+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2797 | |||||||||
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タイトル | single-particle cryo reconstruction of the Large Ribosomal subunit-associated protein Quality Control (RQC) complex | |||||||||
マップデータ | reconstruction of RQC-delta-RING complex generated after enriching for nonribosomal density using a likelihood-based classification algorithm | |||||||||
試料 |
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キーワード | RING domain E3 ubiquitin ligase / translational surveillance / protein quality control / cryo-EM (低温電子顕微鏡法) / listerin/Ltn1 / Tae2/Nemf | |||||||||
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: 9.6 Å | |||||||||
データ登録者 | Lyumkis D / Oliveira dos Passos D / Tahara EB / Webb K / Bennett EJ / Vinterbo S / Potter CS / Carragher B / Joazeiro CAP | |||||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2014 タイトル: Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex. 著者: Dmitry Lyumkis / Dario Oliveira dos Passos / Erich B Tahara / Kristofor Webb / Eric J Bennett / Staal Vinterbo / Clinton S Potter / Bridget Carragher / Claudio A P Joazeiro / 要旨: All organisms have evolved mechanisms to manage the stalling of ribosomes upon translation of aberrant mRNA. In eukaryotes, the large ribosomal subunit-associated quality control complex (RQC), ...All organisms have evolved mechanisms to manage the stalling of ribosomes upon translation of aberrant mRNA. In eukaryotes, the large ribosomal subunit-associated quality control complex (RQC), composed of the listerin/Ltn1 E3 ubiquitin ligase and cofactors, mediates the ubiquitylation and extraction of ribosome-stalled nascent polypeptide chains for proteasomal degradation. How RQC recognizes stalled ribosomes and performs its functions has not been understood. Using single-particle cryoelectron microscopy, we have determined the structure of the RQC complex bound to stalled 60S ribosomal subunits. The structure establishes how Ltn1 associates with the large ribosomal subunit and properly positions its E3-catalytic RING domain to mediate nascent chain ubiquitylation. The structure also reveals that a distinguishing feature of stalled 60S particles is an exposed, nascent chain-conjugated tRNA, and that the Tae2 subunit of RQC, which facilitates Ltn1 binding, is responsible for selective recognition of stalled 60S subunits. RQC components are engaged in interactions across a large span of the 60S subunit surface, connecting the tRNA in the peptidyl transferase center to the distally located nascent chain tunnel exit. This work provides insights into a mechanism linking translation and protein degradation that targets defective proteins immediately after synthesis, while ignoring nascent chains in normally translating ribosomes. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_2797.map.gz | 56.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2797-v30.xml emd-2797.xml | 9.9 KB 9.9 KB | 表示 表示 | EMDBヘッダ |
画像 | EMD-2797.png | 98.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2797 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2797 | 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_2797.map.gz / 形式: CCP4 / 大きさ: 62.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | reconstruction of RQC-delta-RING complex generated after enriching for nonribosomal density using a likelihood-based classification algorithm | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.69 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
-試料の構成要素
-全体 : Large 60S ribosomal subunit in complex with protein quality contr...
全体 | 名称: Large 60S ribosomal subunit in complex with protein quality control components |
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要素 |
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-超分子 #1000: Large 60S ribosomal subunit in complex with protein quality contr...
超分子 | 名称: Large 60S ribosomal subunit in complex with protein quality control components タイプ: sample / ID: 1000 / Number unique components: 1 |
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分子量 | 理論値: 2.5 MDa |
-超分子 #1: large 60S ribosomal subunit-associated protein quality control complex
超分子 | 名称: large 60S ribosomal subunit-associated protein quality control complex タイプ: complex / ID: 1 / Name.synonym: RQC complex / 組換発現: No / Ribosome-details: ribosome-eukaryote: LSU 60S |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) / 株: BY4741 / 別称: Baker's yeast |
分子量 | 理論値: 2.5 MDa |
-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
濃度 | 0.1 mg/mL |
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緩衝液 | pH: 6.8 詳細: 50 mM Hepes-KOH, 100 mM KOAc, 5 mM MgOAc, 1 mM EDTA, 2 mM DTT, 2x protease inhibitors, 0.1% Igepal CA-630 |
グリッド | 詳細: freshly plasma-cleaned holey carbon C-flat grid (Protochips) that had been overlaid with 2 nm thin carbon film |
凍結 | 凍結剤: ETHANE / チャンバー内温度: 93 K / 装置: HOMEMADE PLUNGER 手法: specimens were prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma-cleaned holey carbon C-flat grid (Protochips) that had been overlaid with 2 nm thin carbon film, ...手法: specimens were prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma-cleaned holey carbon C-flat grid (Protochips) that had been overlaid with 2 nm thin carbon film, allowing the sample to adsorb to the grid for 30 s, followed by blotting with filter paper and plunge freezing into liquid ethane using a manual cryoplunger in an ambient environment at 4 C. |
-電子顕微鏡法
顕微鏡 | FEI TECNAI F20 |
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電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 92307 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 62000 |
試料ステージ | 試料ホルダー: 626 / 試料ホルダーモデル: GATAN LIQUID NITROGEN |
温度 | 平均: 93 K |
アライメント法 | Legacy - 非点収差: objective lens astigmatism was corrected by monitoring power spectra of continuously acquired images in leginon |
日付 | 2013年2月23日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) デジタル化 - サンプリング間隔: 15.6 µm / 実像数: 3037 / 平均電子線量: 32 e/Å2 |
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: each particle |
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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: 9.6 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Frealign / 使用した粒子像数: 77962 |
詳細 | see detailed methods in paper |