+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2644 | |||||||||
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タイトル | Structure of the mammalian ribosome-Sec61 complex | |||||||||
マップデータ | Mammalian ribosome in complex with Sec61. Translating active class with mRNA and hybrid tRNAs | |||||||||
試料 |
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キーワード | translation / ribosome / mammalian / sec61 | |||||||||
機能・相同性 | 機能・相同性情報 Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RMTs methylate histone arginines / Protein methylation / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / : ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RMTs methylate histone arginines / Protein methylation / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / : / regulation of cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / 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) / protein-transporting ATPase activity / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / translation at presynapse / protein tyrosine kinase inhibitor activity / embryonic brain development / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / carboxylic acid metabolic process / negative regulation of RNA splicing / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / RHO GTPases Activate Formins / negative regulation of phagocytosis / regulation of establishment of cell polarity / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of mitochondrial depolarization / organelle membrane / negative regulation of Wnt signaling pathway / regulation of cell division / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein localization to nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / cellular response to interleukin-4 / protein targeting / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / signaling adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of smoothened signaling pathway / laminin binding / rough endoplasmic reticulum / 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) / tricarboxylic acid cycle / gastrulation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / SH2 domain binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cyclin binding / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of GTPase activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / innate immune response in mucosa / maturation of SSU-rRNA / neural tube closure / mRNA 3'-UTR binding / small-subunit processome / positive regulation of translation / cellular response to glucose stimulus / protein kinase C binding / maintenance of translational fidelity / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / negative regulation of cell growth / receptor tyrosine kinase binding 類似検索 - 分子機能 | |||||||||
生物種 | Sus scrofa domesticus (ブタ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Voorhees RM / Fernandez IS / Scheres SHW / Hegde R | |||||||||
引用 | ジャーナル: Cell / 年: 2014 タイトル: Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution. 著者: Rebecca M Voorhees / Israel S Fernández / Sjors H W Scheres / Ramanujan S Hegde / 要旨: Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either ...Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies. | |||||||||
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_2644.map.gz | 32.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2644-v30.xml emd-2644.xml | 8.5 KB 8.5 KB | 表示 表示 | EMDBヘッダ |
画像 | EMD-2644.png | 1.6 MB | ||
その他 | emdb_2644_half_map_1.map.gz emdb_2644_half_map_2.map.gz | 210.4 MB 210.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2644 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2644 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_2644_validation.pdf.gz | 322.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_2644_full_validation.pdf.gz | 321.9 KB | 表示 | |
XML形式データ | emd_2644_validation.xml.gz | 7.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2644 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2644 | 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_2644.map.gz / 形式: CCP4 / 大きさ: 276 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Mammalian ribosome in complex with Sec61. Translating active class with mRNA and hybrid tRNAs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.34 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
-添付マップデータ: emdb 2644 half map 1.map
ファイル | emdb_2644_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-添付マップデータ: emdb 2644 half map 2.map
ファイル | emdb_2644_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Mammalian ribosome in complex with Sec61 with the large subunit (...
全体 | 名称: Mammalian ribosome in complex with Sec61 with the large subunit (60S) masked during processing. |
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要素 |
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-超分子 #1000: Mammalian ribosome in complex with Sec61 with the large subunit (...
超分子 | 名称: Mammalian ribosome in complex with Sec61 with the large subunit (60S) masked during processing. タイプ: sample / ID: 1000 / Number unique components: 2 |
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-超分子 #1: Mammalian ribosome
超分子 | 名称: Mammalian ribosome / タイプ: complex / ID: 1 / 組換発現: No / Ribosome-details: ribosome-eukaryote: ALL |
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由来(天然) | 生物種: Sus scrofa domesticus (ブタ) / 別称: domestic pig / 組織: pancreas |
-分子 #1: Sec61
分子 | 名称: Sec61 / タイプ: protein_or_peptide / ID: 1 / 組換発現: No |
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由来(天然) | 生物種: Sus scrofa domesticus (ブタ) / 別称: domestic pig |
-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
緩衝液 | pH: 7.5 詳細: 50mM hepes, 200mM K-acetate, 15mM Mg-acetate, 1mM DTT |
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グリッド | 詳細: Quantifoil R2/2 400 mesh copper grids. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 120 K / 装置: FEI VITROBOT MARK IV 手法: 3uL of sampled was incubated on the grid for 30 seconds before blotting for 9 second |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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日付 | 2014年4月7日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 実像数: 1900 / 平均電子線量: 25 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 0.003 µm / 最小 デフォーカス(公称値): 0.001 µm / 倍率(公称値): 47000 |
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 |
-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) / 解像度のタイプ: BY AUTHOR / 解像度: 3.9 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Relion / 使用した粒子像数: 80019 |