+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4d5l | |||||||||
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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 | |||||||||
要素 |
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キーワード | RIBOSOME / CRPV IRES / TERMINATION / RELEASE FACTORS | |||||||||
機能・相同性 | 機能・相同性情報 laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / 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 ...laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / 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 / translation regulator activity / ribosomal small subunit export from nucleus / 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 / 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 / metal ion binding / plasma membrane / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ORYCTOLAGUS CUNICULUS (ウサギ) | |||||||||
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: 9 Å | |||||||||
データ登録者 | Muhs, M. / Hilal, T. / Mielke, T. / Skabkin, M.A. / Sanbonmatsu, K.Y. / Pestova, T.V. / Spahn, C.M.T. | |||||||||
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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-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 | 4d5l.cif.gz | 1.6 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4d5l.ent.gz | 1.3 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4d5l.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 | 4d5l_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4d5l_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 4d5l_validation.xml.gz | 127.7 KB | 表示 | |
CIF形式データ | 4d5l_validation.cif.gz | 224.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/d5/4d5l ftp://data.pdbj.org/pub/pdb/validation_reports/d5/4d5l | HTTPS FTP |
-関連構造データ
関連構造データ | 2810MC 2813C 4d5nC 4d5yC 4d61C 4d67C 4d66 4d68 C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-RNA鎖 , 1種, 1分子 1
#1: RNA鎖 | 分子量: 602776.875 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ORYCTOLAGUS CUNICULUS (ウサギ) |
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+40S RIBOSOMAL PROTEIN ... , 33種, 33分子 ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
-詳細
配列の詳細 | FOLLOWING HUMAN SEQUENCE USED FOR MODELLING: CHAIN A 1 295 UNP P08865 RSSA_HUMAN 1 295 CHAIN C 1 ...FOLLOWING HUMAN SEQUENCE USED FOR MODELLING: CHAIN A 1 295 UNP P08865 RSSA_HUMAN 1 295 CHAIN C 1 293 UNP P15880 RS2_HUMAN 1 293 CHAIN D 1 243 UNP P23396 RS3_HUMAN 1 243 CHAIN E 1 263 UNP P22090 RS4Y1_HUMAN 1 263 CHAIN I 1 208 UNP P62241 RS8_HUMAN 1 208 CHAIN O 1 151 UNP P62263 RS14_HUMAN 1 151 CHAIN P 1 145 UNP P62841 RS15_HUMAN 1 145 CHAIN R 1 135 UNP P08708 RS17_HUMAN 1 135 CHAIN T 1 145 UNP P39019 RS19_HUMAN 1 145 CHAIN V 1 83 UNP P63220 RS21_HUMAN 1 83 CHAIN Y 1 133 UNP P62847 RS24_HUMAN 1 133 CHAIN a 1 115 UNP P62854 RS26_HUMAN 1 115 CHAIN e 1 59 UNP P62861 RS30_HUMAN 1 59 |
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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: RIBOSOMAL 80S TERMINATION COMPLEX WITH CRPV IRES-RNA AND ERF1 タイプ: RIBOSOME / 詳細: MICROGRAPH SELECTED FOR ASTIGMATISM AND DRIFT |
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緩衝液 | 名称: 20 MM TRIS PH 7.5, 100 MM KCL, 1 MM DTT, 2.5 MM MGCL2, 0.5 MM GTP 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 |
試料 | 濃度: 1.38 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: ETHANE / 詳細: LIQUID ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F20 / 日付: 2012年4月17日 / 詳細: MINIMAL DOSE SYSTEM |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 39000 X / 倍率(補正後): 65520 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 2000 nm / Cs: 2 mm |
撮影 | 電子線照射量: 20 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
画像スキャン | デジタル画像の数: 366 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: DEFOCUS GROUP | ||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 手法: MULTI-REFERENCE TEMPLATE MATCHING / 解像度: 9 Å / 粒子像の数: 109596 / ピクセルサイズ(公称値): 1.56 Å / ピクセルサイズ(実測値): 1.56 Å 倍率補正: CROSS- -CORRELATION DENSITIES WITH REFERENCE STRUCTURE 詳細: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2810. (DEPOSITION ID: 12907). 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / 詳細: METHOD--RIGID BODY | ||||||||||||
原子モデル構築 | PDB-ID: 4CXC 4cxc | ||||||||||||
精密化 | 最高解像度: 9 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 9 Å
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