+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12759 | |||||||||
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タイトル | Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Frameshift / virus / pseudoknot / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal subunit / regulation of G1 to G0 transition / exit from mitosis ...Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal subunit / regulation of G1 to G0 transition / exit from mitosis / laminin receptor activity / 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 / T cell proliferation involved in immune response / protein-RNA complex assembly / erythrocyte development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal small subunit export from nucleus / translation regulator activity / laminin binding / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / 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 / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / ribosome binding / 付加脱離酵素(リアーゼ); P-Oリアーゼ類; - / glucose homeostasis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / regulation of translation / ribosomal small subunit assembly / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / retina development in camera-type eye / Maturation of replicase proteins / virus receptor activity / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / SARS coronavirus main proteinase / small ribosomal subunit / host cell endoplasmic reticulum-Golgi intermediate compartment / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell endosome / cytosolic small ribosomal subunit 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Severe acute respiratory syndrome coronavirus 2 (ウイルス) / Bos taurus (ウシ) | |||||||||
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 | Bhatt PR / Scaiola A | |||||||||
資金援助 | スイス, アイルランド, 2件
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引用 | ジャーナル: Science / 年: 2021 タイトル: Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. 著者: Pramod R Bhatt / Alain Scaiola / Gary Loughran / Marc Leibundgut / Annika Kratzel / Romane Meurs / René Dreos / Kate M O'Connor / Angus McMillan / Jeffrey W Bode / Volker Thiel / David ...著者: Pramod R Bhatt / Alain Scaiola / Gary Loughran / Marc Leibundgut / Annika Kratzel / Romane Meurs / René Dreos / Kate M O'Connor / Angus McMillan / Jeffrey W Bode / Volker Thiel / David Gatfield / John F Atkins / Nenad Ban / 要旨: Programmed ribosomal frameshifting is a key event during translation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows synthesis of the viral RNA-dependent ...Programmed ribosomal frameshifting is a key event during translation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows synthesis of the viral RNA-dependent RNA polymerase and downstream proteins. Here, we present the cryo-electron microscopy structure of a translating mammalian ribosome primed for frameshifting on the viral RNA. The viral RNA adopts a pseudoknot structure that lodges at the entry to the ribosomal messenger RNA (mRNA) channel to generate tension in the mRNA and promote frameshifting, whereas the nascent viral polyprotein forms distinct interactions with the ribosomal tunnel. Biochemical experiments validate the structural observations and reveal mechanistic and regulatory features that influence frameshifting efficiency. Finally, we compare compounds previously shown to reduce frameshifting with respect to their ability to inhibit SARS-CoV-2 replication, establishing coronavirus frameshifting as a target for antiviral intervention. | |||||||||
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_12759.map.gz | 632.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12759-v30.xml emd-12759.xml | 125 KB 125 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12759_fsc.xml | 19.8 KB | 表示 | FSCデータファイル |
画像 | emd_12759.png | 122.7 KB | ||
マスクデータ | emd_12759_msk_1.map emd_12759_msk_2.map | 669.9 MB 669.9 MB | マスクマップ | |
Filedesc metadata | emd-12759.cif.gz | 24.1 KB | ||
その他 | emd_12759_half_map_1.map.gz emd_12759_half_map_2.map.gz | 622 MB 622 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12759 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12759 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12759_validation.pdf.gz | 1.4 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12759_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | emd_12759_validation.xml.gz | 28 KB | 表示 | |
CIF形式データ | emd_12759_validation.cif.gz | 37.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12759 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12759 | 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_12759.map.gz / 形式: CCP4 / 大きさ: 669.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 1.06 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_12759_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 |
-マスク #2
ファイル | emd_12759_msk_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_12759_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_12759_half_map_2.map | ||||||||||||
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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 : Rabbit 80S ribosome colliding in another ribosome stalled by the ...
+超分子 #1: Rabbit 80S ribosome colliding in another ribosome stalled by the ...
