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データを開く
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基本情報
| 登録情報 | ![]() | |||||||||
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| タイトル | 80S ribosome with angiogenin and tRNAAla | |||||||||
マップデータ | 80S ribosome with angiogenin with cleaved tRNA | |||||||||
試料 |
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キーワード | Angiogenin / RNase / RIBOSOME | |||||||||
| 機能・相同性 | 機能・相同性情報angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / 加水分解酵素; エステル加水分解酵素; 3'-リン酸モノエステル産生エンドリボヌクレアーゼ / Adherens junctions interactions / ribosomal subunit ...angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / 加水分解酵素; エステル加水分解酵素; 3'-リン酸モノエステル産生エンドリボヌクレアーゼ / Adherens junctions interactions / ribosomal subunit / oocyte maturation / homeostatic process / hematopoietic stem cell proliferation / rRNA transcription / basement membrane / ubiquitin ligase inhibitor activity / positive regulation of phosphorylation / positive regulation of signal transduction by p53 class mediator / endocytic vesicle / RNA nuclease activity / 90S preribosome / phagocytic cup / protein-RNA complex assembly / ovarian follicle development / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / response to hormone / translation regulator activity / gastrulation / positive regulation of endothelial cell proliferation / actin filament polymerization / MDM2/MDM4 family protein binding / RNA endonuclease activity / cytosolic ribosome / stress granule assembly / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / peptide binding / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / placenta development / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / positive regulation of protein secretion / maturation of SSU-rRNA / small-subunit processome / negative regulation of smooth muscle cell proliferation / spindle / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / antibacterial humoral response / positive regulation of canonical Wnt signaling pathway / cell migration / heparin binding / large ribosomal subunit / actin cytoskeleton / regulation of translation / ribosome binding / chromosome / actin binding / growth cone / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / angiogenesis / endonuclease activity / perikaryon / defense response to Gram-negative bacterium / killing of cells of another organism / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / tRNA binding / response to hypoxia / mitochondrial inner membrane / negative regulation of translation / defense response to Gram-positive bacterium / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / receptor ligand activity / ribonucleoprotein complex / copper ion binding / signaling receptor binding / innate immune response / cell division / DNA repair / neuronal cell body / mRNA binding / apoptotic process 類似検索 - 分子機能 | |||||||||
| 生物種 | ![]() ![]() Homo sapiens (ヒト) / ![]() | |||||||||
| 手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.1 Å | |||||||||
データ登録者 | Loveland AB / Korostelev AA | |||||||||
| 資金援助 | 米国, 1件
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引用 | ジャーナル: Nature / 年: 2024タイトル: Structural mechanism of angiogenin activation by the ribosome. 著者: Anna B Loveland / Cha San Koh / Robin Ganesan / Allan Jacobson / Andrei A Korostelev / ![]() 要旨: Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, ...Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, angiogenin cleaves tRNAs at the anticodon loop, resulting in translation repression. However, the catalytic activity of isolated angiogenin is very low, and the mechanisms of the enzyme activation and tRNA specificity have remained a puzzle. Here we identify these mechanisms using biochemical assays and cryogenic electron microscopy (cryo-EM). Our study reveals that the cytosolic ribosome is the activator of angiogenin. A cryo-EM structure features angiogenin bound in the A site of the 80S ribosome. The C-terminal tail of angiogenin is rearranged by interactions with the ribosome to activate the RNase catalytic centre, making the enzyme several orders of magnitude more efficient in tRNA cleavage. Additional 80S-angiogenin structures capture how tRNA substrate is directed by the ribosome into angiogenin's active site, demonstrating that the ribosome acts as the specificity factor. Our findings therefore suggest that angiogenin is activated by ribosomes with a vacant A site, the abundance of which increases during cellular stress. These results may facilitate the development of therapeutics to treat cancer and neurodegenerative diseases. | |||||||||
| 履歴 |
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構造の表示
| 添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
| マップデータ | emd_44463.map.gz | 794.9 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-44463-v30.xml emd-44463.xml | 108 KB 108 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_44463_fsc.xml | 20.6 KB | 表示 | FSCデータファイル |
| 画像 | emd_44463.png | 185.6 KB | ||
| Filedesc metadata | emd-44463.cif.gz | 19.6 KB | ||
| その他 | emd_44463_half_map_1.map.gz emd_44463_half_map_2.map.gz | 144.8 MB 144.8 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-44463 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44463 | HTTPS FTP |
-検証レポート
| 文書・要旨 | emd_44463_validation.pdf.gz | 966.8 KB | 表示 | EMDB検証レポート |
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| 文書・詳細版 | emd_44463_full_validation.pdf.gz | 966.4 KB | 表示 | |
| XML形式データ | emd_44463_validation.xml.gz | 30 KB | 表示 | |
