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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-5943 | |||||||||
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タイトル | Cryo-EM Map of a yeast ribosome bound to the TSV IRES (Class I) | |||||||||
![]() | Reconstruction of a yeast 80S ribosome bound with the TSV IRES | |||||||||
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![]() | Translation Initiation / Internal Ribosome Entry Site | |||||||||
機能・相同性 | ![]() 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 / RMTs methylate histone arginines / 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 / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / 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 / 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 / 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 / ribosomal small subunit export from nucleus / translation regulator activity / ribosomal 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 / cellular response to amino acid starvation / ribosome assembly / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / 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 / 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 / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / 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: 6.1 Å | |||||||||
![]() | Koh CS / Brilot AF / Grigorieff N / Korostelev AA | |||||||||
![]() | ![]() タイトル: Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center. 著者: Cha San Koh / Axel F Brilot / Nikolaus Grigorieff / Andrei A Korostelev / ![]() 要旨: In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ...In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ribosome entry sites (IRESs) promote translation of mRNAs in a cap-independent manner. We report two structures of the ribosome-bound Taura syndrome virus (TSV) IRES belonging to the family of Dicistroviridae intergenic IRESs. Intersubunit rotational states differ in these structures, suggesting that ribosome dynamics play a role in IRES translocation. Pseudoknot I of the IRES occupies the ribosomal decoding center at the aminoacyl (A) site in a manner resembling that of the tRNA anticodon-mRNA codon. The structures reveal that the TSV IRES initiates translation by a previously unseen mechanism, which is conceptually distinct from initiator tRNA-dependent mechanisms. Specifically, the ORF of the IRES-driven mRNA is established by the placement of the preceding tRNA-mRNA-like structure in the A site, whereas the 40S P site remains unoccupied during this initial step. | |||||||||
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 | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 253.5 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 11 KB 11 KB | 表示 表示 | ![]() |
画像 | ![]() ![]() | 62.6 KB 4.1 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 352 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 351.6 KB | 表示 | |
XML形式データ | ![]() | 7.3 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 3j6yMC ![]() 5942C ![]() 3j6xC C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 273.6 Data #1: Frealign input particle stack [picked particles - multiframe - processed]) |
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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 | Reconstruction of a yeast 80S ribosome bound with the TSV IRES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.0595 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 bound with TSV IRES
全体 | 名称: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES |
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要素 |
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-超分子 #1000: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES
超分子 | 名称: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES タイプ: sample / ID: 1000 / Number unique components: 2 |
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分子量 | 実験値: 3.5 MDa / 理論値: 3.5 MDa |
-超分子 #1: Saccharomyces cerevisiae 80S ribosome
超分子 | 名称: Saccharomyces cerevisiae 80S ribosome / タイプ: complex / ID: 1 / 組換発現: No / データベース: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 実験値: 3.4 MDa / 理論値: 3.4 MDa |
-分子 #1: Internal Ribosome Entry Site
分子 | 名称: Internal Ribosome Entry Site / タイプ: rna / ID: 1 / Name.synonym: IRES / 分類: OTHER / Structure: DOUBLE HELIX / Synthetic?: Yes |
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由来(天然) | 生物種: ![]() |
分子量 | 実験値: 80 KDa / 理論値: 80 KDa |
配列 | 文字列: UAGCACCACC CGAUCGUAAA CUCCAUGUAU UGGUUACCCA UCUGCAUCGA AAACUCUCCG AACACUAGGU GCAGUAAGGC UUUCAUGGAG UGGUUUGCUA UUUAGCGUAC GUGUACCAUA GGCAGCCCCA AAAACACGUG UGAGGAGAAA GUCCCAGUCA CUUUGGGCAA ...文字列: UAGCACCACC CGAUCGUAAA CUCCAUGUAU UGGUUACCCA UCUGCAUCGA AAACUCUCCG AACACUAGGU GCAGUAAGGC UUUCAUGGAG UGGUUUGCUA UUUAGCGUAC GUGUACCAUA GGCAGCCCCA AAAACACGUG UGAGGAGAAA GUCCCAGUCA CUUUGGGCAA AGUAGACAGC CGCGCUUGCG UGGUGGGACU UAAUUAAUGC CUGCUAACCC AGUUGAAAUU GAUAAUUUUG AUACAACAAC |
-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
濃度 | 1.044 mg/mL |
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緩衝液 | pH: 7.5 詳細: 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/ul RNasin |
グリッド | 詳細: C-flat 1.2-1.3 400C |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / 装置: FEI VITROBOT MARK II / 手法: Fresh glow discharge, 7 second blot |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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アライメント法 | Legacy - 非点収差: Corrected using FEI software bundled with Titan Krios/Cs Corrector. |
日付 | 2012年12月26日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON I (4k x 4k) デジタル化 - サンプリング間隔: 14.0 µm / 実像数: 11498 / 平均電子線量: 30 e/Å2 / ビット/ピクセル: 32 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 132138 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 0.01 mm / 最大 デフォーカス(公称値): 6.53 µm / 最小 デフォーカス(公称値): 1.15 µm / 倍率(公称値): 133333 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
CTF補正 | 詳細: CTFFIND3, FREALIGN per micrograph |
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最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 6.1 Å / 解像度の算出法: OTHER ソフトウェア - 名称: EMAN2, IMAGIC, FREALIGN, RSAMPLE, CTFFIND3 使用した粒子像数: 51373 |