+超分子 #2: Rabbit 80S ribosome colliding in another ribosome
+超分子 #3: SARS-CoV-2 pseudoknot
+超分子 #4: Rabbit 80S ribosome colliding in another ribosome
+超分子 #5: Replicase polyprotein 1ab
+分子 #1: 18S rRNA
+分子 #9: mRNA containing SARS-CoV-2 sequence
+分子 #10: A-site Met-tRNA(Met)
+分子 #11: P-site tRNA(Pro)
+分子 #40: 28S rRNA
+分子 #41: 5S rRNA
+分子 #42: 5.8S rRNA
+分子 #2: 40S ribosomal protein S27
+分子 #3: Ribosomal protein S28
+分子 #4: Ribosomal protein S27a
+分子 #5: 40S ribosomal protein S30
+分子 #6: Ribosomal protein eS26
+分子 #7: RACK1
+分子 #8: uS14
+分子 #12: EDF1
+分子 #13: 40S ribosomal protein SA
+分子 #14: 40S ribosomal protein S3a
+分子 #15: Ribosomal protein uS5
+分子 #16: 40S ribosomal protein S3
+分子 #17: Ribosomal protein eS4
+分子 #18: Ribosomal protein S5
+分子 #19: 40S ribosomal protein S6
+分子 #20: 40S ribosomal protein S7
+分子 #21: 40S ribosomal protein S8
+分子 #22: Ribosomal protein S9 (Predicted)
+分子 #23: Ribosomal protein eS10
+分子 #24: 40S ribosomal protein S11
+分子 #25: 40S ribosomal protein S12
+分子 #26: uS15
+分子 #27: 40S ribosomal protein uS11
+分子 #28: 40S ribosomal protein uS19
+分子 #29: uS9
+分子 #30: 40S ribosomal protein eS17
+分子 #31: 40S ribosomal protein S18
+分子 #32: Ribosomal protein eS19
+分子 #33: 40S ribosomal protein uS10
+分子 #34: Ribosomal protein eS21
+分子 #35: Ribosomal protein S15a
+分子 #36: 40S ribosomal protein S23
+分子 #37: 40S ribosomal protein S24
+分子 #38: 40S ribosomal protein S25
+分子 #39: 60s ribosomal protein l41
+分子 #43: Ribosomal protein uL2
+分子 #44: Ribosomal protein L3
+分子 #45: 60S ribosomal protein L4
+分子 #46: Ribosomal_L18_c domain-containing protein
+分子 #47: 60S ribosomal protein L6
+分子 #48: Ribosomal Protein uL30
+分子 #49: Ribosomal protein eL8
+分子 #50: 60S ribosomal protein L9
+分子 #51: 60S ribosomal protein L10
+分子 #52: Ribosomal protein L11
+分子 #53: Replicase polyprotein 1ab
+分子 #54: Ribosomal protein eL13
+分子 #55: Ribosomal protein L14
+分子 #56: Ribosomal protein L15
+分子 #57: Ribosomal protein L13a
+分子 #58: uL22
+分子 #59: Ribosomal protein L18
+分子 #60: 60S ribosomal protein L19
+分子 #61: Ribosomal protein L18a
+分子 #62: eL21
+分子 #63: Ribosomal protein eL22
+分子 #64: Ribosomal protein L23
+分子 #65: eL24
+分子 #66: uL23
+分子 #67: Ribosomal protein L26
+分子 #68: 60S ribosomal protein L27
+分子 #69: 60S ribosomal protein L27a
+分子 #70: 60S ribosomal protein L29
+分子 #71: eL30
+分子 #72: eL31
+分子 #73: eL32
+分子 #74: eL33
+分子 #75: 60S ribosomal protein L34
+分子 #76: uL29
+分子 #77: 60S ribosomal protein L36
+分子 #78: Ribosomal protein L37
+分子 #79: eL38
+分子 #80: eL39
+分子 #81: 60S ribosomal protein L40
+分子 #82: eL42
+分子 #83: eL43
+分子 #84: Ribosomal protein eL28
+分子 #85: 60S acidic ribosomal protein P0
+分子 #86: Ribosomal protein L12
+分子 #87: Ribosomal protein uL1
+分子 #88: MAGNESIUM ION
+分子 #89: UNKNOWN ATOM OR ION
+分子 #90: ZINC ION
+分子 #91: SPERMIDINE
+分子 #92: water
-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
濃度 | 0.3 mg/mL |
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緩衝液 | pH: 7.4 |
グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 1 |
凍結 | 凍結剤: ETHANE-PROPANE / 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 TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 100.0 µm / 倍率(補正後): 56604 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 倍率(公称値): 81000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |