+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14978 | ||||||||||||
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タイトル | Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae | ||||||||||||
マップデータ | locally refined and filtered composite map ligand and ribosome | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / ribosome disassembly / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding ...ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / 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 / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G-protein alpha-subunit binding / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / translation regulator activity / ribosomal subunit export from nucleus / 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) / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / helicase activity / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / ubiquitin binding / maturation of SSU-rRNA / macroautophagy / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / ribosomal large subunit assembly / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / defense response to virus / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / transcription coactivator activity / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / RNA helicase / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / 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 / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / baker's yeast (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: 4.3 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_14978.map.gz | 43.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14978-v30.xml emd-14978.xml | 121.4 KB 121.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_14978_fsc.xml emd_14978_fsc_2.xml | 18.6 KB 18.5 KB | 表示 表示 | FSCデータファイル |
画像 | emd_14978.png | 112.6 KB | ||
マスクデータ | emd_14978_msk_1.map emd_14978_msk_2.map | 669.9 MB 669.9 MB | マスクマップ | |
その他 | emd_14978_additional_1.map.gz emd_14978_additional_2.map.gz emd_14978_additional_3.map.gz emd_14978_additional_4.map.gz emd_14978_additional_5.map.gz emd_14978_half_map_1.map.gz emd_14978_half_map_2.map.gz | 53.5 MB 620.9 MB 5.1 MB 620.9 MB 457.5 MB 622.4 MB 618.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14978 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14978 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_14978_validation.pdf.gz | 979.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_14978_full_validation.pdf.gz | 979.1 KB | 表示 | |
XML形式データ | emd_14978_validation.xml.gz | 28.5 KB | 表示 | |
CIF形式データ | emd_14978_validation.cif.gz | 37.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14978 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14978 | 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_14978.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 | locally refined and filtered composite map ligand and ribosome | ||||||||||||||||||||||||||||||||||||
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_14978_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_14978_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: locally refined and filtered map of the ribosome
ファイル | emd_14978_additional_1.map | ||||||||||||
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注釈 | locally refined and filtered map of the 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 2 of the locally refined ligand
ファイル | emd_14978_additional_2.map | ||||||||||||
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注釈 | halfmap 2 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 and filtered ligand
ファイル | emd_14978_additional_3.map | ||||||||||||
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注釈 | map of the locally refined and filtered 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 1 of the locally refined ligand
ファイル | emd_14978_additional_4.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: composite map of stalled and collided ribosome
ファイル | emd_14978_additional_5.map | ||||||||||||
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注釈 | composite map of stalled and collided ribosome | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: halfmap 2 of the ribosome
ファイル | emd_14978_half_map_1.map | ||||||||||||
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注釈 | halfmap 2 of the ribosome | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: halfmap 1 of the ribosome
ファイル | emd_14978_half_map_2.map | ||||||||||||
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注釈 | halfmap 1 of the 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 : RQC trigger complex bound to the stalled ribosome of a disome unit
+超分子 #1: RQC trigger complex bound to the stalled ribosome of a disome unit
+超分子 #2: ribosome
+超分子 #3: RQC trigger complex with Slh1, Cue3, Rqt4
+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-B
+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: 40S ribosomal protein S26
+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
+分子 #46: RPL9A isoform 1
+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: Ribosomal protein L15
+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: 60S ribosomal protein L41
+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: CUE3 isoform 1
+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 / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE |
-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) 平均電子線量: 44.0 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: OTHER / 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 |