+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2810 | |||||||||
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タイトル | Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state | |||||||||
マップデータ | Reconstruction of mammalian termination complex with CrPV IRES-RNA and eRF1 | |||||||||
試料 |
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キーワード | CrPV IRES / ribosome / Termination / release factors | |||||||||
機能・相同性 | 機能・相同性情報 translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / laminin receptor activity ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / laminin receptor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mammalian oogenesis stage / activation-induced cell death of T cells / Protein hydroxylation / positive regulation of signal transduction by p53 class mediator / Eukaryotic Translation Termination / phagocytic cup / ubiquitin ligase inhibitor activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / ribosomal small subunit export from nucleus / translational termination / cytosolic ribosome / 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 / MDM2/MDM4 family protein binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / glucose homeostasis / virus receptor activity / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / postsynaptic density / rRNA binding / mitochondrial inner membrane / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / cell division / DNA repair / centrosome / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / negative regulation of apoptotic process / nucleolus / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Homo sapiens (ヒト) / Cricket paralysis virus (ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 8.7 Å | |||||||||
データ登録者 | Muhs M / Hilal T / Mielke T / Skabkin MA / Sanbonmatsu KY / Pestova TV / Spahn CMT | |||||||||
引用 | ジャーナル: Mol Cell / 年: 2015 タイトル: Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES. 著者: Margarita Muhs / Tarek Hilal / Thorsten Mielke / Maxim A Skabkin / Karissa Y Sanbonmatsu / Tatyana V Pestova / Christian M T Spahn / 要旨: The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the ...The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the CrPV IRES jumpstarts translation in the elongation phase from the ribosomal A site. Here, we present cryoelectron microscopy (cryo-EM) maps of 80S⋅CrPV-STOP ⋅ eRF1 ⋅ eRF3 ⋅ GMPPNP and 80S⋅CrPV-STOP ⋅ eRF1 complexes, revealing a previously unseen binding state of the IRES and directly rationalizing that an eEF2-dependent translocation of the IRES is required to allow the first A-site occupation. During this unusual translocation event, the IRES undergoes a pronounced conformational change to a more stretched conformation. At the same time, our structural analysis provides information about the binding modes of eRF1 ⋅ eRF3 ⋅ GMPPNP and eRF1 in a minimal system. It shows that neither eRF3 nor ABCE1 are required for the active conformation of eRF1 at the intersection between eukaryotic termination and recycling. | |||||||||
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_2810.map.gz | 86.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2810-v30.xml emd-2810.xml | 19.2 KB 19.2 KB | 表示 表示 | EMDBヘッダ |
画像 | eRF1.png emd_2810.png | 80.3 KB 119.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2810 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2810 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_2810_validation.pdf.gz | 234.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_2810_full_validation.pdf.gz | 233.8 KB | 表示 | |
XML形式データ | emd_2810_validation.xml.gz | 6.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2810 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2810 | 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_2810.map.gz / 形式: CCP4 / 大きさ: 100.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of mammalian termination complex with CrPV IRES-RNA and eRF1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.56 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
-試料の構成要素
-全体 : Ribosomal 80S termination complex with CrPV IRES-RNA and eRF1
全体 | 名称: Ribosomal 80S termination complex with CrPV IRES-RNA and eRF1 |
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要素 |
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-超分子 #1000: Ribosomal 80S termination complex with CrPV IRES-RNA and eRF1
超分子 | 名称: Ribosomal 80S termination complex with CrPV IRES-RNA and eRF1 タイプ: sample / ID: 1000 / 集合状態: CrPV IRES and eRF1 bound to one 80S ribosome / Number unique components: 3 |
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分子量 | 理論値: 4.5 MDa |
-超分子 #1: 80S ribosome