| CIF形式データ | emd_44463_validation.cif.gz | 39.9 KB | 表示 | |
| アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44463 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44463 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 9bdnMC ![]() 9bdlC ![]() 9bdpC C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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| 類似構造データ | 類似検索 - 機能・相同性 F&H 検索 |
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_44463.map.gz / 形式: CCP4 / 大きさ: 857.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| 注釈 | 80S ribosome with angiogenin with cleaved tRNA | ||||||||||||||||||||||||||||||||||||
| 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: 0.87 Å | ||||||||||||||||||||||||||||||||||||
| 密度 |
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| 対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
| 詳細 | EMDB XML:
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-添付データ
-ハーフマップ: 80S ribosome with angiogenin with cleaved tRNA, half map 1
| ファイル | emd_44463_half_map_1.map | ||||||||||||
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| 注釈 | 80S ribosome with angiogenin with cleaved tRNA, half map 1 | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-ハーフマップ: 80S ribosome with angiogenin with cleaved tRNA, half map 1
| ファイル | emd_44463_half_map_2.map | ||||||||||||
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| 注釈 | 80S ribosome with angiogenin with cleaved tRNA, half map 1 | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
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試料の構成要素
+全体 : 80S ribosome with angiogenin and tRNAAla
+超分子 #1: 80S ribosome with angiogenin and tRNAAla
+分子 #1: 18S rRNA
+分子 #2: 28S rRNA
+分子 #3: 5.8S rRNA
+分子 #4: 5S rRNA
+分子 #82: tRNAfMet
+分子 #83: mRNA
+分子 #84: tRNAAla
+分子 #5: 60S ribosomal protein L8
+分子 #6: 60S ribosomal protein L3
+分子 #7: 60S ribosomal protein L4
+分子 #8: 60S ribosomal protein L5
+分子 #9: 60S ribosomal protein L6
+分子 #10: 60S ribosomal protein L7
+分子 #11: Large ribosomal subunit protein eL8
+分子 #12: 60S ribosomal protein L9
+分子 #13: Ribosomal protein L10
+分子 #14: 60S ribosomal protein L11
+分子 #15: uL11
+分子 #16: Large ribosomal subunit protein eL13
+分子 #17: 60S ribosomal protein L14
+分子 #18: 60S ribosomal protein L15
+分子 #19: Large ribosomal subunit protein uL13
+分子 #20: 60S ribosomal protein L17
+分子 #21: Large ribosomal subunit protein eL18
+分子 #22: 60S ribosomal protein L19
+分子 #23: 60S ribosomal protein L18a
+分子 #24: 60S ribosomal protein L21
+分子 #25: Large ribosomal subunit protein eL22
+分子 #26: 60S ribosomal protein L23
+分子 #27: Ribosomal protein L24
+分子 #28: Large ribosomal subunit protein uL23
+分子 #29: 60S ribosomal protein L26
+分子 #30: 60S ribosomal protein L27
+分子 #31: 60S ribosomal protein L27a
+分子 #32: Large ribosomal subunit protein eL29
+分子 #33: 60S ribosomal protein L30
+分子 #34: 60S ribosomal protein L31
+分子 #35: Large ribosomal subunit protein eL32
+分子 #36: 60S ribosomal protein L35a
+分子 #37: 60S ribosomal protein L34
+分子 #38: 60S ribosomal protein L35
+分子 #39: 60S ribosomal protein L36
+分子 #40: 60S ribosomal protein L37
+分子 #41: Large ribosomal subunit protein eL38
+分子 #42: 60S ribosomal protein L39
+分子 #43: Large ribosomal subunit protein eL40
+分子 #44: eL41
+分子 #45: eL42
+分子 #46: 60S ribosomal protein L37a
+分子 #47: 60S ribosomal protein L28
+分子 #48: 60S acidic ribosomal protein P0
+分子 #49: Angiogenin
+分子 #50: Receptor of activated protein C kinase 1
+分子 #51: 40S_SA_C domain-containing protein
+分子 #52: 40S ribosomal protein S3a
+分子 #53: 40S ribosomal protein S2
+分子 #54: 40S ribosomal protein S3
+分子 #55: 40S ribosomal protein S4
+分子 #56: Ribosomal protein S5
+分子 #57: 40S ribosomal protein S6
+分子 #58: Small ribosomal subunit protein eS7
+分子 #59: 40S ribosomal protein S8
+分子 #60: 40S ribosomal protein S9
+分子 #61: 40S ribosomal protein S10
+分子 #62: 40S ribosomal protein S11
+分子 #63: 40S ribosomal protein S12
+分子 #64: 40S ribosomal protein S13
+分子 #65: Small ribosomal subunit protein uS11
+分子 #66: 40S ribosomal protein S15
+分子 #67: Small ribosomal subunit protein uS9
+分子 #68: 40S ribosomal protein S17
+分子 #69: 40S ribosomal protein S18
+分子 #70: Small ribosomal subunit protein eS19
+分子 #71: 40S ribosomal protein S20
+分子 #72: eS21
+分子 #73: 40S ribosomal protein S15a
+分子 #74: 40S ribosomal protein S23
+分子 #75: 40S ribosomal protein S24
+分子 #76: 40S ribosomal protein S25
+分子 #77: eS26
+分子 #78: 40S ribosomal protein S27
+分子 #79: 40S ribosomal protein S28
+分子 #80: 40S ribosomal protein S29
+分子 #81: 40S ribosomal protein S30
-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 |
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試料調製
| 緩衝液 | pH: 7 |
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| グリッド | モデル: Quantifoil R2/1 / 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: 2 |
| 凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 278 K / 装置: FEI VITROBOT MARK IV |
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電子顕微鏡法
| 顕微鏡 | FEI TALOS ARCTICA |
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| 撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 30.0 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: 100.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.5 µm / 最小 デフォーカス(公称値): 0.5 µm |
| 実験機器 | ![]() モデル: Talos Arctica / 画像提供: FEI Company |
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コントローラー
万見について




キーワード

Homo sapiens (ヒト)
データ登録者
米国, 1件
引用






















Z (Sec.)
Y (Row.)
X (Col.)




































解析
FIELD EMISSION GUN


