- EMDB-2650: Structure of the mammalian ribosome-Sec61 complex -
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基本情報
登録情報
データベース: EMDB / ID: EMD-2650
タイトル
Structure of the mammalian ribosome-Sec61 complex
マップデータ
Final map for mammalian ribosome in complex with Sec61 in idle configuration with the large subunit masked along refinement
試料
試料: Mammalian ribosome in complex with Sec61 in a idle configuration with the large subunit (60S) masked during processing.
複合体: Mammalian ribosome
タンパク質・ペプチド: Sec61
キーワード
translation / ribosome / mammalian / sec61
機能・相同性
機能・相同性情報
: / 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) ...: / 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 / embryonic brain development / translation at presynapse / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / 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 / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-RNA complex assembly / protein targeting / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / rough endoplasmic reticulum / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of translation / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / rRNA processing / protein tag activity / large ribosomal subunit / protein transport / ribosome biogenesis / presynapse / regulation of translation / heparin binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / membrane => GO:0016020 / cytoplasmic translation / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / glutamatergic synapse / ubiquitin protein ligase binding / synapse / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm 類似検索 - 分子機能
: / : / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex ...: / : / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L34e / Ribosomal protein L18e signature. / 60S ribosomal protein L19 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L30/YlxQ / 60S ribosomal protein L35 / Ribosomal Protein L6, KOW domain / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7A/L8 / Ribosomal protein L6e / 60S ribosomal protein L6E / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L37ae / Ribosomal protein L7, eukaryotic / Ribosomal protein L31e, conserved site / Ribosomal L37ae protein family / Ribosomal protein L31e signature. / Ribosomal protein L30, N-terminal 類似検索 - ドメイン・相同性
Ribosomal protein L15 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / Protein transport protein Sec61 subunit alpha isoform 1 / 60S ribosomal protein L35a / 60S ribosomal protein L23a / 60S ribosomal protein L3 isoform a / 60S ribosomal protein L36a ...Ribosomal protein L15 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / Protein transport protein Sec61 subunit alpha isoform 1 / 60S ribosomal protein L35a / 60S ribosomal protein L23a / 60S ribosomal protein L3 isoform a / 60S ribosomal protein L36a / 60S ribosomal protein L8 / 60S ribosomal protein L36 / Ribosomal protein L37 / Ribosomal protein L19 / 60S ribosomal protein L23 / 60S ribosomal protein L7 / Protein transport protein Sec61 subunit gamma / 60S ribosomal protein L37a / 60S ribosomal protein L28 isoform 2 / 60S ribosomal protein L13a isoform 1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL15 / 60S ribosomal protein L13 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL39 / Ribosomal protein L18 / 60S ribosomal protein L7a / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL31 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL29 類似検索 - 構成要素
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.
全体 : Mammalian ribosome in complex with Sec61 in a idle configuration ...
全体
名称: Mammalian ribosome in complex with Sec61 in a idle configuration with the large subunit (60S) masked during processing.
要素
試料: Mammalian ribosome in complex with Sec61 in a idle configuration with the large subunit (60S) masked during processing.
複合体: Mammalian ribosome
タンパク質・ペプチド: Sec61
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超分子 #1000: Mammalian ribosome in complex with Sec61 in a idle configuration ...
超分子
名称: Mammalian ribosome in complex with Sec61 in a idle configuration 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
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
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電子顕微鏡法
顕微鏡
FEI TITAN KRIOS
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
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画像解析
CTF補正
詳細: Each particle
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: 3.4 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