+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14181 | |||||||||
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タイトル | Human collided disome (di-ribosome) stalled on XBP1 mRNA | |||||||||
マップデータ | Human collided disome (di-ribosome) stalled on XBP1 mRNA. Composite map filtered according to local resolution. | |||||||||
試料 |
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キーワード | disome / di-ribosome / XBP1 / ribosome / collision / TRANSLATION | |||||||||
機能・相同性 | 機能・相同性情報 Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Major pathway of rRNA processing in the nucleolus and cytosol ...Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / : / negative regulation of protein neddylation / translation at presynapse / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of formation of translation preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of endodeoxyribonuclease activity / negative regulation of DNA repair / poly(U) RNA binding / GAIT complex / supercoiled DNA binding / oxidized purine DNA binding / neural crest cell differentiation / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / alpha-beta T cell differentiation / laminin receptor activity / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / fibroblast growth factor binding / mammalian oogenesis stage / organelle membrane / homeostatic process / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / lung morphogenesis / iron-sulfur cluster binding / positive regulation of activated T cell proliferation / male meiosis I / Protein hydroxylation / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / cellular response to interleukin-4 / protein-RNA complex assembly / erythrocyte development / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Nuclear events stimulated by ALK signaling in cancer / translation regulator activity / laminin binding / rough endoplasmic reticulum / antiviral innate immune response / positive regulation of JUN kinase activity / 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 / negative regulation of protein ubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA 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: 3.0 Å | |||||||||
データ登録者 | Denk TG / Tesina P / Beckmann R | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation. 著者: Momoko Narita / Timo Denk / Yoshitaka Matsuo / Takato Sugiyama / Chisato Kikuguchi / Sota Ito / Nichika Sato / Toru Suzuki / Satoshi Hashimoto / Iva Machová / Petr Tesina / Roland Beckmann / Toshifumi Inada / 要旨: Translational stalling events that result in ribosome collisions induce Ribosome-associated Quality Control (RQC) in order to degrade potentially toxic truncated nascent proteins. For RQC induction, ...Translational stalling events that result in ribosome collisions induce Ribosome-associated Quality Control (RQC) in order to degrade potentially toxic truncated nascent proteins. For RQC induction, the collided ribosomes are first marked by the Hel2/ZNF598 E3 ubiquitin ligase to recruit the RQT complex for subunit dissociation. In yeast, uS10 is polyubiquitinated by Hel2, whereas eS10 is preferentially monoubiquitinated by ZNF598 in human cells for an unknown reason. Here, we characterize the ubiquitination activity of ZNF598 and its importance for human RQT-mediated subunit dissociation using the endogenous XBP1u and poly(A) translation stallers. Cryo-EM analysis of a human collided disome reveals a distinct composite interface, with substantial differences to yeast collided disomes. Biochemical analysis of collided ribosomes shows that ZNF598 forms K63-linked polyubiquitin chains on uS10, which are decisive for mammalian RQC initiation. The human RQT (hRQT) complex composed only of ASCC3, ASCC2 and TRIP4 dissociates collided ribosomes dependent on the ATPase activity of ASCC3 and the ubiquitin-binding capacity of ASCC2. The hRQT-mediated subunit dissociation requires the K63-linked polyubiquitination of uS10, while monoubiquitination of eS10 or uS10 is not sufficient. Therefore, we conclude that ZNF598 functionally marks collided mammalian ribosomes by K63-linked polyubiquitination of uS10 for the trimeric hRQT complex-mediated subunit dissociation. | |||||||||
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_14181.map.gz | 47.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14181-v30.xml emd-14181.xml | 103 KB 103 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_14181_fsc.xml | 21.1 KB | 表示 | FSCデータファイル |
画像 | emd_14181.png | 78.5 KB | ||
Filedesc metadata | emd-14181.cif.gz | 19.8 KB | ||
その他 | emd_14181_additional_1.map.gz emd_14181_additional_2.map.gz | 175.2 MB 174.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14181 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14181 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_14181_validation.pdf.gz | 456.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_14181_full_validation.pdf.gz | 456.2 KB | 表示 | |
XML形式データ | emd_14181_validation.xml.gz | 18.6 KB | 表示 | |
CIF形式データ | emd_14181_validation.cif.gz | 25.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14181 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14181 | HTTPS FTP |
-関連構造データ
関連構造データ | 7qvpMC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_14181.map.gz / 形式: CCP4 / 大きさ: 1000 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Human collided disome (di-ribosome) stalled on XBP1 mRNA. Composite map filtered according to local resolution. | ||||||||||||||||||||||||||||||||||||
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: 1.045 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
-追加マップ: Individually refined first stalled 80S ribosome in the...
