+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7sys | ||||||||||||
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タイトル | Structure of the delta dII IRES eIF2-containing 48S initiation complex, closed conformation. Structure 12(delta dII). | ||||||||||||
要素 |
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キーワード | RIBOSOME / HCV / IRES / 40S | ||||||||||||
機能・相同性 | 機能・相同性情報 regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency ...regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / PERK regulates gene expression / regulation of translational initiation in response to stress / eukaryotic translation initiation factor 2 complex / multi-eIF complex / translation factor activity, RNA binding / ribosomal subunit / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / phagocytic cup / Response of EIF2AK4 (GCN2) to amino acid deficiency / mitophagy / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / erythrocyte development / ribosomal small subunit export from nucleus / translation regulator activity / stress granule assembly / laminin binding / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / response to endoplasmic reticulum stress / translation initiation factor activity / cellular response to amino acid starvation / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / ABC-family proteins mediated transport / PKR-mediated signaling / spindle / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / rRNA processing / cellular response to UV / protein tag activity / ribosomal small subunit biogenesis / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / virus receptor activity / cellular response to oxidative stress / cellular response to heat / small ribosomal subunit / T cell differentiation in thymus / cell body / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / tRNA binding / mitochondrial inner membrane / cell differentiation / postsynaptic density / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of apoptotic process 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) Hepatitis C virus (ウイルス) 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: 3.5 Å | ||||||||||||
データ登録者 | Brown, Z.P. / Abaeva, I.S. / De, S. / Hellen, C.U.T. / Pestova, T.V. / Frank, J. | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: EMBO J / 年: 2022 タイトル: Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. 著者: Zuben P Brown / Irina S Abaeva / Swastik De / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank / 要旨: Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical ...Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining. | ||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7sys.cif.gz | 1.8 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7sys.ent.gz | 1.4 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7sys.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 | 7sys_validation.pdf.gz | 1.6 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7sys_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 7sys_validation.xml.gz | 161 KB | 表示 | |
CIF形式データ | 7sys_validation.cif.gz | 269 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/sy/7sys ftp://data.pdbj.org/pub/pdb/validation_reports/sy/7sys | HTTPS FTP |
-関連構造データ
関連構造データ | 25539MC 7syiC 7syjC 7sykC 7sylC 7syoC 7sypC 7syqC 7syrC 7sytC 7syuC 7syvC 7sywC 7syxC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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 , 3種, 3分子 2zi
#1: RNA鎖 | 分子量: 603100.938 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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#38: RNA鎖 | 分子量: 128746.109 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Hepatitis C virus (isolate 1) (C型肝炎ウイルス) 発現宿主: Escherichia coli (大腸菌) / 参照: GenBank: 149384897 |
#39: RNA鎖 | 分子量: 24231.510 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: GenBank: 174924 |
-Eukaryotic translation initiation factor ... , 2種, 2分子 Aj
#2: タンパク質 | 分子量: 16488.449 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EIF1AX, EIF1A, EIF4C / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P47813 |
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#36: タンパク質 | 分子量: 36161.180 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EIF2S1, EIF2A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P05198 |
+タンパク質 , 33種, 33分子 BCDEFGHIJKLMNOPQRSTUVWXYZabcde...
-タンパク質・ペプチド / 非ポリマー , 2種, 2分子 n
#37: タンパク質・ペプチド | 分子量: 3473.451 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: A0A087WNH4 |
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#40: 化合物 | ChemComp-ZN / |
-詳細
研究の焦点であるリガンドがあるか | N |
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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: 40S ribosomal small subunit with HCV IRES / タイプ: RIBOSOME / Entity ID: #1-#39 / 由来: MULTIPLE SOURCES |
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分子量 | 値: 2 MDa / 実験値: NO |
緩衝液 | pH: 7.5 |
試料 | 濃度: 7.5E-5 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: H2/O2 mixture for 25 seconds at 25W power / グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R0.6/1 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE-PROPANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K / 詳細: 4 second blot time, force 3 |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F30 |
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): 56000 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.26 mm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 平均露光時間: 4 sec. / 電子線照射量: 70.9 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19.1_4122: / 分類: 精密化 | ||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 103813 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
原子モデル構築 |
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拘束条件 |
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