+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20257 | |||||||||
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タイトル | Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3) | |||||||||
マップデータ | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3) | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 ribosomal subunit / regulation of G1 to G0 transition / exit from mitosis / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage ...ribosomal subunit / regulation of G1 to G0 transition / exit from mitosis / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / 90S preribosome / 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 / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal small subunit export from nucleus / translation regulator activity / 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 / maturation of LSU-rRNA / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / 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 / positive regulation of translation / small-subunit processome / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / spindle / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / heparin binding / retina development in camera-type eye / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / T cell differentiation in thymus / large ribosomal subunit rRNA binding / cell body / 5S rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / tRNA binding / mitochondrial inner membrane / cell differentiation / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of apoptotic process / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / cell division / DNA repair / mRNA binding / centrosome / ubiquitin protein ligase binding / dendrite / positive regulation of cell population proliferation / synapse / positive regulation of gene expression / negative regulation of apoptotic process 類似検索 - 分子機能 | |||||||||
生物種 | Rabbit (ウサギ) / Israeli acute paralysis virus (ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.1 Å | |||||||||
データ登録者 | Acosta-Reyes FJ / Neupane R / Frank J / Fernandez IS | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: EMBO J / 年: 2019 タイトル: The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs. 著者: Francisco Acosta-Reyes / Ritam Neupane / Joachim Frank / Israel S Fernández / 要旨: Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a ...Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches. | |||||||||
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_20257.map.gz | 26.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20257-v30.xml emd-20257.xml | 96.5 KB 96.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_20257.png | 208 KB | ||
マスクデータ | emd_20257_msk_1.map | 178 MB | マスクマップ | |
その他 | emd_20257_additional.map.gz emd_20257_half_map_1.map.gz emd_20257_half_map_2.map.gz | 140.7 MB 141.1 MB 141.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20257 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20257 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_20257_validation.pdf.gz | 847.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_20257_full_validation.pdf.gz | 846.8 KB | 表示 | |
XML形式データ | emd_20257_validation.xml.gz | 14.8 KB | 表示 | |
CIF形式データ | emd_20257_validation.cif.gz | 17.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20257 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20257 | 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_20257.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.233 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
-マスク #1
ファイル | emd_20257_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: mammalian 80S ribosome in complex with the Israeli...
ファイル | emd_20257_additional.map | ||||||||||||
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注釈 | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: mammalian 80S ribosome in complex with the Israeli...
ファイル | emd_20257_half_map_1.map | ||||||||||||
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注釈 | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: mammalian 80S ribosome in complex with the Israeli...
ファイル | emd_20257_half_map_2.map | ||||||||||||
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注釈 | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Structure of a mammalian 80S ribosome in complex with the Israeli...
+超分子 #1: Structure of a mammalian 80S ribosome in complex with the Israeli...
+分子 #1: 28S rRNA
+分子 #2: 5S rRNA
+分子 #3: 5.8S rRNA
+分子 #47: 18S rRNA
+分子 #81: IAPV-IRES
+分子 #4: uL2
+分子 #5: uL3
+分子 #6: uL4
+分子 #7: uL18
+分子 #8: eL6
+分子 #9: uL30
+分子 #10: eL8
+分子 #11: uL6
+分子 #12: uL16
+分子 #13: uL11
+分子 #14: eL13
+分子 #15: L14e
+分子 #16: eL15
+分子 #17: uL13
+分子 #18: uL22
+分子 #19: eL18
+分子 #20: eL19
+分子 #21: eL20
+分子 #22: eL21
+分子 #23: eL22
+分子 #24: uL14
+分子 #25: eL24
+分子 #26: eL23
+分子 #27: uL24
+分子 #28: eL27
+分子 #29: uL15
+分子 #30: eL29
+分子 #31: eL30
+分子 #32: eL31
+分子 #33: eL32
+分子 #34: eL33
+分子 #35: eL34
+分子 #36: eL35
+分子 #37: eL36
+分子 #38: eL37
+分子 #39: eL38
+分子 #40: eL39
+分子 #41: eL40
+分子 #42: eL41
+分子 #43: eL42
+分子 #44: eL43
+分子 #45: eL28
+分子 #46: uL1
+分子 #48: uS2
+分子 #49: eS1
+分子 #50: uS5
+分子 #51: uS3
+分子 #52: eS4
+分子 #53: uS7
+分子 #54: eS6
+分子 #55: eS7
+分子 #56: eS8
+分子 #57: uS4
+分子 #58: eS10
+分子 #59: uS17
+分子 #60: eS12
+分子 #61: uS15
+分子 #62: uS11
+分子 #63: uS19
+分子 #64: uS9
+分子 #65: eS17
+分子 #66: uS13
+分子 #67: eS19
+分子 #68: uS10
+分子 #69: eS21
+分子 #70: uS8
+分子 #71: uS12
+分子 #72: eS24
+分子 #73: eS25
+分子 #74: eS26
+分子 #75: eS27
+分子 #76: eS28
+分子 #77: eS29
+分子 #78: eS30
+分子 #79: eS31
+分子 #80: RACK1
-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 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / 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: HOLEY / 支持フィルム - Film thickness: 5.0 nm / 前処理 - タイプ: PLASMA CLEANING / 前処理 - 雰囲気: OTHER / 前処理 - 気圧: 9.33257 kPa 詳細: Plasma cleaning for both holey carbon and holey gold grids was done on a Gatan Solarus with Hydrogen (6.4 sccm gas flow) and Oxygen (27.5 sccm gas flow) and 10 W cleaning power. | ||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV 詳細: Blot force = 3s Wait time = 15s Drain time = 0s Blot time = 2.5 to 3 s. | ||||||||||
詳細 | Ribosomal complexes for the pre-translocated state were assembled at 240-390 nM concentration and applied to plasma treated holey carbon or holey gold grids. |
-電子顕微鏡法
顕微鏡 | FEI TECNAI F30 |
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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: COUNTING / デジタル化 - サイズ - 横: 3710 pixel / デジタル化 - サイズ - 縦: 3838 pixel / 平均電子線量: 42.09 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: BRIGHT FIELD / Cs: 2.26 mm / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.8 µm / 倍率(公称値): 31000 |
試料ステージ | ホルダー冷却材: NITROGEN |
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |