+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14921 | ||||||||||||
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タイトル | Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map | ||||||||||||
マップデータ | composite map of locally refined ribosome and ligand | ||||||||||||
試料 |
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キーワード | collision / RNA binding / RQT / RQC / RIBOSOME | ||||||||||||
機能・相同性 | 機能・相同性情報 RQC-trigger complex / ribosomal subunit / Negative regulators of DDX58/IFIH1 signaling / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / ribosome disassembly / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity ...RQC-trigger complex / ribosomal subunit / Negative regulators of DDX58/IFIH1 signaling / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / ribosome disassembly / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / nonfunctional rRNA decay / Translation initiation complex formation / Ribosomal scanning and start codon recognition / K63-linked polyubiquitin modification-dependent protein binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / Ub-specific processing proteases / positive regulation of protein kinase activity / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / translation regulator activity / cytosolic ribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ubiquitin binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal large subunit biogenesis / helicase activity / translational initiation / small-subunit processome / positive regulation of apoptotic signaling pathway / macroautophagy / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosome biogenesis / regulation of translation / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / defense response to virus / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / negative regulation of translation / rRNA binding / ribosome / RNA helicase / structural constituent of ribosome / protein ubiquitination / translation / ribonucleoprotein complex / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||
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: 4.8 Å | ||||||||||||
データ登録者 | Best KM / Ikeuchi K / Kater L / Best DM / Musial J / Matsuo Y / Berninghausen O / Becker T / Inada T / Beckmann R | ||||||||||||
資金援助 | European Union, ドイツ, 3件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Structural basis for clearing of ribosome collisions by the RQT complex. 著者: Katharina Best / Ken Ikeuchi / Lukas Kater / Daniel Best / Joanna Musial / Yoshitaka Matsuo / Otto Berninghausen / Thomas Becker / Toshifumi Inada / Roland Beckmann / 要旨: Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress responses and quality ...Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress responses and quality control pathways. Ribosome-associated quality control facilitates the degradation of incomplete translation products and requires dissociation of the stalled ribosomes. A central event is therefore the splitting of collided ribosomes by the ribosome quality control trigger complex, RQT, by an unknown mechanism. Here we show that RQT requires accessible mRNA and the presence of a neighboring ribosome. Cryogenic electron microscopy of RQT-ribosome complexes reveals that RQT engages the 40S subunit of the lead ribosome and can switch between two conformations. We propose that the Ski2-like helicase 1 (Slh1) subunit of RQT applies a pulling force on the mRNA, causing destabilizing conformational changes of the small ribosomal subunit, ultimately resulting in subunit dissociation. Our findings provide conceptual framework for a helicase-driven ribosomal splitting mechanism. #1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2018 タイトル: Real-space refinement in PHENIX for cryo-EM and crystallography. 著者: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD | ||||||||||||
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_14921.map.gz | 29.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14921-v30.xml emd-14921.xml | 123.9 KB 123.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_14921_fsc.xml emd_14921_fsc_2.xml | 18.7 KB 18.5 KB | 表示 表示 | FSCデータファイル |
画像 | emd_14921.png | 113.8 KB | ||
マスクデータ | emd_14921_msk_1.map emd_14921_msk_2.map | 669.9 MB 669.9 MB | マスクマップ | |
Filedesc metadata | emd-14921.cif.gz | 21.2 KB | ||
その他 | emd_14921_additional_1.map.gz emd_14921_additional_2.map.gz emd_14921_additional_3.map.gz emd_14921_additional_4.map.gz | 39.9 MB 620.5 MB 5.1 MB 620.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14921 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14921 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_14921_validation.pdf.gz | 491 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_14921_full_validation.pdf.gz | 490.5 KB | 表示 | |
XML形式データ | emd_14921_validation.xml.gz | 17.4 KB | 表示 | |
CIF形式データ | emd_14921_validation.cif.gz | 24.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14921 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14921 | 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_14921.map.gz / 形式: CCP4 / 大きさ: 669.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | composite map of locally refined ribosome and ligand | ||||||||||||||||||||||||||||||||||||
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: 1.045 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_14921_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 |
-マスク #2
ファイル | emd_14921_msk_2.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: map of the locally refined ribosome
ファイル | emd_14921_additional_1.map | ||||||||||||
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注釈 | map of the locally refined ribosome | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: halfmap 1 of the locally refined ligand
ファイル | emd_14921_additional_2.map | ||||||||||||
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注釈 | halfmap 1 of the locally refined ligand | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: map of the locally refined ligand
ファイル | emd_14921_additional_3.map | ||||||||||||
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注釈 | map of the locally refined ligand | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: halfmap 2 of the locally refined ribosome
ファイル | emd_14921_additional_4.map | ||||||||||||
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注釈 | halfmap 2 of the locally refined ribosome | ||||||||||||
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 : ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
+超分子 #1: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
+超分子 #2: RQT complex (Slh1, Cue3 and Rqt4)
+超分子 #3: ribosome
+分子 #1: 18S ribosomal RNA
+分子 #2: 5.8S ribosomal RNA
+分子 #3: 5S ribosomal RNA
+分子 #4: 25S ribosomal RNA
+分子 #5: tRNA
+分子 #6: 40S ribosomal protein S0-A
+分子 #7: 40S ribosomal protein S1-A
+分子 #8: RPS2 isoform 1
+分子 #9: RPS3 isoform 1
+分子 #10: 40S ribosomal protein S4-A
+分子 #11: Rps5p
+分子 #12: 40S ribosomal protein S6-A
+分子 #13: 40S ribosomal protein S7-A
+分子 #14: 40S ribosomal protein S8-A
+分子 #15: 40S ribosomal protein S9-A
+分子 #16: 40S ribosomal protein S10-A
+分子 #17: 40S ribosomal protein S11-A
+分子 #18: 40S ribosomal protein S12
+分子 #19: 40S ribosomal protein S13
+分子 #20: 40S ribosomal protein S14-B
+分子 #21: RPS15 isoform 1
+分子 #22: 40S ribosomal protein S16-A
+分子 #23: 40S ribosomal protein S17-A
+分子 #24: 40S ribosomal protein S18-A
+分子 #25: 40S ribosomal protein S19-A
+分子 #26: RPS20 isoform 1
+分子 #27: 40S ribosomal protein S21-A
+分子 #28: RPS22A isoform 1
+分子 #29: 40S ribosomal protein S23-A
+分子 #30: 40S ribosomal protein S24-A
+分子 #31: 40S ribosomal protein S25
+分子 #32: RPS26B isoform 1
+分子 #33: 40S ribosomal protein S27-A
+分子 #34: RPS28A isoform 1
+分子 #35: RPS29A isoform 1
+分子 #36: 40S ribosomal protein S30-A
+分子 #37: RPS31 isoform 1
+分子 #38: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #39: 60S ribosomal protein L2-A
+分子 #40: 60S ribosomal protein L3
+分子 #41: RPL4A isoform 1
+分子 #42: RPL5 isoform 1
+分子 #43: 60S ribosomal protein L6-B
+分子 #44: 60S ribosomal protein L7-A
+分子 #45: 60S ribosomal protein L8-A
+分子 #46: 60S ribosomal protein L9-A
+分子 #47: RPL10 isoform 1
+分子 #48: RPL11B isoform 1
+分子 #49: 60S ribosomal protein L13-A
+分子 #50: 60S ribosomal protein L14-A
+分子 #51: 60S ribosomal protein L15-A
+分子 #52: 60S ribosomal protein L16-A
+分子 #53: 60S ribosomal protein L17-A
+分子 #54: 60S ribosomal protein L18-A
+分子 #55: 60S ribosomal protein L19-A
+分子 #56: 60S ribosomal protein L20-A
+分子 #57: 60S ribosomal protein L21-A
+分子 #58: 60S ribosomal protein L22-A
+分子 #59: 60S ribosomal protein L23-A
+分子 #60: RPL24A isoform 1
+分子 #61: 60S ribosomal protein L25
+分子 #62: 60S ribosomal protein L26-A
+分子 #63: 60S ribosomal protein L27-A
+分子 #64: 60S ribosomal protein L28
+分子 #65: 60S ribosomal protein L29
+分子 #66: 60S ribosomal protein L30
+分子 #67: 60S ribosomal protein L31-A
+分子 #68: RPL32 isoform 1
+分子 #69: 60S ribosomal protein L33-A
+分子 #70: 60S ribosomal protein L34-A
+分子 #71: 60S ribosomal protein L35-A
+分子 #72: 60S ribosomal protein L36-A
+分子 #73: 60S ribosomal protein L37-A
+分子 #74: RPL38 isoform 1
+分子 #75: 60S ribosomal protein L39
+分子 #76: 60S ribosomal protein L40-A
+分子 #77: RPL41A isoform 1
+分子 #78: 60S ribosomal protein L42-A
+分子 #79: 60S ribosomal protein L43-A
+分子 #80: RQC trigger complex helicase SLH1
+分子 #81: RQC trigger complex subunit CUE3
+分子 #82: RQC trigger complex subunit RQT4
+分子 #83: MAGNESIUM ION
+分子 #84: ZINC ION
-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: 7.5 |
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グリッド | モデル: Quantifoil R3/3 / 材質: COPPER / 支持フィルム - 材質: CARBON |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK II |
-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 K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 43.6 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |