+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-51134 | ||||||||||||||||||
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タイトル | human 40S ribosome bound by a SKI238-exosome complex | ||||||||||||||||||
マップデータ | |||||||||||||||||||
試料 |
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キーワード | RNA-binding / RNA-degradation / cytoplasm / helicase / RIBOSOME | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 DNA deamination / nucleolar exosome (RNase complex) / exoribonuclease II / exoribonuclease II activity / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / U1 snRNA 3'-end processing / Ski complex / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway ...DNA deamination / nucleolar exosome (RNase complex) / exoribonuclease II / exoribonuclease II activity / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / U1 snRNA 3'-end processing / Ski complex / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / mRNA decay by 3' to 5' exoribonuclease / CUT catabolic process / cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / Cdc73/Paf1 complex / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear exosome (RNase complex) / negative regulation of myeloid cell differentiation / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / histone mRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / rRNA catabolic process / 3'-5' RNA helicase activity / nuclear mRNA surveillance / positive regulation of isotype switching / ribosome disassembly / 7S RNA binding / : / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mRNA 3'-UTR AU-rich region binding / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / isotype switching / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / RNA catabolic process / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / oxidized purine DNA binding / NF-kappaB complex / neural crest cell differentiation / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / KSRP (KHSRP) binds and destabilizes mRNA / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / maturation of 5.8S rRNA / Translation initiation complex formation / nuclear chromosome / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / iron-sulfur cluster binding / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / positive regulation of activated T cell proliferation / monocyte chemotaxis / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / regulation of cell division / Association of TriC/CCT with target proteins during biosynthesis / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / mRNA catabolic process / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / nuclear-transcribed mRNA catabolic process / Formation of a pool of free 40S subunits 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Homo sapiens (ヒト) / Cricket paralysis virus (ウイルス) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | ||||||||||||||||||
データ登録者 | Koegel A / Keidel A / Loukeri MJ / Kuhn CC / Langer LM / Schaefer IB / Conti E | ||||||||||||||||||
資金援助 | ドイツ, European Union, デンマーク, 5件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: Structural basis of mRNA decay by the human exosome-ribosome supercomplex. 著者: Alexander Kögel / Achim Keidel / Matina-Jasemi Loukeri / Christopher C Kuhn / Lukas M Langer / Ingmar B Schäfer / Elena Conti / 要旨: The interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated ...The interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated largely by the cytoplasmic exosome, which includes the exoribonuclease complex EXO10 and the helicase complex SKI238 (refs. ). The helicase can extract mRNA from the ribosome and is expected to transfer it to the exoribonuclease core through a bridging factor, HBS1L3 (also known as SKI7), but the mechanisms of this molecular handover remain unclear. Here we reveal how human EXO10 is recruited by HBS1L3 (SKI7) to an active ribosome-bound SKI238 complex. We show that rather than a sequential handover, a direct physical coupling mechanism takes place, which culminates in the formation of a cytoplasmic exosome-ribosome supercomplex. Capturing the structure during active decay reveals a continuous path in which an RNA substrate threads from the 80S ribosome through the SKI2 helicase into the exoribonuclease active site of the cytoplasmic exosome complex. The SKI3 subunit of the complex directly binds to HBS1L3 (SKI7) and also engages a surface of the 40S subunit, establishing a recognition platform in collided disomes. Exosome and ribosome thus work together as a single structural and functional unit in co-translational mRNA decay, coordinating their activities in a transient supercomplex. | ||||||||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_51134.map.gz | 71.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-51134-v30.xml emd-51134.xml | 74.5 KB 74.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_51134_fsc.xml | 29.4 KB | 表示 | FSCデータファイル |
画像 | emd_51134.png | 35.4 KB | ||
マスクデータ | emd_51134_msk_1.map | 2.1 GB | マスクマップ | |
Filedesc metadata | emd-51134.cif.gz | 17.3 KB | ||
その他 | emd_51134_additional_1.map.gz emd_51134_half_map_1.map.gz emd_51134_half_map_2.map.gz | 66.4 MB 1.5 GB 1.5 GB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-51134 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-51134 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_51134_validation.pdf.gz | 750.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_51134_full_validation.pdf.gz | 750.1 KB | 表示 | |
XML形式データ | emd_51134_validation.xml.gz | 37.5 KB | 表示 | |
CIF形式データ | emd_51134_validation.cif.gz | 51.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51134 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51134 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_51134.map.gz / 形式: CCP4 / 大きさ: 2.1 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.8512 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_51134_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: composite map human 40S ribosome bound to the...
ファイル | emd_51134_additional_1.map | ||||||||||||
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注釈 | composite map human 40S ribosome bound to the SKI238 complex and the exosome | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_51134_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_51134_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : human 40S ribosome bound by a SKI238-exosome complex
+超分子 #1: human 40S ribosome bound by a SKI238-exosome complex
+分子 #1: Superkiller complex protein 3
+分子 #2: WD repeat-containing protein 61
+分子 #3: Exosome complex component RRP42
+分子 #4: Exosome complex component CSL4
+分子 #5: Exosome complex component RRP45
+分子 #6: Exosome complex component RRP43
+分子 #7: Exosome complex component RRP41
+分子 #8: Exosome complex component RRP46
+分子 #9: Helicase SKI2W
+分子 #10: Isoform 2 of HBS1-like protein
+分子 #11: Exosome complex component MTR3
+分子 #12: Exosome complex component RRP40
+分子 #13: Exosome complex component RRP4
+分子 #15: 60S ribosomal protein L41
+分子 #16: DIS3-like exonuclease 1
+分子 #18: 40S ribosomal protein SA
+分子 #19: 40S ribosomal protein S3a
+分子 #20: 40S ribosomal protein S2
+分子 #21: 40S ribosomal protein S3
+分子 #22: 40S ribosomal protein S4, X isoform
+分子 #23: 40S ribosomal protein S5
+分子 #24: 40S ribosomal protein S6
+分子 #25: 40S ribosomal protein S7
+分子 #26: 40S ribosomal protein S8
+分子 #27: 40S ribosomal protein S9
+分子 #28: 40S ribosomal protein S10
+分子 #29: 40S ribosomal protein S11
+分子 #30: 40S ribosomal protein S12
+分子 #31: 40S ribosomal protein S13
+分子 #32: 40S ribosomal protein S14
+分子 #33: 40S ribosomal protein S15
+分子 #34: 40S ribosomal protein S16
+分子 #35: 40S ribosomal protein S17
+分子 #36: 40S ribosomal protein S18
+分子 #37: 40S ribosomal protein S19
+分子 #38: 40S ribosomal protein S20
+分子 #39: 40S ribosomal protein S21
+分子 #40: 40S ribosomal protein S15a
+分子 #41: 40S ribosomal protein S23
+分子 #42: 40S ribosomal protein S24
+分子 #43: 40S ribosomal protein S25
+分子 #44: 40S ribosomal protein S26
+分子 #45: 40S ribosomal protein S27
+分子 #46: 40S ribosomal protein S28
+分子 #47: 40S ribosomal protein S29
+分子 #48: 40S ribosomal protein S30
+分子 #49: Ubiquitin
+分子 #50: Receptor of activated protein C kinase 1
+分子 #14: CrPV-IRES RNA
+分子 #17: 18S ribosomal RNA
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.4 |
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グリッド | モデル: Quantifoil R2/1 / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE-PROPANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 64.2 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.4 µm / 最小 デフォーカス(公称値): 0.6 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |