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基本情報
登録情報 | データベース: PDB / ID: 3j7p | ||||||||||||
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タイトル | Structure of the 80S mammalian ribosome bound to eEF2 | ||||||||||||
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![]() | RIBOSOME / mammalian / Sec61 / translocation / translation / eEF2 | ||||||||||||
機能・相同性 | ![]() 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 / 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 ...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 / 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) / : / multicellular organism development / translation at presynapse / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / organelle membrane / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / regulation of cell division / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / phagocytic cup / 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 / translation regulator activity / signaling adaptor activity / cytosolic ribosome / negative regulation of smoothened signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / laminin binding / 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) / rough endoplasmic reticulum / gastrulation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / cyclin binding / SH2 domain binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of GTPase activity / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA / small-subunit processome / positive regulation of translation / cellular response to glucose stimulus / protein kinase C binding / maintenance of translational fidelity / cell cycle / positive regulation of protein-containing complex assembly / negative regulation of cell growth / cellular response to gamma radiation / receptor tyrosine kinase binding / cellular response to growth factor stimulus / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / protein tag activity / large ribosomal subunit / regulation of protein localization / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / rhythmic process / ribosome biogenesis / ribosome binding / presynapse / regulation of translation / virus receptor activity / heparin binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / midbody / 5S rRNA binding / large ribosomal subunit rRNA binding / perikaryon 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() | ||||||||||||
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: 3.5 Å | ||||||||||||
![]() | Voorhees, R.M. / Fernandez, I.S. / Scheres, S.H.W. / Hegde, R.S. | ||||||||||||
![]() | ![]() 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
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 5.4 MB | 表示 | ![]() |
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PDB形式 | ![]() | 表示 | ![]() | |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
-RNA鎖 , 4種, 4分子 578S2
#1: RNA鎖 | 分子量: 1187230.000 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
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#2: RNA鎖 | 分子量: 38691.914 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#3: RNA鎖 | 分子量: 50143.648 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#49: RNA鎖 | 分子量: 561958.812 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
+Ribosomal protein ... , 77種, 77分子 ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
-タンパク質 , 1種, 1分子 4
#48: タンパク質 | 分子量: 95232.875 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
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-非ポリマー , 2種, 170分子 ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#83: 化合物 | ChemComp-MG / #84: 化合物 | ChemComp-ZN / |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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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 |
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試料調製
構成要素 | 名称: The 80S-eEF2 complex purified from porcine pancreas / タイプ: RIBOSOME |
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緩衝液 | 名称: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin pH: 7.5 詳細: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: Quantifoil R2/2 400 mesh copper grids |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / Temp: 120 K 詳細: 3 uL sample was incubated on the grid for 30 seconds and blotted for 9 seconds before being plunged into liquid ethane (FEI VITROBOT MARK IV). |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2014年4月7日 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 59000 X / 倍率(補正後): 104478 X / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 2500 nm / Cs: 2.7 mm |
試料ホルダ | 資料ホルダタイプ: FEI TITAN KRIOS AUTOGRID HOLDER / 温度: 70 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 27 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 詳細: Back-thinned |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
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解析
EMソフトウェア |
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CTF補正 | 詳細: Each particle | |||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||
3次元再構成 | 手法: Single particle / 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 36667 / ピクセルサイズ(公称値): 1.34 Å / 対称性のタイプ: POINT | |||||||||||||||
原子モデル構築 | B value: 37 / プロトコル: OTHER / 空間: RECIPROCAL / Target criteria: R-factor and FSC / 詳細: METHOD--Maximum likelihood | |||||||||||||||
原子モデル構築 |
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精密化ステップ | サイクル: LAST
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