ファイル | emd_14181_additional_1.map | ||||||||||||
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注釈 | Individually refined first stalled 80S ribosome in the P/P E/E post-state. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Individually refined collided human 80S ribosome in the...
ファイル | emd_14181_additional_2.map | ||||||||||||
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注釈 | Individually refined collided human 80S ribosome in the A/P P/E hybrid state. | ||||||||||||
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 : human collided disome stalled on XBP1 staller
+超分子 #1: human collided disome stalled on XBP1 staller
+分子 #1: mRNA
+分子 #2: mRNA
+分子 #3: tRNA P/P
+分子 #4: tRNA P/E
+分子 #5: tNRA E/E
+分子 #6: 5.8S ribosomal RNA
+分子 #7: 28S ribosomal RNA
+分子 #8: 5S ribosomal RNA
+分子 #85: 18S ribosomal RNA
+分子 #9: 60S ribosomal protein L8
+分子 #10: 60S ribosomal protein L3
+分子 #11: 60S ribosomal protein L4
+分子 #12: 60S ribosomal protein L5
+分子 #13: 60S ribosomal protein L6
+分子 #14: 60S ribosomal protein L7
+分子 #15: 60S ribosomal protein L7a
+分子 #16: 60S ribosomal protein L9
+分子 #17: 60S ribosomal protein L10-like
+分子 #18: 60S ribosomal protein L11
+分子 #19: 60S ribosomal protein L13
+分子 #20: 60S ribosomal protein L14
+分子 #21: 60S ribosomal protein L15
+分子 #22: 60S ribosomal protein L13a
+分子 #23: 60S ribosomal protein L17
+分子 #24: 60S ribosomal protein L18
+分子 #25: 60S ribosomal protein L19
+分子 #26: 60S ribosomal protein L18a
+分子 #27: 60S ribosomal protein L21
+分子 #28: 60S ribosomal protein L22
+分子 #29: 60S ribosomal protein L23
+分子 #30: 60S ribosomal protein L24
+分子 #31: 60S ribosomal protein L23a
+分子 #32: KOW domain-containing protein
+分子 #33: 60S ribosomal protein L27
+分子 #34: 60S ribosomal protein L27a
+分子 #35: 60S ribosomal protein L29
+分子 #36: 60S ribosomal protein L30
+分子 #37: 60S ribosomal protein L31
+分子 #38: 60S ribosomal protein L32
+分子 #39: 60S ribosomal protein L35a
+分子 #40: 60S ribosomal protein L34
+分子 #41: 60S ribosomal protein L35
+分子 #42: 60S ribosomal protein L36
+分子 #43: Ribosomal protein L37
+分子 #44: 60S ribosomal protein L38
+分子 #45: 60S ribosomal protein L39
+分子 #46: Ubiquitin-60S ribosomal protein L40
+分子 #47: 60S ribosomal protein L41
+分子 #48: 60S ribosomal protein L36a
+分子 #49: 60S ribosomal protein L37a
+分子 #50: 60S ribosomal protein L28
+分子 #51: 60S ribosomal protein L17
+分子 #52: 40S ribosomal protein SA
+分子 #53: 40S ribosomal protein S3a
+分子 #54: 40S ribosomal protein S2
+分子 #55: 40S ribosomal protein S3
+分子 #56: 40S ribosomal protein S4, X isoform
+分子 #57: 40S ribosomal protein S5
+分子 #58: 40S ribosomal protein S6
+分子 #59: 40S ribosomal protein S7
+分子 #60: 40S ribosomal protein S8
+分子 #61: 40S ribosomal protein S9
+分子 #62: 40S ribosomal protein S10
+分子 #63: 40S ribosomal protein S11
+分子 #64: 40S ribosomal protein S13
+分子 #65: 40S ribosomal protein S14
+分子 #66: 40S ribosomal protein S15
+分子 #67: 40S ribosomal protein S16
+分子 #68: 40S ribosomal protein S17
+分子 #69: 40S ribosomal protein S18
+分子 #70: 40S ribosomal protein S19
+分子 #71: 40S ribosomal protein S20
+分子 #72: 40S ribosomal protein S21
+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: 40S ribosomal protein S26
+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
+分子 #82: 40S ribosomal protein S12
+分子 #83: Receptor of activated protein C kinase 1
+分子 #84: Ubiquitin-40S ribosomal protein S27a
-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 |
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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: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 43.6 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 / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 0.4 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |