06]], [[Resolution|resolution]] 4.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5g06]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5G06 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5g06]] is a 10 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=5G06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5G06 FirstGlance]. <br>
</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exoribonuclease_II Exoribonuclease II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.1 3.1.13.1] </span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.2&#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=5g06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g06 OCA], [http://pdbe.org/5g06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g06 RCSB], [http://www.ebi.ac.uk/pdbsum/5g06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g06 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=5g06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g06 OCA], [https://pdbe.org/5g06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5g06 RCSB], [https://www.ebi.ac.uk/pdbsum/5g06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5g06 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/MTR3_YEAST MTR3_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. MTR3 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.<ref>PMID:8534909</ref> <ref>PMID:10465791</ref> <ref>PMID:17173052</ref>  [[http://www.uniprot.org/uniprot/SKI7_YEAST SKI7_YEAST]] Represses the expression of non-poly(A) mRNAs like L-A or M viruses and is therefore involved in antiviral system. Mediates interactions via its N-terminus between the exosome and the SKI complex which operate in the 3'-to-5' mRNA-decay pathway. By interacting with NAM7, is also required for nonsense-mediated 3'-to-5' mRNA-decay (NMD). May recognize a stalled 80S ribosome at the 3'-end of a nonstop mRNA which leads to the recruitment of the exosome and SKI complexes to the mRNAs to be degraded.<ref>PMID:10074137</ref> <ref>PMID:11027292</ref> <ref>PMID:11514438</ref> <ref>PMID:11532933</ref> <ref>PMID:11910110</ref> <ref>PMID:12769863</ref> <ref>PMID:12881429</ref> <ref>PMID:14671320</ref> <ref>PMID:15933721</ref> <ref>PMID:6371496</ref>  [[http://www.uniprot.org/uniprot/RRP43_YEAST RRP43_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. RRP43 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.<ref>PMID:9390555</ref> <ref>PMID:9973615</ref> <ref>PMID:12364597</ref> <ref>PMID:17173052</ref>  [[http://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>  [[http://www.uniprot.org/uniprot/CSL4_YEAST CSL4_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.<ref>PMID:10465791</ref> <ref>PMID:17173052</ref> <ref>PMID:19060898</ref>  [[http://www.uniprot.org/uniprot/RRP41_YEAST RRP41_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. SKI6 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.<ref>PMID:9390555</ref> <ref>PMID:17173052</ref>  [[http://www.uniprot.org/uniprot/RRP4_YEAST RRP4_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. RRP4 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.<ref>PMID:9390555</ref> <ref>PMID:8600032</ref> <ref>PMID:17173052</ref> <ref>PMID:19060898</ref> [[http://www.uniprot.org/uniprot/RRP45_YEAST RRP45_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. RRP45 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.<ref>PMID:10465791</ref> <ref>PMID:17173052</ref>  [[http://www.uniprot.org/uniprot/RRP46_YEAST RRP46_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. RRP46 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.<ref>PMID:10465791</ref> <ref>PMID:17173052</ref>  [[http://www.uniprot.org/uniprot/RRP44_YEAST RRP44_YEAST]] 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. DIS3 has both 3'-5' exonuclease and endonuclease activities. The exonuclease activity of DIS3 is down-regulated upon association with Exo-9 possibly involving a conformational change in the catalytic domain and threading of the RNA substrate through the complex central channel. Structured substrates can be degraded if they have a 3' single-stranded extension sufficiently long (such as 35 nt poly(A)) to span the proposed complex inner RNA-binding path and to reach the exonuclease site provided by DIS3. Plays a role in mitotic control.<ref>PMID:8896453</ref> <ref>PMID:9390555</ref> <ref>PMID:17173052</ref>  [[http://www.uniprot.org/uniprot/RRP42_YEAST RRP42_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. RRP42 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.<ref>PMID:9390555</ref> <ref>PMID:17173052</ref> 
[https://www.uniprot.org/uniprot/RRP4_YEAST RRP4_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. RRP4 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.<ref>PMID:9390555</ref> <ref>PMID:8600032</ref> <ref>PMID:17173052</ref> <ref>PMID:19060898</ref>  
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<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
<div class="pdbe-citations 5g06" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 5g06" style="background-color:#fffaf0;"></div>
==See Also==
*[[Exosome 3D structures|Exosome 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</SX>
[[Category: Exoribonuclease II]]
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Dai, J B]]
[[Category: Dai JB]]
[[Category: Dong, M Q]]
[[Category: Dong MQ]]
[[Category: Huang, N]]
[[Category: Huang N]]
[[Category: Liu, J J]]
[[Category: Liu JJ]]
[[Category: Liu, Q S]]
[[Category: Liu QS]]
[[Category: Liu, Y]]
[[Category: Liu Y]]
[[Category: Niu, C Y]]
[[Category: Niu CY]]
[[Category: Tan, D]]
[[Category: Tan D]]
[[Category: Wang, H W]]
[[Category: Wang HW]]
[[Category: Wang, Y]]
[[Category: Wang Y]]
[[Category: Wu, Y]]
[[Category: Wu Y]]
[[Category: Yang, X R]]
[[Category: Yang XR]]
[[Category: Ye, M D]]
[[Category: Ye MD]]
[[Category: Zhao, W W]]
[[Category: Zhao WW]]
[[Category: Zhou, K]]
[[Category: Zhou K]]
[[Category: Exosome]]
[[Category: Hydrolase]]
[[Category: Rna decay]]
[[Category: Rna quality control]]

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