+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6sv4 | ||||||
---|---|---|---|---|---|---|---|
タイトル | The cryo-EM structure of SDD1-stalled collided trisome. | ||||||
要素 |
| ||||||
キーワード | TRANSLATION / trisome / ribosome / collision / stalling | ||||||
機能・相同性 | 機能・相同性情報 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 / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...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 / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / hexon binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / 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 / Ribosomal scanning and start codon recognition / 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 / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ub-specific processing proteases / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / 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) / maturation of LSU-rRNA / DNA-(apurinic or apyrimidinic site) endonuclease activity / 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 / ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / viral capsid / ribosome binding / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / host cell nucleus / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / 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 | 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 | ||||||
データ登録者 | Tesina, P. / Buschauer, R. / Cheng, J. / Becker, T. / Beckmann, R. | ||||||
資金援助 | ドイツ, 1件
| ||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2020 タイトル: RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1. 著者: Yoshitaka Matsuo / Petr Tesina / Shizuka Nakajima / Masato Mizuno / Akinori Endo / Robert Buschauer / Jingdong Cheng / Okuto Shounai / Ken Ikeuchi / Yasushi Saeki / Thomas Becker / Roland ...著者: Yoshitaka Matsuo / Petr Tesina / Shizuka Nakajima / Masato Mizuno / Akinori Endo / Robert Buschauer / Jingdong Cheng / Okuto Shounai / Ken Ikeuchi / Yasushi Saeki / Thomas Becker / Roland Beckmann / Toshifumi Inada / 要旨: Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells that is triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation ...Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells that is triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation followed by degradation of nascent peptides. However, endogenous RQC-inducing sequences and the mechanism underlying the ubiquitin-dependent ribosome dissociation remain poorly understood. Here, we identified SDD1 messenger RNA from Saccharomyces cerevisiae as an endogenous RQC substrate and reveal the mechanism of its mRNA-dependent and nascent peptide-dependent translational stalling. In vitro translation of SDD1 mRNA enabled the reconstitution of Hel2-dependent polyubiquitination of collided disomes and, preferentially, trisomes. The distinct trisome architecture, visualized using cryo-EM, provides the structural basis for the more-efficient recognition by Hel2 compared with that of disomes. Subsequently, the Slh1 helicase subunit of the RQC trigger (RQT) complex preferentially dissociates the first stalled polyubiquitinated ribosome in an ATP-dependent manner. Together, these findings provide fundamental mechanistic insights into RQC and its physiological role in maintaining cellular protein homeostasis. | ||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6sv4.cif.gz | 13.1 MB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6sv4.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6sv4.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6sv4_validation.pdf.gz | 2.4 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 6sv4_full_validation.pdf.gz | 3 MB | 表示 | |
XML形式データ | 6sv4_validation.xml.gz | 957 KB | 表示 | |
CIF形式データ | 6sv4_validation.cif.gz | 1.7 MB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/sv/6sv4 ftp://data.pdbj.org/pub/pdb/validation_reports/sv/6sv4 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-RNA鎖 , 7種, 17分子 BQYQZQBRYRZRBSYSZS22b2cnnbncmbmc
#1: RNA鎖 | 分子量: 1097493.875 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 834774822 #2: RNA鎖 | 分子量: 38951.105 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1329886537 #3: RNA鎖 | 分子量: 50376.758 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1489318609 #18: RNA鎖 | 分子量: 579761.938 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 874346701 #80: RNA鎖 | | 分子量: 24468.551 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) #81: RNA鎖 | 分子量: 24501.539 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) #82: RNA鎖 | 分子量: 24802.785 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) |
---|
+60S ribosomal protein ... , 40種, 120分子 AWXWzWBAYAZABEYEZEBIYIZIBMYMZMBOYOZOAAXAzAADXDzDBDYDZDAGXGzG...
+40S ribosomal protein ... , 30種, 90分子 PPbPcQQbQcRRbRcAAbAcSSbScTTbTcUUbUcVVbVcWWbWcCCbCc...
-タンパク質 , 5種, 15分子 BBbBcNNbNcOObOcAOXOzOBUYUZU
#24: タンパク質 | 分子量: 25072.600 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: A0A1L4AA68 #50: タンパク質 | 分子量: 17254.227 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05759 #51: タンパク質 | 分子量: 34841.219 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P38011 #75: タンパク質 | 分子量: 14583.077 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CH08 #79: タンパク質 | 分子量: 33749.121 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05317 |
---|
-詳細
Has protein modification | Y |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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 |
-試料調製
構成要素 | 名称: Trisome assembly of yeast collided ribosomes / タイプ: RIBOSOME / Entity ID: #1-#79, #81-#82, #80 / 由来: NATURAL |
---|---|
由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
緩衝液 | pH: 7.2 |
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 |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 25 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 69054 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
精密化 | 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 107.33 Å2 | ||||||||||||||||||||||||
拘束条件 |
|