超分子 | 名称: 80S 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: Oryctolagus cuniculus (ウサギ) / 別称: Rabbit |
分子量 | 理論値: 4.5 MDa |
-分子 #1: eukaryoric release factor 1
分子 | 名称: eukaryoric release factor 1 / タイプ: protein_or_peptide / ID: 1 / Name.synonym: eRF1 / コピー数: 1 / 集合状態: Monomer / 組換発現: Yes |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human |
分子量 | 理論値: 50 KDa |
組換発現 | 生物種: Escherichia coli BL21 (大腸菌) |
配列 | UniProtKB: Eukaryotic peptide chain release factor subunit 1 |
-分子 #2: Cricket paralysis virus IRES RNA
分子 | 名称: Cricket paralysis virus IRES RNA / タイプ: rna / ID: 2 / Name.synonym: CrPV IRES RNA / 分類: OTHER / Structure: OTHER / Synthetic?: No |
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由来(天然) | 生物種: Cricket paralysis virus (ウイルス) |
配列 | 文字列: AAAAAUGUGA UCUUGCUUGU AAAUACAAUU UUGAGAGGUU AAUAAAUUAC AAGUAGUGCU AUUUUUGUAU UUAGGUUAGC UAUUUAGCUU UACGUUCCAG GAUGCCUAGU GGCAGCCCCA CAAUAUCCAG GAAGCCCUCU CUGCGGUUUU UCAGAUUAGG UAGUCGAAAA ...文字列: AAAAAUGUGA UCUUGCUUGU AAAUACAAUU UUGAGAGGUU AAUAAAUUAC AAGUAGUGCU AUUUUUGUAU UUAGGUUAGC UAUUUAGCUU UACGUUCCAG GAUGCCUAGU GGCAGCCCCA CAAUAUCCAG GAAGCCCUCU CUGCGGUUUU UCAGAUUAGG UAGUCGAAAA ACCUAAGAAA UUUACCUUAA GGCUUCCUCG A |
-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
濃度 | 1.38 mg/mL |
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緩衝液 | pH: 7.5 詳細: 20 mM Tris pH 7.5, 100 mM KCl, 1 mM DTT, 2.5 mM MgCl2, 0.5 mM GTP |
グリッド | 詳細: Quantifoil grids with additional continuous carbon support |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 85 % / 装置: FEI VITROBOT MARK II / 手法: blot for 2/4 seconds before plunging |
-電子顕微鏡法
顕微鏡 | FEI TECNAI F20 |
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温度 | 最低: 77 K |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 200,000 times magnification |
詳細 | minimal dose system |
日付 | 2012年4月17日 |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM / デジタル化 - スキャナー: OTHER / 実像数: 366 / 平均電子線量: 20 e/Å2 / ビット/ピクセル: 16 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 65520 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2 mm / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 2.0 µm / 倍率(公称値): 39000 |
試料ステージ | 試料ホルダーモデル: GATAN LIQUID NITROGEN |
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
-画像解析
詳細 | The particles were selected using SIGNATURE and processed by using SPIDER and SPARX |
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CTF補正 | 詳細: Defocus group |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 8.7 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: SPIDER, SPARX 詳細: The particles were selected using SIGNATURE and processed by using SPIDER and SPARX. 使用した粒子像数: 109596 |
-原子モデル構築 1
初期モデル | PDB ID: 4cxc Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L / Chain - #12 - Chain ID: M / Chain - #13 - Chain ID: N / Chain - #14 - Chain ID: O / Chain - #15 - Chain ID: P / Chain - #16 - Chain ID: Q / Chain - #17 - Chain ID: R / Chain - #18 - Chain ID: S / Chain - #19 - Chain ID: T / Chain - #20 - Chain ID: U / Chain - #21 - Chain ID: V / Chain - #22 - Chain ID: W / Chain - #23 - Chain ID: X / Chain - #24 - Chain ID: Y / Chain - #25 - Chain ID: Z / Chain - #26 - Chain ID: a / Chain - #27 - Chain ID: b / Chain - #28 - Chain ID: c / Chain - #29 - Chain ID: d / Chain - #30 - Chain ID: e / Chain - #31 - Chain ID: f / Chain - #32 - Chain ID: g / Chain - #33 - Chain ID: 1 |
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ソフトウェア | 名称: CHIMERA |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-4d5l: PDB-4d5n: PDB-4d5y: |
-原子モデル構築 2
初期モデル | PDB ID: 4cxd Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: L / Chain - #11 - Chain ID: M / Chain - #12 - Chain ID: N / Chain - #13 - Chain ID: O / Chain - #14 - Chain ID: P / Chain - #15 - Chain ID: Q / Chain - #16 - Chain ID: R / Chain - #17 - Chain ID: S / Chain - #18 - Chain ID: T / Chain - #19 - Chain ID: U / Chain - #20 - Chain ID: V / Chain - #21 - Chain ID: W / Chain - #22 - Chain ID: X / Chain - #23 - Chain ID: Y / Chain - #24 - Chain ID: Z / Chain - #25 - Chain ID: a / Chain - #26 - Chain ID: b / Chain - #27 - Chain ID: c / Chain - #28 - Chain ID: d / Chain - #29 - Chain ID: e / Chain - #30 - Chain ID: f / Chain - #31 - Chain ID: g / Chain - #32 - Chain ID: h / Chain - #33 - Chain ID: i / Chain - #34 - Chain ID: j / Chain - #35 - Chain ID: k / Chain - #36 - Chain ID: l / Chain - #37 - Chain ID: m / Chain - #38 - Chain ID: n / Chain - #39 - Chain ID: o / Chain - #40 - Chain ID: p / Chain - #41 - Chain ID: t / Chain - #42 - Chain ID: u |
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ソフトウェア | 名称: CHIMERA |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-4d5l: PDB-4d5n: PDB-4d5y: |