+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j7o | ||||||||||||
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タイトル | Structure of the mammalian 60S ribosomal subunit | ||||||||||||
要素 |
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キーワード | RIBOSOME / mammalian | ||||||||||||
機能・相同性 | 機能・相同性情報 Protein hydroxylation / 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) / translation at presynapse / alpha-beta T cell differentiation ...Protein hydroxylation / 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) / translation at presynapse / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / 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 / organelle membrane / G1 to G0 transition / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein localization to nucleus / protein-RNA complex assembly / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / rough endoplasmic reticulum / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / innate immune response in mucosa / positive regulation of translation / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / antibacterial humoral response / presynapse / heparin binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / protein stabilization / rRNA binding / defense response to Gram-positive bacterium / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / synapse / positive regulation of gene expression / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / extracellular space / nucleoplasm / identical protein binding / nucleus / cytoplasm 類似検索 - 分子機能 | ||||||||||||
生物種 | Sus scrofa (ブタ) | ||||||||||||
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: 3.4 Å | ||||||||||||
データ登録者 | Voorhees, R.M. / Fernandez, I.S. / Scheres, S.H.W. / Hegde, R.S. | ||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3j7o.cif.gz | 3.4 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j7o.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 3j7o.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 | 3j7o_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3j7o_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 3j7o_validation.xml.gz | 230.1 KB | 表示 | |
CIF形式データ | 3j7o_validation.cif.gz | 382.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j7/3j7o ftp://data.pdbj.org/pub/pdb/validation_reports/j7/3j7o | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
-RNA鎖 , 3種, 3分子 578
#1: RNA鎖 | 分子量: 1187230.000 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 器官: pancreas |
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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) Sus scrofa (ブタ) / 器官: pancreas |
#3: RNA鎖 | 分子量: 50143.648 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 器官: pancreas |
+Ribosomal protein ... , 42種, 42分子 ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-非ポリマー , 2種, 133分子
#46: 化合物 | ChemComp-MG / #47: 化合物 | |
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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 |
-試料調製
構成要素 | 名称: The 60S ribosomal subunit 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). |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: OTHER |
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 |
-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: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 80019 / 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 | 解像度: 3.5→268 Å / Cor.coef. Fo:Fc: 0.856 / SU B: 22.493 / SU ML: 0.34 / σ(F): 0 / ESU R: 0.873 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 0 Å2 / Biso mean: 48.645 Å2 / Biso min: 0 Å2
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拘束条件 |
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LS精密化 シェル | 解像度: 3.5→3.591 Å / Total num. of bins used: 20 /
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