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基本情報
登録情報 | データベース: PDB / ID: 5m1j | |||||||||
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タイトル | Nonstop ribosomal complex bound with Dom34 and Hbs1 | |||||||||
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![]() | RIBOSOME / mRNA surveillance | |||||||||
機能・相同性 | ![]() Eukaryotic Translation Elongation / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling ...Eukaryotic Translation Elongation / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / ribosome disassembly / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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) / preribosome, small subunit precursor / 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 / regulation of cellular amino acid metabolic process / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / positive regulation of translational initiation / meiotic cell cycle / translation elongation factor activity / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / translational termination / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / RNA endonuclease activity / maturation of 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) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of translation / translational initiation / macroautophagy / protein kinase C binding / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosome biogenesis / 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 / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / cell division / negative regulation of gene expression / response to antibiotic / GTPase activity 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() synthetic construct (人工物) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | |||||||||
![]() | Hilal, T. / Yamamoto, H. / Loerke, J. / Buerger, J. / Mielke, T. / Spahn, C.M.T. | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution. 著者: Tarek Hilal / Hiroshi Yamamoto / Justus Loerke / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / ![]() 要旨: The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational ...The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational machinery. During ribosomal rescue, arrested ribosomes are specifically recognized by the conserved eukaryotic proteins Dom34 and Hbs1, to initiate their recycling. Here we solve the structure of Dom34 and Hbs1 bound to a yeast ribosome programmed with a nonstop mRNA at 3.3 Å resolution using cryo-electron microscopy. The structure shows that Domain N of Dom34 is inserted into the upstream mRNA-binding groove via direct stacking interactions with conserved nucleotides of 18S rRNA. It senses the absence of mRNA at the A-site and part of the mRNA entry channel by direct competition. Thus, our analysis establishes the structural foundation for the recognition of aberrantly stalled 80S ribosomes by the Dom34·Hbs1·GTP complex during Dom34-mediated mRNA surveillance pathways. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 4.9 MB | 表示 | ![]() |
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PDB形式 | ![]() | 表示 | ![]() | |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
-タンパク質 , 5種, 5分子 A1g2f2m5A6
#1: タンパク質 | 分子量: 43574.344 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Hexahistidine-tagged protein 由来: (組換発現) ![]() ![]() 遺伝子: DOM34, YNL001W, N2016 / 発現宿主: ![]() ![]() 参照: UniProt: P33309, 加水分解酵素; エステル加水分解酵素 |
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#14: タンパク質 | 分子量: 34710.023 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#35: タンパク質 | 分子量: 8101.675 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#61: タンパク質 | 分子量: 6032.321 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#80: タンパク質 | 分子量: 68812.383 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Hexahistidine tagged protein 由来: (組換発現) ![]() ![]() 遺伝子: HBS1, YKR084C, YKR404 / 発現宿主: ![]() ![]() |
+40S ribosomal protein ... , 31種, 31分子 A2a2B2b2C2c2D2d2E2e2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W2X2Y2Z2
-RNA鎖 , 6種, 6分子 22143444X7A3
#34: RNA鎖 | 分子量: 579126.562 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
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#36: RNA鎖 | 分子量: 1097493.875 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#37: RNA鎖 | 分子量: 38951.105 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#38: RNA鎖 | 分子量: 50682.922 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#81: RNA鎖 | 分子量: 6494.952 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: synthetic mRNA / 由来: (合成) synthetic construct (人工物) |
#82: RNA鎖 | 分子量: 24890.121 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: N-acetylated Phe-tRNA / 由来: (天然) ![]() ![]() |
+60S ribosomal protein ... , 40種, 40分子 a5A5b5B5c5C5D5d5e5f5F5g5G5h5H5i5I5J5j5k5l5L5M5N5o5p5P5Q5S5U5...
-非ポリマー , 5種, 1081分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/5CR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/5CR.gif)
![](data/chem/img/HOH.gif)
#83: 化合物 | ChemComp-ZN / #84: 化合物 | ChemComp-MG / #85: 化合物 | ChemComp-GNP / | #86: 化合物 | ChemComp-5CR / | #87: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 | 名称: Nonstop ribosomal complex bound with Dom34-Hbs1-GMPPNP タイプ: RIBOSOME / Entity ID: #1-#82 / 由来: MULTIPLE SOURCES |
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分子量 | 値: 3.6 MDa / 実験値: NO |
緩衝液 | pH: 7.6 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai Polara / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI POLARA 300 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 80645 X / 最大 デフォーカス(公称値): 4500 nm / 最小 デフォーカス(公称値): 500 nm / Cs: 2 mm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 平均露光時間: 5 sec. / 電子線照射量: 25 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 4797 |
画像スキャン | 動画フレーム数/画像: 25 / 利用したフレーム数/画像: 1-25 |
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解析
ソフトウェア | 名称: PHENIX / バージョン: dev_2415: / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 520612 | ||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 73391 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||||||
精密化 | 最高解像度: 3.3 Å | ||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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