+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0194 | |||||||||||||||
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タイトル | Structure of the rabbit 80S ribosome on globin mRNA in the rotated state with A/P and P/E tRNAs | |||||||||||||||
マップデータ | Rabbit 80S ribosome on globin mRNA in the rotated state with A/P and P/E tRNAs | |||||||||||||||
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 / phagocytic cup ...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 / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / ribosomal small subunit export from nucleus / cytosolic ribosome / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / cytoplasmic translation / cell differentiation / tRNA binding / postsynaptic density / protein stabilization / rRNA binding / mitochondrial inner membrane / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / cell division / DNA repair / centrosome / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA 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: 3.8 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_0194.map.gz | 24.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0194-v30.xml emd-0194.xml | 95.1 KB 95.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0194_fsc.xml | 12.6 KB | 表示 | FSCデータファイル |
画像 | emd_0194.png | 200.3 KB | ||
マスクデータ | emd_0194_msk_1.map | 172.1 MB | マスクマップ | |
その他 | emd_0194_half_map_1.map.gz emd_0194_half_map_2.map.gz | 135.6 MB 135.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0194 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0194 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0194_validation.pdf.gz | 432.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0194_full_validation.pdf.gz | 431.3 KB | 表示 | |
XML形式データ | emd_0194_validation.xml.gz | 18.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0194 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0194 | 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_0194.map.gz / 形式: CCP4 / 大きさ: 172.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Rabbit 80S ribosome on globin mRNA in the rotated state with A/P and P/E tRNAs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.52 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_0194_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: Collided half2 map
ファイル | emd_0194_half_map_1.map | ||||||||||||
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注釈 | Collided half2 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: Collided half1 map
ファイル | emd_0194_half_map_2.map | ||||||||||||
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注釈 | Collided 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 ribosome translating globin mRNA in the rotated state ...
+超分子 #1: Rabbit 80S ribosome translating globin mRNA in the rotated state ...
+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 RNA
+分子 #82: mRNA
+分子 #83: P/E tRNA
+分子 #5: uS2
+分子 #6: 40S ribosomal protein S3a
+分子 #7: uS5
+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: uL1
+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 |