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基本情報
登録情報 | データベース: EMDB / ID: EMD-2010 | |||||||||
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タイトル | 3D reconstruction of a translating yeast 80S ribosome in complex with Dom34p and Rli1p | |||||||||
![]() | This map represents a stalled yeast 80S ribosome in complex with Dom34 and Rli1 before sorting for P-site tRNA. | |||||||||
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![]() | translation / ribosome recycling / no-go mRNA decay | |||||||||
機能・相同性 | ![]() Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / mTORC1-mediated signalling / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition ...Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / mTORC1-mediated signalling / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / positive regulation of translational initiation / ribosomal subunit export from nucleus / translational termination / RNA endonuclease activity / translational initiation / translation initiation factor activity / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / meiotic cell cycle / ribosomal large subunit biogenesis / positive regulation of translation / small-subunit processome / ribosomal large subunit assembly / cytoplasmic stress granule / rRNA processing / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / iron ion binding / translation / cell division / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.2 Å | |||||||||
![]() | Becker T / Franckenberg S / Wickles S / Shoemaker CJ / Anger AM / Armache J-P / Sieber H / Ungewickell C / Berninghausen O / Daberkow I ...Becker T / Franckenberg S / Wickles S / Shoemaker CJ / Anger AM / Armache J-P / Sieber H / Ungewickell C / Berninghausen O / Daberkow I / Karcher A / Thomm M / Hopfner K-P / Green R / Beckmann R | |||||||||
![]() | ![]() タイトル: Structural basis of highly conserved ribosome recycling in eukaryotes and archaea. 著者: Thomas Becker / Sibylle Franckenberg / Stephan Wickles / Christopher J Shoemaker / Andreas M Anger / Jean-Paul Armache / Heidemarie Sieber / Charlotte Ungewickell / Otto Berninghausen / Ingo ...著者: Thomas Becker / Sibylle Franckenberg / Stephan Wickles / Christopher J Shoemaker / Andreas M Anger / Jean-Paul Armache / Heidemarie Sieber / Charlotte Ungewickell / Otto Berninghausen / Ingo Daberkow / Annette Karcher / Michael Thomm / Karl-Peter Hopfner / Rachel Green / Roland Beckmann / ![]() 要旨: Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation ...Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron-sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation. | |||||||||
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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ヘッダ (付随情報) | ![]() ![]() | 13 KB 13 KB | 表示 表示 | ![]() |
画像 | ![]() | 238 KB | ||
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-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | This map represents a stalled yeast 80S ribosome in complex with Dom34 and Rli1 before sorting for P-site tRNA. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.2375 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : Saccharomyces cerevisiae 80S ribosome stalled by a synthetic stem...
全体 | 名称: Saccharomyces cerevisiae 80S ribosome stalled by a synthetic stem-loop mRNA in complex with Dom34p and Rli1p |
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要素 |
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-超分子 #1000: Saccharomyces cerevisiae 80S ribosome stalled by a synthetic stem...
超分子 | 名称: Saccharomyces cerevisiae 80S ribosome stalled by a synthetic stem-loop mRNA in complex with Dom34p and Rli1p タイプ: sample / ID: 1000 集合状態: One 80S ribosome binds one Dom34p and one Rli1p Number unique components: 3 |
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-超分子 #1: S. cerevisiae 80S ribosome
超分子 | 名称: S. cerevisiae 80S ribosome / タイプ: complex / ID: 1 / Name.synonym: Baker's yeast 80S ribosome / 組換発現: No / Ribosome-details: ribosome-eukaryote: ALL |
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由来(天然) | 生物種: ![]() ![]() |
-分子 #1: Rli1p
分子 | 名称: Rli1p / タイプ: protein_or_peptide / ID: 1 / Name.synonym: ABCE1 / 集合状態: Monomer / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
組換発現 | 生物種: ![]() ![]() |
-分子 #2: Dom34p
分子 | 名称: Dom34p / タイプ: protein_or_peptide / ID: 2 / Name.synonym: Pelota / 集合状態: Monomer / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
組換発現 | 生物種: ![]() ![]() |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7 詳細: 20 mM Tris/HCl pH 7.0, 150 mM KOAc, 10 mM Mg(OAc)2, 1.5 mM DTT, 0.005% Nikkol, 0.01 mg/ml Cycloheximide, 0.3% (w/v) Digitonin, 0.5 mM ADPNP |
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グリッド | 詳細: Quantifoil grids (3/3) with 2 nm carbon on top |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / 装置: OTHER / 詳細: Vitrification instrument: Vitrobot 手法: Blot for 10 seconds before plunging, use 2 layer of filter paper |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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詳細 | Final magnification of the object on the CCD image is 128200 |
撮影 | カテゴリ: CCD / フィルム・検出器のモデル: FEI EAGLE (4k x 4k) / デジタル化 - サンプリング間隔: 15 µm / 実像数: 5610 / 平均電子線量: 25 e/Å2 / ビット/ピクセル: 16 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 4.5 µm / 最小 デフォーカス(公称値): 1.4 µm / 倍率(公称値): 75000 |
試料ステージ | 試料ホルダー: Dual tilt autoloader cartridge / 試料ホルダーモデル: OTHER |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
詳細 | mammalian Sec61 complex was added to saturate hydrophobic nascent polypeptide chains |
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CTF補正 | 詳細: Wiener Filter |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 7.2 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: SPIDER 詳細: sorting for ribosome conformation and ligand presence was performed. This map represents the step after sorting for ligand presence but before sorting for p_site tRNA. 使用した粒子像数: 45700 |
最終 角度割当 | 詳細: SPIDER |
-原子モデル構築 1
初期モデル | PDB ID: Chain - Chain ID: 0 |
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ソフトウェア | 名称: MDFF |
詳細 | PDBEntryID_givenInChain. Protocol: rigid body followed by molecular dynamics flexible fitting. rigid body fitting of individual domains followed by molecular dynamics flexible fitting |
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
得られたモデル | ![]() PDB-3j16: |
-原子モデル構築 2
初期モデル | PDB ID: Chain - Chain ID: A |
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ソフトウェア | 名称: MDFF |
詳細 | PDBEntryID_givenInChain. Protocol: rigid body followed by molecular dynamics flexible fitting. rigid body followed by molecular dynamics flexible fitting |
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
得られたモデル | ![]() PDB-3j16: |