+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9703 | |||||||||
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タイトル | Cryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv) | |||||||||
マップデータ | ||||||||||
試料 |
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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 / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation release factor activity, codon specific / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation release factor activity, codon specific / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / translation at presynapse / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / axial mesoderm development / protein methylation / positive regulation of respiratory burst involved in inflammatory response / ribosomal protein import into nucleus / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of formation of translation preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / IRE1-RACK1-PP2A complex / 90S preribosome assembly / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / TORC2 complex binding / sequence-specific mRNA binding / GAIT complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / middle ear morphogenesis / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / aminoacyl-tRNA hydrolase activity / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / A band / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / regulation of G1 to G0 transition / laminin receptor activity / exit from mitosis / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / protein kinase A binding / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / response to aldosterone / Translation initiation complex formation / pigmentation / retinal ganglion cell axon guidance / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / G1 to G0 transition / homeostatic process / activation-induced cell death of T cells / macrophage chemotaxis / negative regulation of Wnt signaling pathway / lung morphogenesis / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / male meiosis I / iron-sulfur cluster binding / regulation of cell division / Protein hydroxylation / monocyte chemotaxis / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / phagocytic cup / blastocyst development / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Yokoyama T / Shigematsu H / Shirouzu M / Imataka H / Ito T | |||||||||
資金援助 | 日本, 1件
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引用 | ジャーナル: Mol Cell / 年: 2019 タイトル: HCV IRES Captures an Actively Translating 80S Ribosome. 著者: Takeshi Yokoyama / Kodai Machida / Wakana Iwasaki / Tomoaki Shigeta / Madoka Nishimoto / Mari Takahashi / Ayako Sakamoto / Mayumi Yonemochi / Yoshie Harada / Hideki Shigematsu / Mikako ...著者: Takeshi Yokoyama / Kodai Machida / Wakana Iwasaki / Tomoaki Shigeta / Madoka Nishimoto / Mari Takahashi / Ayako Sakamoto / Mayumi Yonemochi / Yoshie Harada / Hideki Shigematsu / Mikako Shirouzu / Hisashi Tadakuma / Hiroaki Imataka / Takuhiro Ito / 要旨: Translation initiation of hepatitis C virus (HCV) genomic RNA is induced by an internal ribosome entry site (IRES). Our cryoelectron microscopy (cryo-EM) analysis revealed that the HCV IRES binds to ...Translation initiation of hepatitis C virus (HCV) genomic RNA is induced by an internal ribosome entry site (IRES). Our cryoelectron microscopy (cryo-EM) analysis revealed that the HCV IRES binds to the solvent side of the 40S platform of the cap-dependently translating 80S ribosome. Furthermore, we obtained the cryo-EM structures of the HCV IRES capturing the 40S subunit of the IRES-dependently translating 80S ribosome. In the elucidated structures, the HCV IRES "body," consisting of domain III except for subdomain IIIb, binds to the 40S subunit, while the "long arm," consisting of domain II, remains flexible and does not impede the ongoing translation. Biochemical experiments revealed that the cap-dependently translating ribosome becomes a better substrate for the HCV IRES than the free ribosome. Therefore, the HCV IRES is likely to efficiently induce the translation initiation of its downstream mRNA with the captured translating ribosome as soon as the ongoing translation terminates. | |||||||||
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_9703.map.gz | 265 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9703-v30.xml emd-9703.xml | 92.6 KB 92.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_9703_fsc.xml | 14.8 KB | 表示 | FSCデータファイル |
画像 | emd_9703.png | 161.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9703 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9703 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9703_validation.pdf.gz | 622.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9703_full_validation.pdf.gz | 622.2 KB | 表示 | |
XML形式データ | emd_9703_validation.xml.gz | 14.2 KB | 表示 | |
CIF形式データ | emd_9703_validation.cif.gz | 19.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9703 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9703 | 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_9703.map.gz / 形式: CCP4 / 大きさ: 282.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.49 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 : Human 80S ribosome
+超分子 #1: Human 80S ribosome
+分子 #1: 28S ribosomal RNA
+分子 #2: 5S ribosomal RNA
+分子 #3: 5.8S ribosomal RNA
+分子 #46: 18S ribosomal RNA
+分子 #80: mRNA
+分子 #83: P-site tRNA
+分子 #84: HCV-IRES RNA
+分子 #4: 60S ribosomal protein L8
+分子 #5: 60S ribosomal protein L3
+分子 #6: 60S ribosomal protein L4
+分子 #7: 60S ribosomal protein L5
+分子 #8: 60S ribosomal protein L6
+分子 #9: 60S ribosomal protein L7
+分子 #10: 60S ribosomal protein L7a
+分子 #11: 60S ribosomal protein L9
+分子 #12: 60S ribosomal protein L10-like
+分子 #13: 60S ribosomal protein L11
+分子 #14: 60S ribosomal protein L13
+分子 #15: 60S ribosomal protein L14
+分子 #16: 60S ribosomal protein L15
+分子 #17: 60S ribosomal protein L13a
+分子 #18: 60S ribosomal protein L17
+分子 #19: 60S ribosomal protein L18
+分子 #20: 60S ribosomal protein L19
+分子 #21: 60S ribosomal protein L18a
+分子 #22: 60S ribosomal protein L21
+分子 #23: 60S ribosomal protein L22
+分子 #24: 60S ribosomal protein L23
+分子 #25: 60S ribosomal protein L24
+分子 #26: 60S ribosomal protein L23a
+分子 #27: 60S ribosomal protein L26
+分子 #28: 60S ribosomal protein L27
+分子 #29: 60S ribosomal protein L27a
+分子 #30: 60S ribosomal protein L29
+分子 #31: 60S ribosomal protein L30
+分子 #32: 60S ribosomal protein L31
+分子 #33: 60S ribosomal protein L32
+分子 #34: 60S ribosomal protein L35a
+分子 #35: 60S ribosomal protein L34
+分子 #36: 60S ribosomal protein L35
+分子 #37: 60S ribosomal protein L36
+分子 #38: 60S ribosomal protein L37
+分子 #39: 60S ribosomal protein L38
+分子 #40: 60S ribosomal protein L39
+分子 #41: Ubiquitin-60S ribosomal protein L40
+分子 #42: 60S ribosomal protein L41
+分子 #43: 60S ribosomal protein L36a
+分子 #44: 60S ribosomal protein L37a
+分子 #45: 60S ribosomal protein L28
+分子 #47: 40S ribosomal protein SA
+分子 #48: 40S ribosomal protein S3a
+分子 #49: 40S ribosomal protein S3
+分子 #50: 40S ribosomal protein S4, X isoform
+分子 #51: 40S ribosomal protein S5
+分子 #52: 40S ribosomal protein S7
+分子 #53: 40S ribosomal protein S8
+分子 #54: 40S ribosomal protein S10
+分子 #55: 40S ribosomal protein S11
+分子 #56: 40S ribosomal protein S15
+分子 #57: 40S ribosomal protein S16
+分子 #58: 40S ribosomal protein S17
+分子 #59: 40S ribosomal protein S18
+分子 #60: 40S ribosomal protein S19
+分子 #61: 40S ribosomal protein S20
+分子 #62: 40S ribosomal protein S21
+分子 #63: 40S ribosomal protein S23
+分子 #64: 40S ribosomal protein S26
+分子 #65: 40S ribosomal protein S28
+分子 #66: 40S ribosomal protein S29
+分子 #67: Receptor of activated protein C kinase 1
+分子 #68: 40S ribosomal protein S2
+分子 #69: 40S ribosomal protein S6
+分子 #70: 40S ribosomal protein S9
+分子 #71: 40S ribosomal protein S12
+分子 #72: 40S ribosomal protein S13
+分子 #73: 40S ribosomal protein S14
+分子 #74: 40S ribosomal protein S15a
+分子 #75: 40S ribosomal protein S24
+分子 #76: 40S ribosomal protein S25
+分子 #77: 40S ribosomal protein S27
+分子 #78: 40S ribosomal protein S30
+分子 #79: Ubiquitin-40S ribosomal protein S27a
+分子 #81: Eukaryotic peptide chain release factor subunit 1
+分子 #82: nascent peptide
-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
緩衝液 | pH: 7.5 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TECNAI ARCTICA |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 倍率(補正後): 33557 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 倍率(公称値): 23500 |
試料ステージ | ホルダー冷却材: NITROGEN |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |