+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0197 | |||||||||||||||
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タイトル | Multi-body refined map of the rabbit 80S collided with a stalled 80S | |||||||||||||||
マップデータ | Multi-body refined rabbit 80S ribosome collided with the stalled 80S ribosome | |||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of G1 to G0 transition / 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 / 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 ...regulation of G1 to G0 transition / 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 / 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 / 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 / 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 / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / T cell differentiation in thymus / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cell body / cytoplasmic translation / perikaryon / cytosolic large ribosomal subunit / defense response to Gram-negative bacterium / killing of cells of another organism / tRNA binding / mitochondrial inner membrane / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of apoptotic process / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / cell division / DNA repair / mRNA binding / centrosome / dendrite / ubiquitin protein ligase binding / positive regulation of cell population proliferation / synapse / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / DNA binding 類似検索 - 分子機能 | |||||||||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Rabbit (ウサギ) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.5 Å | |||||||||||||||
データ登録者 | Juszkiewicz S / Chandrasekaran V / Lin Z / Kraatz S / Ramakrishnan V / Hegde RS | |||||||||||||||
資金援助 | 英国, フランス, 4件
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引用 | ジャーナル: Mol Cell / 年: 2018 タイトル: ZNF598 Is a Quality Control Sensor of Collided Ribosomes. 著者: Szymon Juszkiewicz / Viswanathan Chandrasekaran / Zhewang Lin / Sebastian Kraatz / V Ramakrishnan / Ramanujan S Hegde / 要旨: Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates ...Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status. | |||||||||||||||
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_0197.map.gz | 23.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0197-v30.xml emd-0197.xml | 94.9 KB 94.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0197_fsc.xml | 17.6 KB | 表示 | FSCデータファイル |
画像 | emd_0197.png | 157.7 KB | ||
マスクデータ | emd_0197_msk_1.map | 476.8 MB | マスクマップ | |
その他 | emd_0197_half_map_1.map.gz emd_0197_half_map_2.map.gz | 325.9 MB 324.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0197 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0197 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0197_validation.pdf.gz | 408.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0197_full_validation.pdf.gz | 407.2 KB | 表示 | |
XML形式データ | emd_0197_validation.xml.gz | 22.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0197 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0197 | 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_0197.map.gz / 形式: CCP4 / 大きさ: 476.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Multi-body refined rabbit 80S ribosome collided with the stalled 80S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.14 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_0197_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 |
-ハーフマップ: Body2 half1 map
ファイル | emd_0197_half_map_1.map | ||||||||||||
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注釈 | Body2 half1 map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Body2 half1 map
ファイル | emd_0197_half_map_2.map | ||||||||||||
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注釈 | Body2 half1 map | ||||||||||||
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 on globin mRNA in the rotated state with A/P and P/E tRNAs
+超分子 #1: Rabbit 80S on globin mRNA in the rotated state with A/P and P/E tRNAs
+分子 #1: 28S ribosomal RNA
+分子 #2: 5S ribosomal RNA
+分子 #3: 5.8S ribosomal RNA
+分子 #4: 18S ribosomal RNA
+分子 #79: A/P tRNA
+分子 #82: mRNA
+分子 #83: P/E tRNA
+分子 #5: uS2
+分子 #6: 40S ribosomal protein S3a
+分子 #7: eS1
+分子 #8: uS3
+分子 #9: eS4
+分子 #10: Ribosomal protein S5
+分子 #11: 40S ribosomal protein S6
+分子 #12: 40S ribosomal protein S7
+分子 #13: eS8
+分子 #14: Ribosomal protein S9 (Predicted)
+分子 #15: eS10
+分子 #16: Ribosomal protein S11
+分子 #17: 40S ribosomal protein S12
+分子 #18: uS15
+分子 #19: uS11
+分子 #20: uS19
+分子 #21: Ribosomal protein S16
+分子 #22: eS17
+分子 #23: uS13
+分子 #24: eS19
+分子 #25: uS10
+分子 #26: eS21
+分子 #27: Ribosomal protein S15a
+分子 #28: uS12
+分子 #29: eS24
+分子 #30: eS25
+分子 #31: eS26
+分子 #32: 40S ribosomal protein S27
+分子 #33: Ribosomal protein S28
+分子 #34: uS14
+分子 #35: 40S ribosomal protein S30
+分子 #36: Ribosomal protein S27a
+分子 #37: RACK1
+分子 #38: Ribosomal protein L8
+分子 #39: uL3
+分子 #40: uL4
+分子 #41: 60S ribosomal protein L5
+分子 #42: 60S ribosomal protein L6
+分子 #43: uL30
+分子 #44: eL8
+分子 #45: uL6
+分子 #46: 60S ribosomal protein L10
+分子 #47: Ribosomal protein L11
+分子 #48: eL13
+分子 #49: Ribosomal protein L14
+分子 #50: Ribosomal protein L15
+分子 #51: uL13
+分子 #52: uL22
+分子 #53: eL18
+分子 #54: eL19
+分子 #55: eL20
+分子 #56: eL21
+分子 #57: eL22
+分子 #58: Ribosomal protein L23
+分子 #59: uL23
+分子 #60: Ribosomal protein L26
+分子 #61: 60S ribosomal protein L27
+分子 #62: uL15
+分子 #63: eL29
+分子 #64: eL30
+分子 #65: eL31
+分子 #66: eL32
+分子 #67: eL33
+分子 #68: eL34
+分子 #69: uL29
+分子 #70: 60S ribosomal protein L36
+分子 #71: Ribosomal protein L37
+分子 #72: eL38
+分子 #73: eL39
+分子 #74: eL40
+分子 #75: eL41
+分子 #76: eL42
+分子 #77: eL43
+分子 #78: eL28
+分子 #80: uL10
+分子 #81: Ribosomal protein L12
+分子 #84: Ribosomal protein
+分子 #85: nascent chain
+分子 #86: MAGNESIUM ION
+分子 #87: ZINC ION
-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: 7.4 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: INTEGRATING / 平均電子線量: 1.79 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |