登録情報 データベース : EMDB / ID : EMD-18329 ダウンロードとリンクタイトル yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate マップデータ 詳細 試料複合体 : yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrateタンパク質・ペプチド : x 12種RNA : x 1種リガンド : x 1種 詳細 キーワード Helicase / RNA binding / RNA degradation / HYDROLASE機能・相同性 機能・相同性情報分子機能 ドメイン・相同性 構成要素
Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Ski complex / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / regulatory ncRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process ... Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Ski complex / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / regulatory ncRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing / : / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / nuclear mRNA surveillance / rRNA catabolic process / nonfunctional rRNA decay / sulfur compound metabolic process / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドリボヌクレアーゼ / RNA catabolic process / translational elongation / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / RNA processing / translation elongation factor activity / RNA endonuclease activity / protein catabolic process / mRNA processing / protein-macromolecule adaptor activity / regulation of translation / manganese ion binding / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / 3'-5'-RNA exonuclease activity / endonuclease activity / defense response to virus / tRNA binding / RNA helicase activity / RNA helicase / translation / GTPase activity / mRNA binding / protein-containing complex binding / nucleolus / GTP binding / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 : / Ski2, beta-barrel domain / Ski2, N-terminal domain / : / Ski2 N-terminal region / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain ... : / Ski2, beta-barrel domain / Ski2, N-terminal domain / : / Ski2 N-terminal region / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / RRP4, S1 domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / PIN domain / Exosome complex exonuclease RRP4 N-terminal region / : / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Large family of predicted nucleotide-binding domains / PIN domain / K Homology domain, type 1 / K Homology domain, type 1 superfamily / PIN-like domain superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase 類似検索 - ドメイン・相同性 RRP46 isoform 1 / Exosome complex component RRP43 / Antiviral helicase SKI2 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 ... RRP46 isoform 1 / Exosome complex component RRP43 / Antiviral helicase SKI2 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / Superkiller protein 7 / Exosome complex component RRP42 類似検索 - 構成要素生物種 Saccharomyces cerevisiae (パン酵母)手法 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度 : 2.55 Å 詳細 データ登録者Keidel A / Koegel A / Reichelt P / Kowalinski E / Schaefer IB / Conti E 資金援助 ドイツ, 1件 詳細 詳細を隠すOrganization Grant number 国 Max Planck Society ドイツ
引用ジャーナル : Mol Cell / 年 : 2023タイトル : Concerted structural rearrangements enable RNA channeling into the cytoplasmic Ski238-Ski7-exosome assembly.著者 : Achim Keidel / Alexander Kögel / Peter Reichelt / Eva Kowalinski / Ingmar B Schäfer / Elena Conti / 要旨 : The Ski2-Ski3-Ski8 (Ski238) helicase complex directs cytoplasmic mRNAs toward the nucleolytic exosome complex for degradation. In yeast, the interaction between Ski238 and exosome requires the ... The Ski2-Ski3-Ski8 (Ski238) helicase complex directs cytoplasmic mRNAs toward the nucleolytic exosome complex for degradation. In yeast, the interaction between Ski238 and exosome requires the adaptor protein Ski7. We determined different cryo-EM structures of the Ski238 complex depicting the transition from a rigid autoinhibited closed conformation to a flexible active open conformation in which the Ski2 helicase module has detached from the rest of Ski238. The open conformation favors the interaction of the Ski3 subunit with exosome-bound Ski7, leading to the recruitment of the exosome. In the Ski238-Ski7-exosome holocomplex, the Ski2 helicase module binds the exosome cap, enabling the RNA to traverse from the helicase through the internal exosome channel to the Rrp44 exoribonuclease. Our study pinpoints how conformational changes within the Ski238 complex regulate exosome recruitment for RNA degradation. We also reveal the remarkable conservation of helicase-exosome RNA channeling mechanisms throughout eukaryotic nuclear and cytoplasmic exosome complexes. 履歴 登録 2023年8月25日 - ヘッダ(付随情報) 公開 2024年1月10日 - マップ公開 2024年1月10日 - 更新 2024年1月10日 - 現状 2024年1月10日 処理サイト : PDBe / 状態 : 公開
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