+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2451 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of the CSFV IRES in complex with eIF3, small ribosomal 40S subunit and DHX29 | |||||||||
マップデータ | Reconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29. | |||||||||
試料 |
| |||||||||
キーワード | Internal Ribosomal Entry Site / 5'-end independent initiation / HCV-like IRES / eIF3/HCV-like IRES interaction | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation ...positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / metal-dependent deubiquitinase activity / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Ribosomal scanning and start codon recognition / Translation initiation complex formation / protein deubiquitination / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of translational initiation / translation initiation factor binding / translational initiation / translation initiation factor activity / positive regulation of translation / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / PML body / fibrillar center / metallopeptidase activity / ribosome binding / microtubule / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / postsynaptic density / cadherin binding / mRNA binding / synapse / chromatin / nucleolus / structural molecule activity / proteolysis / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Classical swine fever virus (豚コレラウイルス) / Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 9.3 Å | |||||||||
データ登録者 | Hashem Y / des-Georges A / Dhote V / Langlois R / Liao HY / Grassucci RA / Pestova TV / Hellen CUT / Frank J | |||||||||
引用 | ジャーナル: Nature / 年: 2013 タイトル: Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. 著者: Yaser Hashem / Amedee des Georges / Vidya Dhote / Robert Langlois / Hstau Y Liao / Robert A Grassucci / Tatyana V Pestova / Christopher U T Hellen / Joachim Frank / 要旨: Hepatitis C virus (HCV) and classical swine fever virus (CSFV) messenger RNAs contain related (HCV-like) internal ribosome entry sites (IRESs) that promote 5'-end independent initiation of ...Hepatitis C virus (HCV) and classical swine fever virus (CSFV) messenger RNAs contain related (HCV-like) internal ribosome entry sites (IRESs) that promote 5'-end independent initiation of translation, requiring only a subset of the eukaryotic initiation factors (eIFs) needed for canonical initiation on cellular mRNAs. Initiation on HCV-like IRESs relies on their specific interaction with the 40S subunit, which places the initiation codon into the P site, where it directly base-pairs with eIF2-bound initiator methionyl transfer RNA to form a 48S initiation complex. However, all HCV-like IRESs also specifically interact with eIF3 (refs 2, 5-7, 9-12), but the role of this interaction in IRES-mediated initiation has remained unknown. During canonical initiation, eIF3 binds to the 40S subunit as a component of the 43S pre-initiation complex, and comparison of the ribosomal positions of eIF3 and the HCV IRES revealed that they overlap, so that their rearrangement would be required for formation of ribosomal complexes containing both components. Here we present a cryo-electron microscopy reconstruction of a 40S ribosomal complex containing eIF3 and the CSFV IRES. Remarkably, although the position and interactions of the CSFV IRES with the 40S subunit in this complex are similar to those of the HCV IRES in the 40S-IRES binary complex, eIF3 is completely displaced from its ribosomal position in the 43S complex, and instead interacts through its ribosome-binding surface exclusively with the apical region of domain III of the IRES. Our results suggest a role for the specific interaction of HCV-like IRESs with eIF3 in preventing ribosomal association of eIF3, which could serve two purposes: relieving the competition between the IRES and eIF3 for a common binding site on the 40S subunit, and reducing formation of 43S complexes, thereby favouring translation of viral mRNAs. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_2451.map.gz | 37.9 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-2451-v30.xml emd-2451.xml | 12.1 KB 12.1 KB | 表示 表示 | EMDBヘッダ |
画像 | EMD-2451-40S-IRES-DHX29-eIF3-500X500.jpg | 108.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2451 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2451 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_2451_validation.pdf.gz | 351.3 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_2451_full_validation.pdf.gz | 350.9 KB | 表示 | |
XML形式データ | emd_2451_validation.xml.gz | 5.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2451 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2451 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_2451.map.gz / 形式: CCP4 / 大きさ: 39.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Reconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.245 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
-全体 : Reconstruction of a mutant Classical Swine Fever Virus IRES bound...
全体 | 名称: Reconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29. |
---|---|
要素 |
|
-超分子 #1000: Reconstruction of a mutant Classical Swine Fever Virus IRES bound...
超分子 | 名称: Reconstruction of a mutant Classical Swine Fever Virus IRES bound to eukaryotic initiation factor 3, the Rabbit 40S subunit and DHX29. タイプ: sample / ID: 1000 集合状態: one 40S, one CSFV IRES, one eIF3 and one DHX29 Number unique components: 4 |
---|---|
分子量 | 理論値: 2.6 MDa |
-超分子 #1: eukaryotic small ribosmal subunit
超分子 | 名称: eukaryotic small ribosmal subunit / タイプ: complex / ID: 1 / Name.synonym: 40S subunit / 組換発現: No / Ribosome-details: ribosome-eukaryote: SSU 40S, SSU RNA 18S |
---|---|
由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) / 別称: Rabbit / 組織: blood / 細胞: reticulocytes |
分子量 | 理論値: 1.5 MDa |
-分子 #1: Internal Ribosomal Entry Site
分子 | 名称: Internal Ribosomal Entry Site / タイプ: rna / ID: 1 / Name.synonym: IRES / 分類: OTHER / Structure: DOUBLE HELIX / Synthetic?: Yes |
---|---|
由来(天然) | 生物種: Classical swine fever virus (豚コレラウイルス) 別称: CSFV |
分子量 | 理論値: 100 KDa |
配列 | 文字列: GACUAGCCGU AGUGGCGAGC UCCCUGGGUG GUCUAAGUCC UGAGUACAGG ACAGUCGUCA GUAGUUCGAC GUGAGCACUA GCCCACCUCG AGAUGCUACG UGGACGAGGG CAUGCCCAAG ACACACCUUA ACCCUGGCGG GGGUCGCUAG GGUGAAAUCA CAUUAUGUGA ...文字列: GACUAGCCGU AGUGGCGAGC UCCCUGGGUG GUCUAAGUCC UGAGUACAGG ACAGUCGUCA GUAGUUCGAC GUGAGCACUA GCCCACCUCG AGAUGCUACG UGGACGAGGG CAUGCCCAAG ACACACCUUA ACCCUGGCGG GGGUCGCUAG GGUGAAAUCA CAUUAUGUGA UGGGGGUACG ACCUGAUAGG GUGCUGCAGA GGCCCACUAG CAGGCUAGUA UAAAAAUCUC UGC |
-分子 #2: DHX29
分子 | 名称: DHX29 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 集合状態: Monomer / 組換発現: Yes |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human |
分子量 | 理論値: 150 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
-分子 #3: eukaryotic initiation factor 3
分子 | 名称: eukaryotic initiation factor 3 / タイプ: protein_or_peptide / ID: 3 / Name.synonym: eIF3 / コピー数: 1 / 集合状態: Monomer / 組換発現: No |
---|---|
由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) / 別称: Rabbit / 組織: Blood / 細胞: Reticulocytes |
分子量 | 理論値: 850 KDa |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.105 mg/mL |
---|---|
緩衝液 | pH: 7.5 詳細: 20 mM Tris , 75 mM KCl, 5 mM Mg, 2 mM DTT and 0.25 mM spermidine |
グリッド | 詳細: 300 mesh copper/molybdenum holey carbon-coated Quantifoil 2/4 grid (Quantifoil Micro Tools GmbH) containing an additional continuous thin layer of carbon |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 120 K / 装置: FEI VITROBOT MARK II 手法: 30 seconds waiting after sample deposition on the grid, blotting for seconds before plunging |
-電子顕微鏡法
顕微鏡 | FEI TECNAI F20 |
---|---|
温度 | 平均: 110 K |
日付 | 2013年2月1日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) 実像数: 12000 / 平均電子線量: 12 e/Å2 / ビット/ピクセル: 32 |
電子線 | 加速電圧: 120 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 51570 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.26 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): -1.0 µm |
試料ステージ | 試料ホルダー: Gatan CT3500 side-entry cryo-holder / 試料ホルダーモデル: OTHER |
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
-画像解析
詳細 | The particles constituting this reconstruction were sorted using RELION. |
---|---|
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) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 9.3 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Spider, Relion / 使用した粒子像数: 26000 |