+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j8b | |||||||||
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タイトル | Model of the human eIF3 PCI-MPN octamer docked into the 43S-HCV IRES EM map | |||||||||
要素 | (Eukaryotic translation initiation factor 3 subunit ...) x 8 | |||||||||
キーワード | TRANSLATION | |||||||||
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 | Homo sapiens (ヒト) | |||||||||
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: 9.3 Å | |||||||||
データ登録者 | Erzberger, J.P. / Ban, N. | |||||||||
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 |
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Remark 0 | THIS ENTRY 3J8B CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-2451) DETERMINED ...THIS ENTRY 3J8B CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-2451) DETERMINED ORIGINALLY BY AUTHORS: Y.HASHEM, A.DES-GEORGES, V.DHOTE, R.LANGLOIS, H.Y.LIAO, R.A.GRASSUCCI, T.V.PESTOVA, C.U.T.HELLEN, J.FRANK | |||||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-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 | 3j8b.cif.gz | 367.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j8b.ent.gz | 222.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j8b.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 | 3j8b_validation.pdf.gz | 913.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3j8b_full_validation.pdf.gz | 931.9 KB | 表示 | |
XML形式データ | 3j8b_validation.xml.gz | 54.5 KB | 表示 | |
CIF形式データ | 3j8b_validation.cif.gz | 89.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j8/3j8b ftp://data.pdbj.org/pub/pdb/validation_reports/j8/3j8b | 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
-Eukaryotic translation initiation factor 3 subunit ... , 8種, 8分子 ACEFHKLM
#1: タンパク質 | 分子量: 61036.340 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q14152*PLUS |
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#2: タンパク質 | 分子量: 62812.340 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q99613*PLUS |
#3: タンパク質 | 分子量: 48854.117 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P60228*PLUS |
#4: タンパク質 | 分子量: 32756.850 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O00303*PLUS, ubiquitinyl hydrolase 1 |
#5: タンパク質 | 分子量: 35125.961 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O15372*PLUS |
#6: タンパク質 | 分子量: 23533.061 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9UBQ5*PLUS |
#7: タンパク質 | 分子量: 63008.434 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9Y262*PLUS |
#8: タンパク質 | 分子量: 40404.781 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q7L2H7*PLUS |
-詳細
配列の詳細 | ENTRY CONTAINS EIF3 PROTEINS FROM HOMO SAPIENS FITTED INTO ELECTRON MICROSCOPY DATA DERIVED FROM ...ENTRY CONTAINS EIF3 PROTEINS FROM HOMO SAPIENS FITTED INTO ELECTRON MICROSCOPY |
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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: CSFV IRES in complex with eIF3, small ribosomal 40S subunit and DHX29 タイプ: RIBOSOME |
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緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: 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: 2013年2月1日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 120 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): -4000 nm / 最小 デフォーカス(公称値): -1000 nm |
撮影 | 電子線照射量: 12 e/Å2 フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) |
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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対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 9.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 26000 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model
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精密化ステップ | サイクル: LAST
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